biology

An Introduction to Ebolavirus Biology

November 4, 2025November 4, 2025By logancollins No Comments

PDF version: An Introduction to Ebolavirus Biology – Logan Thrasher Collins

I wrote this educational primer as a fun exploration of a topic not related to my current research. While such knowledge may be useful in the event of some future ebolavirus epidemic, it is mostly just an exercise in curiosity and intellectual enrichment. I hope that you too enjoy learning about this fascinating (but scary!) virus as you browse my writeup. Also, if you’re an ebolavirus expert with concepts, edits, and/or ideas to offer, feel free to reach out with your additional insights! Shoutout: I’d like to give a special shoutout/thanks to Jain et al. (reference 4) and Bodmer et al. (reference 2). I used their papers extensively throughout the creation of writeup!

Genome

The ebolavirus genome consists of an 18.9 kb negative-sense single-stranded RNA (ssRNA) which encodes seven genes.^1,2 Each gene is flanked by a 3’ and 5’ untranslated region (3’UTR and 5’UTR) which contain start and end signals. The start signals have the consensus sequence of 3’-CUNCUUCUAAUU-5’ and the end signals have the consensus sequence 3’-UAAUUC(U)_5/6-5’. Since 3’UAAUU-5’ is found in both the start and end signals, they can overlap and (for most types of ebolavirus) do so at the junctions between the VP35-VP40, GP-VP30, and VP24-L genes. The rest of the genes have intergenic regions with non-overlapping start and end signals between them.

The 5’ and 3’ ends of the genome contain elements called the 5’ trailer and 3’ leader. The 5’ trailer contains parts of the antigenomic replication promoter and the 3’ leader contains parts of the genomic replication promoter. There is also a second genomic replication promoter in the NP untranslated region. Genomic replication promoters initiate RNA-dependent RNA polymerase (RdRP) replication of the negative-sense ssRNA genome while antigenomic replication promoters initiate replication of the positive-sense copy version of the ssRNA genome.

In total, the ebolavirus genome encodes seven proteins.¹ The seven proteins encoded by the ebolavirus genome include NP (nucleoprotein), VP24 (membrane-associated protein interfering with interferon signaling), VP30 and VP35 (polymerase matrix protein acting as interferon antagonist), L (the RdRP for replication), VP40 (matrix protein), and GP (glycoprotein).^1,2 The proteins will be discussed with more detail in the next section.

The GP RNA itself undergoes mRNA editing, so the GP can take three different forms.^2,3 The unedited GP mRNA (~80% of transcripts) encodes a precursor of soluble glycoprotein or sGP. The edited GP₀ mRNA (~20% of transcripts)^4,5 arises from viral polymerase stuttering at a slippage region sequence of seven consecutive uridines, which leads to addition of an adenosine and a frameshift allowing expression of GP_1,2. VP30 may help facilitate resolution of a stem loop involved in the stuttering of the viral polymerase.⁶ Finally, sometimes either two adenosines are added or one adenosine is omitted from the mRNA (5% of transcripts), leading instead to expression of a small soluble GP precursor protein (ssGP).^2,3

Structure

At a glance, ebolavirus consists of its ssRNA genome, a nucleocapsid and accessory proteins, and an envelope bearing its glycoproteins. The NP adopts a helical structure when complexed with the ssRNA genome, forming the nucleocapsid.⁷ VP35 and VP24 associate with the surface of the NP-RNA complex. VP40 forms the matrix between the envelope and the nucleocapsid. VP30 also binds the nucleocapsid and is important for transcription initiation.⁴ GP is a transmembrane protein which plays roles in cellular attachment and transduction.

NP’s main function is to encapsidate the ssRNA genome, forming a helical ssRNA-NP complex (the nucleocapsid).^2,8 The NPs form a left-handed helix with 24 subunits per turn. Each NP subunit binds six nucleotides of ssRNA via a positively charged cleft on the outside of the NP helix. The NP forms the core of a repeating asymmetric unit consisting of two NPs associated with two oppositely-oriented VP24 proteins, one of which in turn associates with a VP35 protein.

Image adapted from reference 8 (Sugita et al.)

In the cryo-EM structure⁸ above, the nucleocapsid helix of NP and ssRNA is displayed. VP24 and VP35 are not shown, though they also associate with the nucleocapsid.

VP24

VP24’s interactions and association with NP are required for nucleocapsid formation as well as for helping package the nucleocapsid into virions.⁴ It is involved in the initiation of viral budding. VP24 additionally inhibits the host cell’s immune responses. It inhibits IFN responses by blocking p38 phosphorylation, which inhibits the p38 MAPK pathway. It also can block NF-κB activation, precluding multiple downstream IFN gene expression pathways. VP24 can inhibit nuclear translocation of the phosphorylated transcription factor STAT1 by interacting with importins of the NPI-1 subfamily of importin-α.

VP35

VP35 is a tetrameric protein which plays a structural role in ebolavirus by associating with the surface of the nucleocapsid. It furthermore acts as a polymerase cofactor which bridges the NP-RNA complex with L (the polymerase) during replication.⁷ It has helicase and NTPase activities, which indicate that it may unwind RNA helices and hydrolyze NTPs to facilitate transcription and replication.⁴ VP35 also helps facilitate genome packaging and nucleocapsid assembly.

In addition, VP35 inhibits host cell immune responses.⁴ It interferes with the dimerization, phosphorylation, and nuclear localization of interferon regulatory factor 3 (IRF-3). It accomplishes this by preventing proteins TBK-1 and IKKε from interacting with IRF-3. Under normal circumstances, phosphorylation and dimerization of IRF-3 causes it to translocate to the nucleus and induce transcription of IFNα, IFNβ, and other genes. VP35 furthermore suppresses interferon transcription by enhancing SUMOylation of IRF-7 via interaction with PIAS1 (a type of SUMO ligase). VP35 also blocks PACT (which prevents activation of PACT-induced RIG-I ATPase) as well as inactivating PKR.

VP30

VP30 forms a hexamer composed of three dimers.⁴ It is required for RNA transcription initiation. It should be noted that VP30 has a disordered arginine-rich region in the middle of its sequence which interacts with the viral RNA. VP30 also interacts with NP, an interaction which must occur at a certain threshold level for optimal transcriptional activity. VP30 binds zinc, an essential capability for viral transcription initiation.

For transcription to occur, VP30 must either exhibit no phosphorylation (on serines and threonines) or have only partial phosphorylation along with constant phosphorylation-dephosphorylation activity. Partial phosphorylation is only acceptable at some stages of viral replication. By contrast, when it is phosphorylated, VP30 binds NP more robustly. This allows it to tightly associate with the nucleocapsid as new ebolavirus particles are synthesized.

VP40 (matrix protein)

Ebolavirus VP40 is abundantly expressed and associates with the plasma membrane of the host cell, where it facilitates viral assembly and budding.⁴ It contains two late budding domains (L-domains) of four amino acids each: PTAP and PPEY. The PTAP domain interacts with tumor susceptibility gene 101 protein (tsg101), which recruits VP40 to lipid raft domains on the plasma membrane. PPEY interacts with ubiquitin ligase Nedd4 and ubiquitin ligase ITCH E3, causing ubiquitination of the matrix proteins in certain ways, a requirement for budding.

VP40 can form dimers, hexamers, filaments, and octamers. Dimerization of VP40 is essential for binding to Sec24c and trafficking to the plasma membrane. Sec24c is a component of the coat protein complex II (COPII) which facilitates formation of transport vesicles traveling from the endoplasmic reticulum to the Golgi apparatus, enabling eventual transport to the plasma membrane.⁹ Dimers can assemble into filaments via VP40’s C-terminal domain residues, which is crucial for matrix assembly and budding.⁴

VP40 contains a C-terminal domain with a hydrophobic interface which penetrates the plasma membrane to anchor the matrix protein and facilitate assembly and budding.¹⁰ Interestingly, VP40 has been shown to selectively anchor onto the plasma membrane via interactions with the enriched anionic phospholipids like phosphatidylserine found in the plasma membrane. At the membrane, the dimers assemble into linear hexamers which are also important for assembly and budding. VP40 can additionally form octameric rings which are essential for VP40-ssRNA binding. Oligomers of VP40 have also been implicated as inhibitory regulators of viral transcription.¹¹

L protein

The L protein is the RNA-dependent RNA polymerase (RdRP) of the ebolavirus.⁴ It is a fairly large (2212 amino acids) protein consisting of five domains: (i) the RdRP domain which facilitates transcription and replication and polyadenylation, (ii) the capping domain which has polyribonucleotidyl transferase activity, (iii) a connector domain, (iv) a methyltransferase domain, and (v) a small C-terminal domain. The capping domain transfers a GDP to the 5’ phosphate of the viral mRNA. The methyltransferase then methylates the first nucleotide at the 2’-O position and the guanosine cap at the N-7 position. The small C-terminal domain plays a role in recruiting RNAs before methylation.

Additionally, the first 450 amino acids contain a homo-oligomerization domain which overlaps with the RdRP domain. The first 380 amino acids furthermore contain a domain for interaction with the VP35 protein, allowing localization of the L protein into viral inclusion bodies during assembly.

GP (glycoprotein) is a fusogenic transmembrane protein.⁴ It has a cathepsin binding site which is cleaved inside the endosome as a step in viral infection. It is also post-translationally cleaved by furin from its precursor GP₀ to make GP1 and GP2 subunits, which remain linked by disulfide bonds. Three GP_1,2 complexes associate to form the trimeric GP that is displayed on the ebolavirus envelope surface.⁵

GP1 mediates attachment to host cell receptors via its receptor binding domain (RBD).⁴ There is a heavily glycosylated mucin-like domain (MLD) in GP1, which can stimulate host dendritic cells by activating their MAPK and NF-κB pathways. GP1 furthermore contains another important heavily glycosylated domain called the glycan cap (though it is in the middle of the GP1 sequence).¹²

GP2 facilitates fusion of viral envelopes with host cell membranes. It does this by inserting a hydrophobic loop domain into the endosomal membrane, bringing the envelope into close contact with said endosomal membrane.⁴ GP2 also contains a transmembrane anchor domain to help tether the GP to the envelope. GP2 furthermore can inhibit cellular antiviral responses. Firstly, it interferes with tetherin activity (tetherins are host cell proteins that aim to prevent viral budding by “tethering” the virus). It also interferes with NF-κB signaling pathways. GP2 can additionally trigger lymphocyte apoptosis and cytokine dysregulation via an immunosuppressive C-terminal motif.

GP is subject to heavy post-translational glycosylation, protecting the protein against host antibodies.⁴ GP1 contains 95 glycosylation sites and GP2 contains an additional 2 known glycosylation sites. In particular, MLD is highly glycosylated, allowing it to mask cell-surface proteins like MHC-I (thus inhibiting CD8⁺ T cell responses).

GP_1,2 can be cleaved away from the viral envelope by the host enzyme TACE (TNF-α converting enzyme), leading to shed GP.^4,13 The shed GP can sequester antibodies, acting as an immunological decoy. Shed GP furthermore contributes to triggering various inflammatory cytokines.

GP_1,2 expression makes up only 20% of the total expressed protein from the GP gene.^4,5 The other 80% consists of soluble secreted glycoprotein (sGP), Δ peptide, and small soluble secreted glycoprotein (ssGP). Both the GP_1,2 and the ssGP are transcribed only when different ribosomal stuttering events occur during transcription as described earlier (in the genome section).

The sGP is a secreted protein which may serve as an immunological decoy which (as with shed GP) binds antibodies and thereby reduces the available antibodies that can bind to the virus itself.^4,5 It has 7 glycosylation sites. In addition, sGP might inhibit inflammatory cytokines and chemokines, further helping the virus evade immunological responses.⁴

A small C-terminal region of sGP can be cleaved off to form Δ peptide.^4,5 The Δ peptide also acts as an immunological decoy. Δ peptide can inhibit entry of ebolavirus into certain cells, preventing superinfection. In addition, Δ peptide may act as a viroporin, forming pores in mammalian cells.

The ssGP consists of an N-terminal region of 295 amino acids which are identical to GP₀ and sGP and a C-terminal region of 3 amino acids which are distinct. It is secreted as a disulfide bonded homodimer which undergoes glycosylation. Its function remains unknown.⁴

Life Cycle

Attachment

Ebolavirus begins its life cycle by leveraging GP_1,2 to attach to host cell receptors.² There are three known mechanisms for attachment including (i) binding of C-type lectins, (ii) interaction with phosphatidylserine-binding receptors, and (iii) antibody-dependent enhancement.

C-type lectins bind the GP’s glycans found on the MLD as well as the glycan cap.² Such lectins are mainly expressed on antigen presenting cells (dendritic cells, monocytes, macrophages, etc.) which are a primary target cell of ebolaviruses. However, they are not required or sufficient for entry, so they act as accessory receptors.

During budding, ebolavirus incorporates the host scramblase XKR8 into its envelope (via interactions with GP_1,2),² which randomly swaps phospholipids between inner and outer membrane leaflets. It should be noted that other scramblases like TMEM16F might also be used by the virus in the same way. The scramblases expose phosphatidylserine on the envelope’s surface (phosphatidylserine is normally found on the inner leaflet rather than the outer leaflet). As a result, phosphatidylserine receptors (TIM-1, TIM-4, Axl, and Mer) on the host cell membrane can bind the phosphatidylserine on the viral envelope. Since exposure of phosphatidylserine is normally used by the host to induce phagocytosis of apoptotic cell debris, the presence of phosphatidylserine on the ebolavirus envelope targets it for uptake into phagocytes. This is called “apoptotic mimicry”.

Antibody-dependent enhancement is when anti-ebolavirus antibodies bind to the virus and immune cell Fc receptors bind the antibodies.² Complement factor C1q can also bind the ebolavirus-antibody complexes and attach virions to immune cell surfaces. Though these pathways normally facilitate clearing of viruses by endocytic uptake and degradation, ebolavirus may leverage the process for infection instead.

Endosomal trafficking and fusion

After binding the cell surface, the ebolavirus is endocytosed via macropinocytosis, preferentially near host cell membrane lipid rafts.² Virions are trafficked from the early endosome to the late endosome. In the late endosome, the GP’s MLD and glycan cap are cleaved off by cathepsin B, cathepsin L, and/or other host cell proteases. This allows the GP to bind the intracellular receptor NPC1 (Niemann–Pick C1), which is found on the inner surface of the endosome. Low pH in the endosome causes acidification in the virus, which triggers disassociation of the VP40 matrix protein from the envelope, granting the virus more flexibility. It is thought that this flexibility may represent an additional prerequisite for fusion. Finally, the GP experiences a conformal change that causes insertion of GP2’s hydrophobic loop domain into the endosomal membrane, facilitating fusion with the envelope (a process dependent on certain pH and Ca²⁺ levels). After fusion, the nucleocapsid is released into the cytosol.

Transcription

Condensed nucleocapsids in the cytosol next begin RNA synthesis.² To do this, they use a ribonucleoprotein complex consisting of L, NP, VP35, and VP30. Primary transcription relies on proteins from the incoming virion while secondary transcription can also utilize proteins newly produced inside the host cell. L (along with its VP35 cofactor) catalyzes RNA polymerization as well as methylation (capping) of viral mRNAs as discussed earlier.

Cytosolic transcription initiated by the polymerase complex is assisted by VP30.² L starts at a site at the 3’ end of the genome and scans for the start signal of the first gene, which is the NP gene. The mRNA’s polyadenylation is triggered via polymerase slippage at the poly-uridine end signals which were discussed previously. L continues scanning the genome for the next start signal. It should be noted that scanning can occur in both directions along the genome. If the polymerase disassociates from the genome during scanning, it must return to the 3’ end to reinitiate. Because of this, genes close to the 3’ end of the genome are transcribed at a higher level than genes towards the 5’ end, a transcriptional gradient which might have functional significance.

Primary transcription occurs within 1-2 hours after infection.² After ~10 hours post-infection, ebolavirus causes the formation of cytosolic inclusion bodies that serve to facilitate secondary transcription and genome replication. These inclusion bodies are rich in L, NP, VP35, and VP30 as well as VP24, VP40, and certain host proteins such as CAD, STAU1, SMYD3, RBBP6, PEG10, hnRNP L, and RUVBL1. Ebolavirus inclusion bodies occur as membraneless phase-separated condensates driven by NP oligomerization interactions.

Viral mRNAs are exported from inclusion bodies by recruiting host NFX1 (nuclear RNA export factor 1).² NFX1 binds mRNAs within inclusion bodies and transports them out into the cytosol, where translation can occur. It has been shown that hypusinated eIF5A (eukaryotic initiation 5A) is required for viral mRNA translation. Note that hypusination is a post-translational modification where a lysine in eIF5A is converted to a non-canonical amino acid called hypusine.¹⁴ In addition, ADAR1 (adenosine deaminase acting on RNA 1) edits 3’ untranslated regions within viral mRNAs and thus alters some of their negative regulatory elements to no longer downregulate translation.²

The transition from transcription to replication is thought to involve VP30 phosphorylation.² Non-phosphorylated VP30 associates more strongly with the L-VP35 complex than its phosphorylated form. Phosphorylation of VP30 (and its lower affinity for L-VP35 in this form) may shift the focus of L-VP35 towards replication. When VP30 is phosphorylated, it also interacts more strongly with NP, which helps VP30 incorporate itself into new virions. That said, this process is not fully understood. Cellular kinases (SRPK1 and SRPK2) and phosphatases (PP2A-B56 and PP1) are sequestered into viral inclusion bodies to facilitate VP30 phosphorylation and dephosphorylation.

Replication

Only L, VP35, and NP are needed for ebolavirus replication (unlike transcription, which also needs VP30).² For replication, the genome is copied into an antigenome. Replication is initiated at the first C in the genome, which is actually position 2 in the sequence. As a result, the copies initially lack the 3’-terminal nucleotide. To fix this, it is believed that the 3’ region of the RNA folds into a hairpin structure which back-primes addition of the missing nucleotide. Both the genome and the antigenome are encapsidated by NP.² During the replication process, VP35 acts as a chaperone for monomeric NP that has not yet bound RNA. VP24 may cause nucleocapsids to transition from a relaxed state to a more condensed state.

Assembly and budding

After release from inclusion bodies, the nucleocapsids are transported along actin filaments to the plasma membrane where budding takes place.² GP_1,2 reaches the plasma membrane through the secretory pathway since it is a transmembrane protein. VP40 mediates budding by taking over parts of the host’s ESCRT (endosomal sorting complex required for transport) pathway. VP40 has a motif which recruits Tsg101 (an ESCRT-I component) to lipid rafts in the membrane. VP40 also has a motif which interacts with ubiquitin protein ligases (NEDD4, ITCH, WWP1, and SMURF2). These ubiquitin ligases ubiquitinate VP40, which facilitates its activity in budding. VP40 may also induce curvature across membrane phospholipids via its oligomerization. VP40 has a basic patch in its C-terminal domain which interacts with phosphatidylserine, which causes phosphatidylserine to cluster. Indeed, it has been shown that proper matrix layer formation requires phosphatidylserine clustering, so the interaction likely has functional importance.

References

1. Ghosh, S., Saha, A., Samanta, S. & Saha, R. P. Genome structure and genetic diversity in the Ebola virus. Curr. Opin. Pharmacol. 60, 83–90 (2021).

2. Bodmer, B. S., Hoenen, T. & Wendt, L. Molecular insights into the Ebola virus life cycle. Nat. Microbiol. 9, 1417–1426 (2024).

3. Martin, B., Hoenen, T., Canard, B. & Decroly, E. Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry. Antiviral Res. 135, 1–14 (2016).

4. Jain, S., Martynova, E., Rizvanov, A., Khaiboullina, S. & Baranwal, M. Structural and Functional Aspects of Ebola Virus Proteins. Pathogens vol. 10 at https://doi.org/10.3390/pathogens10101330 (2021).

5. Lee, J. E. & Saphire, E. O. Ebolavirus Glycoprotein Structure and Mechanism of Entry. Future Virol. 4, 621–635 (2009).

6. Mehedi, M. et al. Ebola Virus RNA Editing Depends on the Primary Editing Site Sequence and an Upstream Secondary Structure. PLOS Pathog. 9, e1003677 (2013).

7. Fujita-Fujiharu, Y. et al. Structural basis for Ebola virus nucleocapsid assembly and function regulated by VP24. Nat. Commun. 16, 2171 (2025).

8. Sugita, Y., Matsunami, H., Kawaoka, Y., Noda, T. & Wolf, M. Cryo-EM structure of the Ebola virus nucleoprotein–RNA complex at 3.6 Å resolution. Nature 563, 137–140 (2018).

9. Mancias, J. D. & Goldberg, J. Structural basis of cargo membrane protein discrimination by the human COPII coat machinery. EMBO J. 27, 2918–2928 (2008).

10. Adu-Gyamfi, E. et al. The Ebola Virus Matrix Protein Penetrates into the Plasma Membrane. J. Biol. Chem. 288, 5779–5789 (2013).

11. T., H. et al. Oligomerization of Ebola Virus VP40 Is Essential for Particle Morphogenesis and Regulation of Viral Transcription. J. Virol. 84, 7053–7063 (2010).

12. Peng, W. et al. Glycan shield of the ebolavirus envelope glycoprotein GP. Commun. Biol. 5, 785 (2022).

13. Ning, Y.-J., Deng, F., Hu, Z. & Wang, H. The roles of ebolavirus glycoproteins in viral pathogenesis. Virol. Sin. 32, 3–15 (2017).

14. McKenna, S. The first step of hypusination. Nat. Chem. Biol. 19, 664 (2023).

Key facts about protein vault biology

June 3, 2025June 5, 2025By logancollins No Comments

PDB 4V60: structure of a protein vault (MVP only)

Structure and organization:

Wild-type vaults consist of multiple copies of major vault protein (MVP), VPARP, and TEP1 proteins as well as small untranslated RNAs called vRNAs (Pupols, 2011).

Vaults are ~13 MDa in mass if VPARP, TEP1, and vRNAs are included along with the 78 MVPs (Galbiati et al., 2018). Each of the 78 MVP copies is ~97 kDa (Champion et al., 2009), so the hollow vault mass is ~7.7 MDa.

VPARP catalyzes poly-ADP ribosylation. It has been found to ribosylate itself and MVP. Its function is unknown. It contains the INT domain, which binds to the interior waist region of the vault (Pupols, 2011).

TEP1 (telomerase-associated protein 1) is found both associated with nuclear telomerase complexes and with cytosolic vaults. Its function is unknown (Pupols, 2011).

vRNAs are untranslated RNA polymerase III transcripts ranging from 80-150 nucleotides in length. Their function is unknown (Pupols, 2011).

Physiology and dynamics:

Vaults are found inside every cell in the human body at copy numbers of ~10⁴ vaults per cell in most cells but ~10⁵ in certain cell types (e.g. some immune cells) (Travis, 2024). They are especially abundant in tissues exposed to external stressors such as bronchus, renal proximal tubules, digestive tract, macrophages, and dendritic cells (Pupols, 2011). In embryonic tissues, vaults sometimes can occur at an impressive ~10⁷ copies per cell (Suprenant, 2002).

Vaults do not self-assemble from MVP on its own. They can only be made co-translationally on eukaryotic polyribosomes (Mrazek et al., 2014). Two copies of MVP, oriented in opposite directions, are first translated by two ribosomes. The N-terminal regions of these MVPs dimerize. As more ribosome pairs arrive in line, more MVP dimers are made. Lateral interactions between the dimers begin assembling the wall of the vault. In total, 39 copies of MVP dimer are translated on the polyribosome, leading to the formation of the final barrel-shaped vault structure.

Vaults have consistently been found as contaminants in purified extracellular vesicle (EV) preparations. There is evidence that vaults associate with the outside of EVs and are not protected beneath vesicular membranes (Liu et al., 2023). However, vaults have also been found to be released from cells in an EV-independent fashion wherein they are not bound to the outside of the EVs (Jeppesen et al., 2019). As such, they might be co-released alongside EVs.

Vaults frequently exchange halves when in solution, indicating their dynamic structural nature (Yang et al., 2010). Indeed, vaults have been proposed to experience a structural “breathing” motion.

Vaults disassemble at low pH, through mechanisms of half vault separation (Goldsmith et al., 2007) and/or weakening of the lateral associations between MVP copies (Llauró et al., 2016).

Vaults are cytosolic particles, but small amounts of them associate with the nuclear membrane at nuclear pore complexes and in some cell types (e.g. U373 glioblastoma cell line) about 5% of MVP is localized to the nucleus (Slesina et al., 2005).

As MVP is a self-protein, it is usually invisible to the immune system (Champion et al., 2009). Indeed, repeated intranasal administration of vaults carrying non-immunogenic proteins like mCherry-INT does not induce anti-vault antibodies even when MVP is fused to Z peptide (an Fc-binding peptide often used to conjugate antibodies for vault targeting to specific cell types). That said, the immune system’s tolerance to vaults can be broken if vaults carrying highly immunogenic proteins like chlamydia major outer membrane protein with INT (MOMP-INT). Repeated administration of vaults carrying MOMP-INT has been shown to induce anti-MVP antibodies.

Hints at function:

MVP knockout mice are viable but have lower survival rates when challenged with Pseudomonas aeruginosa (Frascotti et al., 2021).

Vault overexpression is found in multidrug resistant cancers, but so far this seems more of a correlation than a causation. Experimentally, overexpression of vaults alone does not produce the multidrug resistant phenotype (Frascotti et al., 2021).

In neurons, vaults localize at neurite tips and along axonal and dendritic microtubule networks. Vaults can co-precipitate with cytoplasmic RNAs that are known to be translated in response to synaptic activity (Frascotti et al., 2021).

Vaults are highly conserved (Daly et al., 2013; Slinning et al., 2024). They occur in mammals, amphibians, birds, fish, sea urchins, slime molds, and more. That said, insects, plants, and fungi do not have vaults.

References:

Champion, C. I., Kickhoefer, V. A., Liu, G., Moniz, R. J., Freed, A. S., Bergmann, L. L., Vaccari, D., Raval-Fernandes, S., Chan, A. M., Rome, L. H., & Kelly, K. A. (2009). A Vault Nanoparticle Vaccine Induces Protective Mucosal Immunity. PLOS ONE, 4(4), e5409. https://doi.org/10.1371/journal.pone.0005409

Daly, T. K., Sutherland-Smith, A. J., & Penny, D. (2013). In Silico Resurrection of the Major Vault Protein Suggests It Is Ancestral in Modern Eukaryotes. Genome Biology and Evolution, 5(8), 1567–1583. https://doi.org/10.1093/gbe/evt113

Frascotti, G., Galbiati, E., Mazzucchelli, M., Pozzi, M., Salvioni, L., Vertemara, J., & Tortora, P. (2021). The Vault Nanoparticle: A Gigantic Ribonucleoprotein Assembly Involved in Diverse Physiological and Pathological Phenomena and an Ideal Nanovector for Drug Delivery and Therapy. In Cancers (Vol. 13, Issue 4). https://doi.org/10.3390/cancers13040707

Galbiati, E., Avvakumova, S., La Rocca, A., Pozzi, M., Messali, S., Magnaghi, P., Colombo, M., Prosperi, D., & Tortora, P. (2018). A fast and straightforward procedure for vault nanoparticle purification and the characterization of its endocytic uptake. Biochimica et Biophysica Acta (BBA) – General Subjects, 1862(10), 2254–2260. https://doi.org/https://doi.org/10.1016/j.bbagen.2018.07.018

Goldsmith, L. E., Yu, M., Rome, L. H., & Monbouquette, H. G. (2007). Vault Nanocapsule Dissociation into Halves Triggered at Low pH. Biochemistry, 46(10), 2865–2875. https://doi.org/10.1021/bi0606243

Jeppesen, D. K., Fenix, A. M., Franklin, J. L., Higginbotham, J. N., Zhang, Q., Zimmerman, L. J., Liebler, D. C., Ping, J., Liu, Q., Evans, R., Fissell, W. H., Patton, J. G., Rome, L. H., Burnette, D. T., & Coffey, R. J. (2019). Reassessment of Exosome Composition. Cell, 177(2), 428-445.e18. https://doi.org/10.1016/j.cell.2019.02.029

Liu, X., Nizamudeen, Z., Hill, C. J., Parmenter, C., Arkill, K. P., Lambert, D. W., & Hunt, S. (2023). Vault particles are common contaminants of extracellular vesicle preparations. BioRxiv, 2023.11.09.566362. https://doi.org/10.1101/2023.11.09.566362

Llauró, A., Guerra, P., Kant, R., Bothner, B., Verdaguer, N., & de Pablo, P. J. (2016). Decrease in pH destabilizes individual vault nanocages by weakening the inter-protein lateral interaction. Scientific Reports, 6(1), 34143. https://doi.org/10.1038/srep34143

Mrazek, J., Toso, D., Ryazantsev, S., Zhang, X., Zhou, Z. H., Fernandez, B. C., Kickhoefer, V. A., & Rome, L. H. (2014). Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles. ACS Nano, 8(11), 11552–11559. https://doi.org/10.1021/nn504778h

Pupols, M. D. (2011). Packaging RNA into Vault Nanoparticles to Develop a Novel Delivery System for RNA Therapeutics. In ProQuest Dissertations and Theses. University of California, Los Angeles PP – United States — California.

Slesina, M., Inman, E. M., Rome, L. H., & Volknandt, W. (2005). Nuclear localization of the major vault protein in U373 cells. Cell and Tissue Research, 321(1), 97–104. https://doi.org/10.1007/s00441-005-1086-8

Slinning, M. S., Nthiga, T. M., Eichner, C., Khadija, S., Rome, L. H., Nilsen, F., & Dondrup, M. (2024). Major vault protein is part of an extracellular cement material in the Atlantic salmon louse (Lepeophtheirus salmonis). Scientific Reports, 14(1), 15240. https://doi.org/10.1038/s41598-024-65683-0

Suprenant, K. A. (2002). Vault Ribonucleoprotein Particles: Sarcophagi, Gondolas, or Safety Deposit Boxes? Biochemistry, 41(49), 14447–14454. https://doi.org/10.1021/bi026747e

Travis, J. (2024). The vault guy. Science (New York, NY), 384(6700), 1058–1062.

Yang, J., Kickhoefer, V. A., Ng, B. C., Gopal, A., Bentolila, L. A., John, S., Tolbert, S. H., & Rome, L. H. (2010). Vaults Are Dynamically Unconstrained Cytoplasmic Nanoparticles Capable of Half Vault Exchange. ACS Nano, 4(12), 7229–7240. https://doi.org/10.1021/nn102051r

The Virus Zoo: A Primer on Molecular Virology

July 27, 2022January 29, 2023By logancollins 4 Comments

Click here for a PDF version of the virus zoo

Human Immunodeficiency Virus (HIV)

Genome and Structure:

HIV’s genome is a 9.7 kb linear positive-sense ssRNA.¹ There is a m⁷G-cap (specifically the standard eukaryotic m⁷GpppG as added by the host’s enzymes) at the 5’ end of the genome and a poly-A tail at the 3’ end of the genome.² The genome also has a 5’-LTR and 3’-LTR (long terminal repeats) that aid its integration into the host genome after reverse transcription, that facilitate HIV genetic regulation, and that play a variety of other important functional roles. In particular, it should be noted that the integrated 5’UTR contains the HIV promoter called U3.^3,4

HIV’s genome translates three polyproteins (as well as several accessory proteins). The Gag polyprotein contains the HIV structural proteins. The Gag-Pol polyprotein contains (within its Pol component) the enzymes viral protease, reverse transcriptase, and integrase. The Gag-Pol polyprotein is produced via a –1 ribosomal frameshift at the end of Gag translation. Because of the lower efficiency of this frameshift, Gag-Pol is synthesized 20-fold less frequently than Gag.⁵ The frameshift’s mechanism depends upon a slippery heptanucleotide sequence UUUUUUA and a downstream RNA secondary structure called the frameshift stimulatory signal (FSS).⁶ This FSS controls the efficiency of the frameshift process.

The HIV RNA genome undergoes alternative splicing to produce the rest of the viral proteins. One splicing event produces an RNA that separately encodes the Vpu protein and the Env protein (also called gp160).^6–8 A mechanism called ribosome shunting is used to transition from Vpu’s open reading frame to Env’s open reading frame. The Env protein contains the gp41 and gp120 proteins. Env is post-translationally cleaved into gp41 and gp120 by a host furin enzyme in the endoplasmic reticulum.⁹ It is important to note that Env is also heavily glycosylated post-translationally to help HIV evade the immune system. Several other complex splicing events lead to the production of RNAs encoding Tat, Rev, Nef, Vif, and Vpr.

HIV viral protease cleaves the Gag polyprotein and thus produces structural proteins including the capsid protein CA (also called p24), the matrix protein MA (also called p17), the nucleocapsid protein NC (also called p7), and the p6 peptide.¹⁰ The HIV core capsid is shaped like a truncated cone and consists of about 1500 CA monomers. Most of the CA proteins assemble into hexamers, but a few pentamers are present. The pentamers help give the core capsid its conical morphology by providing extra curvature near the top and bottom. Each core capsid contains two copies of the HIV genomic RNA, complexed with NC protein. Reverse transcriptase, integrase, and viral accessory proteins are also held within the core capsid. HIV’s core capsid is packaged into a lipid envelope that bears gp41-gp120 glycoprotein heterodimers. The MA protein forms a layer between the core capsid and the envelope.

Accessory proteins Vpu, Tat, Rev, Nef, Vif, and Vpr facilitate a variety of functions. Vpu induces degradation of CD4 proteins within the endoplasmic reticulum of host CD4+ T cells. It does this by using its cytosolic domain as a molecular adaptor between CD4 and a ubiquitin ligase (which subsequently triggers proteosomal degradation of the CD4).¹¹ The reason that Vpu does this is to prevent HIV superinfection wherein two different types of HIV might infect the same cell and interfere with each other. This is an example of competition between viruses.¹² Vpu also enhances release of HIV virions from infected cells by using its cytosolic domain to inhibit a host protein called tetherin (also known as BST-2).¹¹ Without Vpu, tetherin would bind the viral envelope to the cell surface as well to other HIV virus particles, impeding release.

Tat, also called the viral transactivator protein, is necessary for efficient transcriptional elongation of the HIV genome after integration into the host DNA.¹³ Tat binds the viral transactivation response element (TAR), a structured RNA motif present at the beginning of the HIV transcripts. It then recruits protein positive transcription elongation factor b (P-TEFb). This allows P-TEFb to phosphorylate certain residues in the C-terminal domain of RNA polymerase II, stimulating transcriptional elongation. Tat also recruits several of the host cell’s histone acetyltransferases to the viral 5’-LTR so as to open the chromatin around the U3 promoter and related parts of the integrated HIV genome.^3,4 Finally, Tat is secreted from infected cells¹⁴ and acts as an autocrine and paracrine signaling molecule.⁴ It inhibits antigen-specific lymphocyte proliferation, stimulates expression of certain cytokines and cytokine receptors, modulates the activities of various host cell types, causes neurotoxicity in the brain, and more.

Rev facilitates nuclear export of the unspliced and singly spliced HIV RNAs by binding to a sequence located in the Env coding region called the Rev response element (RRE).¹³ The Rev protein forms a dimer upon binding to the RRE and acts as an adaptor, binding a host nuclear export factor called CRM1. Rev is also known to form higher-order oligomers via cooperative multimerization of the RNA-bound dimers.

Nef is a myristoylated protein that downregulates certain host T cell proteins and thereby increases production of virus. Nef is localized to the cytosol and the plasma membrane. It specifically inhibits CD4, Lck, CTLA-4, and Bad.¹⁵ Downregulating CD4 contributes to the prevention of superinfection that also occurs with Vpu’s inhibition of CD4. Nef induces endocytosis of plasma membrane Lck protein and traffics it to recycling endosomes and the trans-Golgi network. At these intracellular compartments, Lck signals for Ras and Erk activation, which triggers IL-2 production. IL-2 causes T cells to grow and proliferate, leading to more T cells that HIV can infect and leading to activation of the machinery HIV needs to replicate itself within infected T cells. Nef triggers lysosomal degradation of CTLA-4. This is because CTLA-4 can serve as an off-switch for T cells, which would lead to inhibition of HIV replication if active. Nef inactivates the Bad protein via phosphorylation. Bad participates in apoptotic cascades, so Nef prevents apoptosis of the infected host cell in this way.

Vif forms a complex with the host antiviral proteins APOBEC3F and APOBEC3G and induces their ubiquitination and subsequent degradation by the proteosome.¹⁶ It also may inhibit these proteins through other mechanisms. APOBEC3F and APOBEC3G are cytidine deaminases that hypermutate the negative-sense strand of HIV cDNA, leading to weak or nonviable viruses.¹⁷ These proteins also interfere with reverse transcription by blocking tRNALys3 from binding to the HIV RNA 5’UTR (tRNALys3 usually acts as a primer to initiate reverse transcription of the HIV genome).¹⁸

Vpr facilitates nuclear import of the HIV pre-integration complex.¹⁹ The pre-integration complex consists of viral cDNA and associated proteins (uncoating and reverse transcription have already occurred at this stage). Vpr binds the pre-integration complex and recruits host importins to enable nuclear import. It may further enhance nuclear import through interactions with some of the nuclear pore proteins. In addition to nuclear import, Vpr has several more functions: it acts as a coactivator (along with other proteins) of the HIV 5’UTR’s U3 promoter, might influence NF-κB regulation, may modulate apoptotic pathways, and arrests the cell cycle at the G₂ stage.

Life cycle:

CD4+ T cells represent the primary targets of HIV, though the virus is also capable of infecting other cell types such as dendritic cells.²⁰ HIV infects CD4+ T cells through binding its gp120 glycoprotein to the CD4 receptor and the CCR5 coreceptor or the CXCR4 coreceptor.¹⁰ This triggers fusion of the viral envelope with the plasma membrane and allows the core capsid to enter the cytosol.

HIV’s core capsid is transported by motor proteins along microtubules to dock at nuclear pores. The nuclear pore complex has flexible cytosolic filaments composed primarily of the Nup358 protein, which interacts with the core capsid.²¹ These interactions guide the narrow end of the core capsid into the nuclear pore’s central channel. Next, the core capsid interacts with the central channel’s unstructured phenylalanine-glycine (FG) repeats that exist in a hydrogel-like liquid phase. As the core capsid translocates through the central pore, it binds the Nup153 protein, a component of the nuclear pore complex’s basket. Finally, many copies of the nucleoplasmic CPSF6 protein coat the core capsid and escort it towards its genomic site of integration. It is thought that the reverse transcription process begins inside of the core capsid at this point, leading to cDNA synthesis.^21,22 Buildup of newly made cDNA within the core capsid likely results in pressure that helps rupture the capsid structure, facilitating uncoating.

Tetrameric HIV integrase binds both of the viral LTRs and facilitates integration of the cDNA into the host genome.²³ Though integration sites vary widely, they are not entirely random. Host chromatin structure and other factors influence where the viral cDNA integrates.²⁴ Transcription of HIV RNAs can then proceed from the U3 promoter with the aid of the Tat protein and host factors. As described earlier, a series of RNA splicing events produce the various RNAs necessary to synthesize all of the different HIV proteins and polyproteins.

Env protein is trafficked to the cell membrane through the secretory pathway. It is cleaved by a host furin enzyme into gp41 and gp160 components during its time in the endoplasmic reticulum.⁹ Gag and Gag-Pol polyproteins are expressed cytosolically. Since Gag is post-translationally modified by amino-terminal myristoylation, it anchors to the cell membrane by inserting its myristate tail into the lipid bilayer.²⁵ Gag and a smaller number of Gag-Pol accumulate on the inner membrane surface and incorporate gp41-gp160 complexes. NC domains in the Gag proteins bind and help package the two copies of HIV genomic RNA. The p6 region of the Gag protein (located at the C-terminal end) then recruits host ESCRT-I and ALIX proteins, which subsequently sequester host ESCRT-III and VPS4 complexes to drive budding and membrane scission, releasing virus into the extracellular space. After this, the HIV viral protease (from within the Gag-Pol polyprotein) cleaves the Gag and Gag-Pol polyproteins into their constituent proteins, facilitating maturation of the released HIV particles.

SARS-CoV-2

Genome and Structure:

The SARS-CoV-2 genome consists of about 30 kb of linear positive-sense ssRNA. There is a m⁷G-cap (specifically m⁷GpppA₁) at the 5’ end of the genome and a 30-60 nucleotide poly-A tail at the 3’ end of the genome. These protective structures minimize exonuclease degradation.²⁶ The genome also has a 5’ UTR and a 3’ UTR which contain sequences that aid in transcriptional regulation and in packaging. The SARS-CoV-2 genome directly translates two partially overlapping polyproteins, ORF1a and ORF1b. There is a –1 ribosomal frameshift in ORF1b relative to ORF1a. Within the polyproteins, two self-activating proteases (Papain-like protease PLpro and 3-chymotrypsin-like protease 3CLpro) perform cleavage events that lead to the generation of the virus’s 16 non-structural proteins (nsps). It should be noted that the 3CLpro is also known as the main protease or M^pro. The coronavirus also produces 4 structural proteins, but these are not translated until after the synthesis of corresponding subgenomic RNAs via the viral replication complex. To create these subgenomic RNAs, negative-sense RNA must first be made and then undergo conversion back to positive-sense RNA for translation. Genes encoding the structural proteins are located downstream of the ORF1b section.

SARS-CoV-2’s four structural proteins include the N, E, M, and S proteins. Many copies of the N (nucleocapsid) protein bind the RNA genome and organize it into a helical ribonucelocapsid complex. The complex undergoes packaging into the viral envelope during coronavirus budding. Interactions between the N protein and the other structural proteins may facilitate this packaging process. The N protein also inhibits host immune responses by antagonizing viral suppressor RNAi and by blocking the signaling of interferon production pathways.²⁷

The transmembrane E (envelope) protein forms pentamers and plays a key but poorly understood role in the budding of viral envelopes into the endoplasmic reticulum Golgi intermediate compartment (ERGIC).^28–30 Despite its importance in budding, mature viral particles do not incorporate very many E proteins into their envelopes. One of the posttranslational modifications of the E protein is palmitoylation. This aids subcellular trafficking and interactions with membranes. E protein pentamers also act as ion channels that alter membrane potential.^31,32 This may lead to inflammasome activation, a contributing factor to cytokine storm induction.

The M (membrane) protein is the most abundant protein in the virion and drives global curvature in the ERGIC membrane to facilitate budding.^30,33 It forms transmembrane dimers that likely oligomerize to induce this curvature.³⁴ The M protein also has a cytosolic (and later intravirion) globular domain that likely interacts with the other structural proteins. M protein dimers also induce local curvature through preferential interactions with phosphatidylserine and phosphatidylinositol lipids.^29,30 M proteins help sequester S proteins into the envelopes of budding viruses.³⁵

The S (spike) protein of SARS-CoV-2 has been heavily studied due to its central roles in the infectivity and immunogenicity of the coronavirus. It forms a homotrimer that protrudes from the viral envelope and is heavily glycosylated. It binds the host’s ACE2 receptor (angiotensin-converting enzyme 2 receptor) and undergoes conformational changes to promote viral fusion.³⁶ The S protein undergoes cleavage into S1 and S2 subunits by the host’s furin protease during viral maturation.^37,38 This enhances SARS-CoV-2 entry into lung cells and may partially explain the virus’s high degree of transmissibility. The S1 fragment contains the receptor binding domain (RBD) and associated machinery while the S2 fragment facilitates fusion. Prior to cellular infection, most S proteins exist in a closed prefusion conformation where the RBDs of each monomer are hidden most of the time.³⁹ After the S protein binds ACE2 during transient exposure of one of its RBDs, the other two RBDs quickly bind as well. This binding triggers a conformational change in the S protein that loosens the structure, unleashing the S2 fusion component and exposing another proteolytic cleavage site called S2’. Host transmembrane proteases such as TMPRSS2 cut at S2’, causing the full activation of the S2 fusion subunit and the dramatic elongation of the S protein into the postfusion conformation. This results in the viral envelope fusing with the host membrane and uptake of the coronavirus’s RNA into the cell.

The 16 nsps of SARS-CoV-2 play a variety of roles. For instance, nsp1 shuts down host cell translation by plugging the mRNA entry channel of the ribosome, inhibiting the host cell’s immune responses and maximizing viral production.^40,41 Viral proteins still undergo translation because a conserved sequence in the coronavirus RNA helps circumvent the blockage through a poorly understood mechanism. The nsp5 protein is the protease 3CLpro.⁴² The nsp3 protein contains several subcomponents, including the protease PLpro. The nsp12, nsp7, and nsp8 proteins come together to form the RNA-dependent RNA polymerase (RdRp) that replicates the viral genome.^42,43 The nsp2 protein is likely a topoisomerase which functions in RNA replication. The nsp4 and nsp6 proteins as well as certain subcomponents of nsp3 restructure intracellular host membranes into double-membrane vesicles (DMVs) which compartmentalize viral replication.⁴⁴

Beyond the 4 structural proteins and 16 nsps of SARS-CoV-2, the coronaviral genome also encodes some poorly understood accessory proteins including ORF3a, ORF3b, ORF6, ORF7a, ORF7b, ORF8 and ORF9b.⁴⁵ These accessory proteins are non-essential for replication in vitro, but they are thought to be required for the virus’s full degree of virulence in vivo.

Life cycle:

As mentioned, SARS-CoV-2 infects cells by first binding a S protein RBD to the ACE2 receptor. This triggers a conformational change that elongates the S protein’s structure and reveals the S2 fusion fragment, facilitating fusion of the virion envelope with the host cell membrane.³⁹ Cleavage of the S’ site by proteases like TMPRSS2 aid this change from the prefusion to postfusion configurations. Alternatively, SARS-CoV-2 can enter the cell by binding to ACE2, undergoing endocytosis, and fusing with the endosome to release its genome (as induced by endosomal cathepsin proteases).⁴⁵ After release of the SARS-CoV-2 genome into the cytosol, the N protein disassociates and allows translation of ORF1a and ORF1b, producing polyproteins which are cleaved into mature proteins by the PLpro and 3CLpro proteases as discussed earlier.

The RdRp complex synthesizes negative-sense full genomic RNAs as well as negative-sense subgenomic RNAs. In the latter case, discontinuous transcription is employed, a process by which the RdRp jumps over certain sections of the RNA and initiates transcription separately from the rest of the genome.⁴⁶ The negative-sense RNAs are subsequently converted back into positive-sense full genomic RNAs and positive-sense subgenomic RNAs. The subgenomic RNAs are translated to make structural proteins and some accessory proteins.⁴⁵

As described earlier, the nsp4, nsp6, and parts of nsp3 proteins remodel host endoplasmic reticulum (ER) to create DMVs.⁴⁵ These DMVs are the site of the coronaviral genomic replication and serve to shield the viral RNA and RdRp complex from cellular innate immune factors. DMVs cluster together and are continuous with the ER mostly through small tubular connections. After replication, the newly synthesized coronavirus RNAs undergo export into the cytosol through molecular pore complexes that span both membranes of the DMVs.⁴⁷ These molecular pore complexes are composed of nsp3 domains and possibly other viral and/or host proteins.

Newly replicated SARS-CoV-2 genomic RNAs complex with N proteins to form helical nucleocapsids. To enable packaging, the nucleocapsids interact with M protein cytosolic domains which protrude at the ERGIC.⁴⁸ M proteins, E proteins, and S proteins are all localized to the ERGIC membrane. The highly abundant M proteins induce curvature of the membrane to facilitate budding. As mentioned, E proteins also play essential roles in budding, but the mechanisms are poorly understood. Once the virions have budded into the ERGIC, they are shuttled through the Golgi via a series of vesicles and eventually secreted out of the cell.

Adeno-associated virus (AAV)

Genome and Structure:

AAV genomes are about 4.7 kb in length and are composed of ssDNA. Inverted terminal repeats (ITRs) form hairpin structures at ends of the genome. These ITR structures are important for AAV genomic packaging and replication. Rep genes (encoded via overlapping reading frames) include Rep78, Rep68, Rep52, Rep40.⁴⁹ These proteins facilitate replication of the viral genome. As a Dependoparvovirus, additional helper functions from adenovirus (or certain other viruses) are needed for AAVs to replicate.

AAV capsids are about 25 nm in diameter. Cap genes include VP1, VP2, VP3 and are transcribed from overlapping reading frames.⁵⁰ The VP3 protein is the smallest capsid protein. The VP2 protein is the same as VP3 except that it includes an N-terminal extension with a nuclear localization sequence. The VP1 protein is the same as VP2 except that it includes a further N-terminal extension encoding a phospholipase A2 (PLA2) that facilitates endosomal escape during infection. In the AAV capsid, VP1, VP2, and VP3 are present at a ratio of roughly 1:1:10. It should be noted that this ratio is actually the average of a distribution, not a fixed number.

Frame-shifted start codons in the Cap gene region transcribe AAP (assembly activating protein) and MAAP (membrane associated accessory protein). These proteins help facilitate packaging and other aspects of the AAV life cycle.

Life cycle:

There are a variety of different AAV serotypes (AAV2, AAV6, AAV9, etc.) that selectively infect certain tissue types. AAVs bind to host cell receptors and are internalized by endocytosis. The particular receptors involved can vary depending on the AAV serotype, though some receptors are consistent across many serotypes. Internalization occurs most often via clathrin-coated pits, but some AAVs are internalized by other routes such as macropinocytosis or the CLIC/GEEC tubulovesicular pathway.⁵¹

After endocytosis, conformational changes in the AAV capsid lead to exposure of the PLA2 VP1 domain, which facilitates endosomal escape. The AAV is then transported to the nucleus mainly by motor proteins on cytoskeletal highways. It enters via nuclear pores and finishes uncoating its genome.

AAV genomes initiate replication using the ends of their ITR hairpins as primers. This leads to a series of complex steps involving strand displacement and nicking.⁴⁹ In the end, new copies of the AAV genome are synthesized. The Rep proteins are key players in this process. It is important to realize that AAVs can only replicate in cells which have also been infected by adenovirus or similar helper viruses (this is why they are called “adeno-associated viruses”). Adenoviruses provide helper genes encoding proteins (e.g. E4, E2a, VA) that are vital for the successful completion of the AAV life cycle. After new AAV capsids have assembled from VP1, VP2, and VP3 and once AAV genomes have been replicated, the ssDNA genomes are threaded into the capsids via pores at their five-fold vertices.

AAVs are nonpathogenic, though a large fraction of people possess antibodies against at least some serotypes, so exposure to them is fairly common.

Adenovirus

Genome and Structure:

Adenovirus genomes are about 36 kb in size and are composed of linear dsDNA. They possess inverted terminal repeats (ITRs) which help facilitate replication and other functions. These genomes contain a variety of transcriptional units which are expressed at different times during the virus’s life cycle.⁵² E1A, E1B, E2A, E2B, E3, and E4 transcriptional units are expressed early during cellular infection. Their proteins are involved in DNA replication, transcriptional regulation, and suppression of host immune responses. The L1, L2, L3, L4, and L5 transcriptional units are expressed later in the life cycle. Their products include most of the capsid proteins as well as other proteins involved in packaging and assembly. Each transcriptional unit can produce multiple mRNAs through the host’s alternative splicing machinery.

The capsid of the adenovirus is about 90 nm in diameter and consists of three major proteins (hexon, penton, and fiber proteins) as well as a variety of minor proteins and core proteins. Hexon trimer is the most abundant protein in the capsid, the pentameric pentons occur at the vertices, and trimeric fibers are positioned on top of the pentons.⁵³ The fibers point outwards from the capsid and end in knob domains which bind to cellular receptors. In Ad5, a commonly studied type of adenovirus, the fiber knob primarily binds to the coxsackievirus and adenovirus receptor (CAR). That said, it should be noted that Ad5’s fiber knob can also bind to alternative receptors such as vascular cell adhesion molecule 1 and heparan sulfate proteoglycans.

Minor capsid proteins include pIX, pIIIa, pVI, and pVIII. The pIX protein interlaces between hexons and helps stabilize the capsid. Though pIX is positioned in the crevices between the hexons, it is still exposed to the outside environment. By contrast, the pIIIa, pVI, and pVIII proteins bind to the inside of the capsid and contribute further structural stabilization. When the adenovirus is inside of the acidic endosome during infection, conformational changes in the capsid release the pVI protein, which facilitates endosomal escape through membrane lytic activity.

Adenovirus core proteins include pV, pVII, protein μ (also known as pX), adenovirus proteinase (AVP), pIVa2, and terminal protein (TP).⁵⁴ The pVII protein has many positively-charged arginine residues and so functions to condense the viral DNA. The pV protein bridges the core with the capsid through interactions with pVII and with pVI. AVP cleaves various adenoviral proteins (pIIIa, TP, pVI, pVII, pVIII, pX) to convert them to their mature forms.⁵⁵ The pIVa2 and pX proteins interact with the viral DNA and may play roles in packaging or replication. TP binds to the ends of the genome and is essential for localizing the viral DNA in the nucleus and for viral replication.

Life Cycle:

Adenovirus infects cells by binding its fiber knob to cellular receptors such as CAR (in the case of Ad5). The penton then binds certain α_v integrins, positioning the viral capsid for endocytosis.⁵⁶ When the endosome acidifies, the adenovirus capsid partially disassembles, fibers and pentons fall away, and pVI is released.⁵⁷ The pVI protein’s membrane lytic activity facilitates endosomal escape. Partially disassembled capsids then undergo dynein-mediated transport along microtubules and dock at the entrance to nuclear pores. The capsids further disassemble and releases DNA through the nuclear pore. This DNA remains complexed with pVII after it enters the nucleus.

Adenoviral transcription is initiated by the E1A protein, inducing expression of early genes.⁵⁸ This subsequently leads to expression of the E2, E3, and E4 transcriptional units, which help the virus escape immune responses. This cascade leads to expression of the L1, L2, L3, L4, and L5 transcriptional units, which mainly synthesize viral structural proteins and facilitate capsid assembly.

In the nucleus, adenovirus genomes replicate within dense complexes of protein that can be seen as spots via fluorescence microscopy. Replication begins at the ITRs and is primed by TP.⁵⁹ Several more viral proteins and host proteins also aid the initiation of replication. Nontemplate strands are displaced during replication but may reanneal and act as template strands later. Adenovirus DNA binding protein and adenovirus DNA polymerase play important roles in replication. Once the genome has been replicated, TP undergoes cleavage into its mature form, signaling for packaging of new genomes.

The adenoviral capsid assembly and maturation process occurs in the nucleus.⁵⁸ Once enough assembled adenoviruses have accumulated, they rupture the nuclear membrane using adenoviral death protein and subsequently lyse the cell, releasing adenoviral particles.

Herpes Simplex Virus 1 (HSV-1)

Genome and Structure:

HSV-1 genomes are about 150 kb in size and are composed of linear dsDNA. These genomes include a unique long (U_L) region and a unique short (U_S) region.⁶⁰ The U_L and U_S regions are both flanked by their own inverted repeats. The terminal inverted repeats are called TR_L and TR_S while the internal inverted repeats are called IR_L and IR_S. HSV-1 contains approximately 80 genes, though the complexity of its genomic organization makes an exact number of genes difficult to obtain. As with many other viruses, HSV-1 genomes encode early, middle, and late genes. The early genes activate and regulate transcription of the middle and late genes. Middle genes facilitate genome replication and late genes mostly encode structural proteins.

The diameter of HSV-1 ranges around 155 nm to 240 nm.⁶¹ Its virions include an inner icosahedral capsid (with a 125 nm diameter) surrounded by tegument proteins which are in turn enveloped by a lipid membrane containing glycoproteins.

HSV-1’s icosahedral capsid consists of a variety of proteins. Some of the most important capsid proteins are encoded by the UL19, UL18, UL38, UL6, UL17, and UL25 genes.⁶² The UL19 gene encodes the major capsid protein VP5, which forms pentamers and hexamers for the capsid. These VP5 pentamers and hexamers are glued together by triplexes consisting of two copies of VP23 (encoded by UL18) and one copy of VP19C (encoded by UL38).⁶³ The UL6 gene encodes the protein that makes up the portal complex, a structure used by HSV-1 to release its DNA during infection. Each HSV-1 capsid has a single portal (composed of 12 copies of the portal protein) located at one of the vertices. UL17 and UL25 encode additional structural proteins that stabilize the capsid by binding on top of the other vertices. These two proteins also serve as a bridge between the capsid core and the tegument proteins.

The tegument of HSV-1 contains dozens of distinct proteins. Some examples include pUL36, pUL37, pUL7, and pUL51 proteins. The major tegument proteins are pUL36 and pUL37. The pUL36 protein binds on top of the UL17-UL25 complexes at the capsid’s vertices.⁶⁴ The pUL37 protein subsequently associates with pUL36. The pUL51 protein associates with cytoplasmic membranes in infected cells and recruits the pUL7 protein.⁶⁵ This pUL51-pUL7 interaction is important for HSV-1 assembly. HSV-1 has many more tegument proteins which play various functional roles.

HSV-1’s envelope contains up to 16 unique glycoproteins. Four of these glycoproteins (gB, gD, gH, and gL) are essential for viral entry into cells.⁶⁶ The gD glycoprotein first binds to one of its cellular receptors (nectin-1, herpesvirus entry mediator or HVEM, or 3-O-sulfated heparan sulfate). This binding event triggers a conformational change in gD that allows it to activate the gH/gL heterodimer. Next, gH/gL activate gB which induces fusion of HSV-1’s envelope with the cell membrane. Though the remaining 12 envelope glycoproteins are poorly understood, it is thought that they also play roles that influence cellular tropism and entry.

Life cycle:

After binding to cellular receptors via its glycoproteins, HSV-1 induces fusion of its envelope with the host cell membrane.⁶⁷ The capsid is trafficked to nuclear pores via microtubules. Since the capsid is too large to pass through a nuclear pore directly, the virus instead ejects its DNA through the pore via the portal complex.⁶⁸

HSV-1 replicates its genome and assembles its capsids in the nucleus. But the assembled capsids are again too large to exist the nucleus through nuclear pores. To overcome this issue, HSV-1 first buds via the inner nuclear membrane into the perinuclear cleft (the space between nuclear membranes), acquiring a primary envelope.⁶⁷ This process is driven by a pair of proteins (pUL34 and pUL31) which together form the nuclear egress complex. Next, the primary envelope fuses with the outer nuclear membrane, releasing the assembled capsids into the cytosol.

To acquire its final envelope, the HSV-1 capsid likely buds into the trans-Golgi network or into certain tubular vesicular organelles.⁶⁹ These membrane sources contain the envelope proteins of the virus as produced by transcription and various secretory pathways. One player is the pUL51 tegument protein that starts associated with the membrane into which the virus buds. The interaction between pUL51 and pUL7 helps facilitate recruitment of the capsid to the membrane. (Capsid envelopment is also coupled in many other ways to formation of the outer tegument). The enveloped virion eventually undergoes trafficking through the secretory system and eventually is packaged into exosomes that fuse with the cell membrane and release completed virions into the extracellular environment.

In humans, HSV-1 infects the epithelial cells first and produces viral particles.⁷⁰ It subsequently enters the termini of sensory neurons, undergoes retrograde transport into the brain, and remains in the central nervous system in a dormant state. During periods of stress in the host, the virus is reactivated and undergoes anterograde transport to infect epithelial cells once again.

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Resource: List of Biotechnology Companies to Watch

May 10, 2021November 17, 2025By logancollins 5 Comments

PDF version: List of Biotechnology Companies to Watch – by Logan Thrasher Collins

I created this list of organizations (162 total to date) to serve as a resource to help people learn about and keep track of key biotechnology companies. Some of these are emerging startups, some are established giants, and some provide useful services. Some notable nonprofit research organizations are included as well. Though this list is far from comprehensive, I have tried to cover as many of the key players as possible. It is also important to realize that this landscape is constantly changing, so some of the information on this list will eventually transition into antiquity. The list was originally started over the course of 2021, updated during the summer of 2022, updated during the summer of 2024, updated in January 2025, and updated in September-October 2025. I hope you enjoy delving into the exciting world of biotechnology!

Global Highlights in Neuroengineering 2005-2018

January 14, 2019January 24, 2019By logancollins No Comments

PDF version: global highlights in neuroengineering 2005-2018 – logan thrasher collins

Optogenetic stimulation using ChR2

(Boyden, Zhang, Bamberg, Nagel, & Deisseroth, 2005)

Ed Boyden, Karl Deisseroth, and colleagues developed optogenetics, a revolutionary technique for stimulating neural activity.
Optogenetics involves engineering neurons to express light-gated ion channels. The first channel used for this purpose was ChR2 (a protein originally found in bacteria which responds to blue light). In this way, a neuron exposed to an appropriate wavelength of light will be stimulated.
Over time, optogenetics has gained a place as an essential experimental tool for neuroscientists across the world. It has been expanded upon and improved in numerous ways and has even allowed control of animal behavior via implanted fiber optics and other light sources. Optogenetics may eventually be used in the development of improved brain-computer interfaces.

optogenetics

Blue Brain Project cortical column simulation

(Markram, 2006)

In the early stages of the Blue Brain Project, neuronal cell types from the layers of the rat neocortex were reconstructed. Furthermore, their electrophysiology was experimentally characterized.
Next, a virtual neocortical column with about 10,000 multicompartmental Hodgkin-Huxley-type neurons and over ten million synapses was built. Its connectivity was defined according the patterns of connectivity found in biological rats, (though this involved the numbers of inputs and outputs quantified for given cell types rather than explicit wiring). In addition, the spatial distributions of boutons forming synaptic terminals upon target cells reflected biological data.
The cortical column was emulated using the Blue Gene/L supercomputer and the dynamics of the emulation reflected its biological counterpart.

Optogenetic silencing using halorhodopsin

(Han & Boyden, 2007)

Ed Boyden continued developing optogenetic tools to manipulate neural activity. Along with Xue Han, he expressed a codon-optimized version of a bacterial halorhodopsin (along with the ChR2 protein) in neurons.
Upon exposure to yellow light, halorhodopsin pumps chloride ions into the cell, hyperpolarizing the membrane and inhibiting neural activity.
Using halorhodopsin and ChR2, neurons could be easily activated and inhibited using yellow and blue light respectively.

halorhodopsin and chr2 wavelengths

Brainbow

(Livet et al., 2007)

Lichtman and colleagues used Cre/Lox recombination tools to create genes which express a randomized set of three or more differently-colored fluorescent proteins (XFPs) in a given neuron, labeling the neuron with a unique combination of colors. About ninety distinct colors were emitted across a population of genetically modified neurons.
The detailed structures within neural tissue equipped with the Brainbow system can be imaged much more easily since neurons can be distinguished via color contrast.
As a proof-of-concept, hundreds of synaptic contacts and axonal processes were reconstructed in a selected volume of the cerebellum. Several other neural structures were also imaged using Brainbow.
The fluorescent proteins expressed by the Brainbow system are usable in vivo.

High temporal precision optogenetics

(Gunaydin et al., 2010)

Karl Deisseroth, Peter Hegemann, and colleagues used protein engineering to improve the temporal resolution of optogenetic stimulation.
Glutamic acid at position 123 in ChR2 was mutated to threonine, producing a new ion channel protein (dubbed ChETA).
The ChETA protein allows for induction of spike trains with frequencies up to 200 Hz and greatly decreases the incidence of unintended spikes. Furthermore, ChETA eliminates plateau potentials (a phenomenon which interferes with precise control of neural activity).

ultrafast optogenetics

Hippocampal prosthesis in rats

(Berger et al., 2012)

Theodore Berger and his team developed an artificial replacement for neurons which transmit information from the CA3 region to the CA1 region of the hippocampus.
This cognitive prosthesis employs recording and stimulation electrodes along with a multi-input multi-output (MIMO) model to encode the information in CA3 and transfer it to CA1.
The hippocampal prosthesis was shown to restore and enhance memory in rats as evaluated by behavioral testing and brain imaging.

In vivo superresolution microscopy for neuroimaging

(Berning, Willig, Steffens, Dibaj, & Hell, 2012)

Stefan Hell (2014 Nobel laureate in chemistry) developed stimulated emission depletion microscopy (STED), a type of superresolution fluorescence microscopy which allows imaging of synapses and dendritic spines.
STED microscopy uses a torus-shaped de-excitation laser that interferes with the excitation laser to deplete fluorescence except in a very small spot. In this way, the diffraction limit is surpassed since the resulting light illuminates extremely small regions of the sample.
Neurons in transgenic mice (equipped with glass-sealed holes in their skulls) were imaged using STED. Synapses and dendritic spines were observed up to fifteen nanometers below the surface of the brain tissue.

In vivo three-photon microscopy

(Horton et al., 2013)

Multi-photon excitation uses pulsed lasers to excite fluorophores with two or more photons of light with long wavelengths. During the excitation, the photons undergo a nonlinear recombination process, yielding a single emitted photon with a much shorter wavelength. Because the excitation photons possess long wavelengths, they can penetrate tissue much more deeply than traditional microscopy allows.
Horton and colleagues developed a three-photon excitation method to facilitate even deeper tissue penetration than the commonly used two-photon microscopic techniques.
Since three photons were involved per excitation event, even longer excitation wavelengths (about 1,700 nm) were usable, allowing the construction of a 3-dimensional image stack that reached a depth of up to 1.4 mm within the living mouse brain.
Blood vessels and RFP-labeled neurons were imaged using this approach. Furthermore, the depth was sufficient to enable imaging of neurons within the mouse hippocampus.

3-photon microscopy

Whole-brain functional recording from larval zebrafish

(Ahrens, Orger, Robson, Li, & Keller, 2013)

Laser-scanning light-sheet microscopy was used to volumetrically image the entire brains of larval zebrafish (an optically transparent organism).
The genetically encoded calcium sensor GCaMP5G facilitated functional recording at single-cell resolution from about 80% of the total neurons in the larval zebrafish brains. Computational methods were used to distinguish between individual neurons.
Populations of neurons that underwent correlated activity patterns were identifiedto show the technique’s utility for uncovering the dynamics of neural circuits. These populations included hindbrain neurons that were functionally linked to neural activity in the spinal cord and a population of neurons which showed coupled oscillations on the left and right halves.

whole-brain recording from larval zebrafish

Eyewire: crowdsourcing method for retina mapping

(Marx, 2013)

The Eyewire project was created by Sebastian Seung’s research group. It is a crowdsourcing initiative for connectomic mapping within the retina towards uncovering neural circuits involved in visual processing.
Laboratories first collect data via serial electron microscopy as well as functional data from two-photon microscopy.
In the Eyewire game, images of tissue slices are provided to players who then help reconstruct neural morphologies and circuits by “coloring in” the parts of the images which correspond to cells and stacking many images on top of each other to generate 3D maps. Artificial intelligence tools help provide initial “best guesses” and guide the players, but the people ultimately perform the task of reconstruction.
By November 2013, around 82,000 participants had played the game. Its popularity continues to grow.

eyewire

The BRAIN Initiative

(“Fact Sheet: BRAIN Initiative,” 2013)

The BRAIN Initiative (Brain Research through Advancing Innovative Technologies) provided neuroscientists with $110 million in governmental funding and $122 million in funding from private sources such as the Howard Hughes Medical Institute and the Allen Institute for Brain Science.
The BRAIN Initiative focused on funding research which develops and utilizes new technologies for functional connectomics. It helped to accelerate research on tools for decoding the mechanisms of neural circuits in order to understand and treat mental illness, neurodegenerative diseases, and traumatic brain injury.
The BRAIN Initiative emphasized collaboration between neuroscientists and physicists. It also pushed forward nanotechnology-based methods to image neural tissue, record from neurons, and otherwise collect neurobiological data.

The CLARITY method for making brains translucent

(Chung & Deisseroth, 2013)

Karl Deisseroth and colleagues developed a method called CLARITY to make samples of neural tissue optically translucent without damaging the fine cellular structures in the tissue. Using CLARITY, entire mouse brains have been turned transparent.
Mouse brains were infused with hydrogel monomers (acrylamide and bisacrylamide) as well as formaldehyde and some other compounds for facilitating crosslinking. Next, the hydrogel monomers were crosslinked by incubating the brains at 37°C. Lipids in the hydrogel-stabilized mouse brains were extracted using hydrophobic organic solvents and electrophoresis.
CLARITY allows antibody labeling, fluorescence microscopy, and other optically-dependent techniques to be used for imaging entire brains. In addition, it renders the tissue permeable to macromolecules, which broadens the types of experimental techniques that these samples can undergo (i.e. macromolecule-based stains, etc.)

X-ray microtomography used to reconstruct Drosophila brain hemisphere

(Mizutani, Saiga, Takeuchi, Uesugi, & Suzuki, 2013)

Mizutani and colleagues stained Drosophila brains with silver nitrate and tetrachloroaurate (a gold-containing compound), facilitating 3-dimensional imaging using X-ray microtomography at a voxel size of 220 × 328 × 314 nm.
To generate the X-rays, a synchrotron source was used. It should be noted that synchrotron sources require large facilities to operate.
Neuronal tracing was performed manually on the 3-dimensional X-ray images of the fly brain, a process which took about 1,700 person-hours. Some neuronal processes were too dense to be resolved, so they were “fused” into unified structures. Furthermore, some neuronal traces were fragmented and most of the cell bodies were not considered. This decreased the number of traces to one third of the estimated number of actual processes in the hemisphere.
Mizutani’s investigation represents an early effort at large-scale connectomics that sets the stage for further initiatives as neuronal tracing, sample preparation, and X-ray microtomography technologies continue to improve.

traced drosophila brain hemisphere

Telepathic rats engineered using hippocampal prosthesis

(S. Deadwyler et al., 2013)

Berger’s hippocampal prosthesis was implanted in pairs of rats. When “donor” rats were trained to perform a task, they developed neural representations (memories) which were recorded by their hippocampal prostheses.
The donor rat memories were run through the MIMO model and transmitted to the stimulation electrodes of the hippocampal prostheses implanted in untrained “recipient” rats. After receiving the memories, the recipient rats showed significant improvements on the task that they had not been trained to perform.

Integrated Information Theory 3.0

(Oizumi, Albantakis, & Tononi, 2014)

Integrated information theory (IIT) was originally proposed by Giulio Tononi in 2004. IIT is a quantitative theory of consciousness which may help explain the hard problem of consciousness.
IIT begins by assuming the following phenomenological axioms; each experience is characterized by how it differs from other experiences, an experience cannot be reduced to interdependent parts, and the boundaries which distinguish individual experiences are describable as having defined “spatiotemporal grains.”
From these phenomenological axioms and the assumption of causality, IIT identifies maximally irreducible conceptual structures (MICS) associated with individual experiences. MICS represent particular patterns of qualia that form unified percepts.
IIT also outlines a mathematical measure of an experience’s quantity. This measure is called integrated information or ϕ.

Openworm

(Szigeti et al., 2014)

The anatomical elegans connectome was originally mapped in 1976 by Albertson and Thomson. More data has since been collected on neurotransmitters, electrophysiology, cell morphology, and other characteristics.
Szigeti, Larson, and their colleagues made an online platform for crowdsourcing research on elegans computational neuroscience, with the goal of completing an entire “simulated worm.”
The group also released software called Geppetto, a program that allows users to manipulate both multicompartmental Hodgkin-Huxley models and highly efficient soft-body physics simulations (for modeling the worm’s electrophysiology and anatomy).

Expansion microscopy

(F. Chen, Tillberg, & Boyden, 2015)

The Boyden group developed expansion microscopy, a method which enlarges neural tissue samples (including entire brains) with minimal structural distortions and so facilitates superior optical visualization of the scaled-up neural microanatomy. Furthermore, expansion microscopy greatly increases the optical translucency of treated samples.
Expansion microscopy operates by infusing a swellable polymer network into brain tissue samples along with several chemical treatments to facilitate polymerization and crosslinking and then triggering expansion via dialysis in water. With 4.5-fold enlargement, expansion microscopy only distorts the tissue by about 1% (computed using a comparison between control superresolution microscopy of easily-resolvable cellular features and the expanded version).
Before expansion, samples can express various fluorescent proteins to facilitate superresolution microscopy of the enlarged tissue once the process is complete. Furthermore, expanded tissue is highly amenable to fluorescent stains and antibody-based labels.

expansion microscopy

Japan’s Brain/MINDS project

(Okano, Miyawaki, & Kasai, 2015)

In 2014, the Brain/MINDS (Brain Mapping by Integrated Neurotechnologies for Disease Studies) project was initiated to further neuroscientific understanding of the brain. This project received nearly $30 million in funding for its first year alone.
Brain/MINDS focuses on studying the brain of the common marmoset (a non-human primate abundant in Japan), developing new technologies for brain mapping, and understanding the human brain with the goal of finding new treatments for brain diseases.

The TrueNorth chip from DARPA and IBM

(Akopyan et al., 2015)

The TrueNorth neuromorphic computing chip was constructed and validated by DARPA and IBM. TrueNorth uses circuit modules which mimic neurons. Inputs to these fundamental circuit modules must overcome a threshold in order to trigger “firing.”
The chip can emulate up to a million neurons with over 250 million synapses while requiring far less power than traditional computing devices.

Human Brain Project cortical mesocircuit reconstruction and simulation

(Markram et al., 2015)

The Human Brain Project reconstructed a 0.29 mm³ region of rat cortical tissue including about 31,000 neurons and 37 million synapses based on morphological data, statistical connectivity rules (rather than exact connectivity), and other datasets. The cortical mesocircuit was emulated using the Blue Gene/Q supercomputer.
This emulation was sufficiently accurate to reproduce emergent neurological processes and yield insights on the mechanisms of their computations.

Recording from C. elegans neurons reveals motor operations

(Kato et al., 2015)

Live elegans worms were immobilized in microfluidic devices and the neurons in their head ganglia as well as some of their motor systems were imaged and recorded from using the calcium indicator GCaMP. As the C. elegans connectome is well-characterized, Kato and colleagues were able to determine the identities of most of the cells that underwent imaging (with the help of computational segmentation techniques).
Principal component analysis was used to reduce the dimensionality of the neural activity datasets since over 100 neurons per worm were recorded from simultaneously.
Next, phase space analysis was utilized to visualize the patterns formed by the recording data. Motor behaviors including dorsal turns, ventral turns, forward movements, and backward movements were found to correspond to specific sequences of neural events as uncovered by examining the patterns found in the phase plots. Further analyses revealed various insights about these brain dynamics and their relationship to motor actions.

c. elegans brain dynamics

Neural lace

(Liu et al., 2015)

Charles Lieber’s group developed a syringe-injectable electronic mesh made of submicrometer-thick wiring for neural interfacing.
The meshes were constructed using novel soft electronics for biocompatibility. Upon injection, the neural lace expands to cover and record from centimeter-scale regions of tissue.
Neural lace may allow for “invasive” brain-computer interfaces to circumvent the need for surgical implantation. Lieber has continued to develop this technology towards clinical application.

BigNeuron initiative towards standardized neuronal morphology acquisition

(Peng et al., 2015)

Because of the inconsistencies between neuronal reconstruction methods and lack of standardization found in neuronal morphology databases, BigNeuron was established as a community effort to improve the situation.
BigNeuron tests as many automated neuronal reconstruction algorithms as possible using large-scale microscopy datasets (from several types of light microscopy). It uses the Vaa3D neuronal reconstruction software as a central platform. Reconstruction algorithms are added to Vaa3D as plugins. These computational tests are performed on supercomputers.
BigNeuron aims to create a superior community-oriented neuronal morphology database, a set of greatly improved tools for neuronal reconstruction, a standardized protocol for future neuronal reconstructions, and a library of morphological feature definitions to facilitate classification.

Human telepathy during a 20 questions game

(Stocco et al., 2015)

Using an interactive question-and-answer setup, Stocco and colleagues demonstrated real-time telepathic communication between pairs of individuals via EEG and transcranial magnetic stimulation. Five pairs of participants played games of 20 questions and attempted to identify unknown objects.
EEG data were recorded from the respondent, computationally processed, and transmitted as transcranial magnetic stimulation signals into the mind (occipital lobe stimulation) of a respondent. The respondent’s answers were translated into higher-intensity transcranial magnetic stimulation pulses corresponding to “yes” answers or lower-intensity transcranial magnetic stimulation pulses corresponding to “no” answers.
When compared to control trials in which sham interfaces were used, the people using the brain-brain interfaces were significantly more successful at playing 20 questions games.

Expansion FISH

(F. Chen et al., 2016)

Boyden, Chen, Marblestone, Church, and colleagues combined fluorescent in situ hybridization (FISH) with expansion microscopy to image the spatial localization of RNA in neural tissue.
The group developed a chemical linker to covalently attach intracellular RNA to the infused polymer network used in expansion microscopy. This allowed for RNAs to maintain their relative spatial locations within each cell post-expansion.
After the tissue was enlarged, FISH was used to fluorescently label targeted RNA molecules. In this way, RNA localization was more effectively resolved.
As a proof-of-concept, expansion FISH was used to reveal the nanoscale distribution of long noncoding RNAs in nuclei as well as the locations of RNAs within dendritic spines.

Neural dust

(Seo et al., 2016)

Michel Maharbiz’s group invented implantable, ~ 1 mm biosensors for wireless neural recording and tested them in rats.
This neural dust could be miniaturized to less than 0.5 mm or even to microscale dimensions using customized electronic components.
Neural dust motes consist of two recording electrodes, a transistor, and a piezoelectric crystal.
The neural dust received external power from ultrasound. Neural signals were recorded by measuring disruptions to the piezoelectric crystal’s reflection of the ultrasound waves. Signal processing mathematics allowed precise detection of activity.

The China Brain Project

(Poo et al., 2016)

The China Brain Project was launched to help understand the neural mechanisms of cognition, develop brain research technology platforms, develop preventative and diagnostic interventions for brain disorders, and to improve brain-inspired artificial intelligence technologies.
This project will be take place from 2016 until 2030 with the goal of completing mesoscopic brain circuit maps.
China’s population of non-human primates and preexisting non-human primate research facilities give the China Brain Project an advantage. The project will focus on studying rhesus macaques.

Somatosensory cortex stimulation for spinal cord injuries

(Flesher et al., 2016)

Gaunt, Flesher, and colleagues found that microstimulation of the primary somatosensory cortex (S1) partially restored tactile sensations to a patient with a spinal cord injury.
Electrode arrays were implanted into the S1 regions of a patient with a spinal cord injury. The array performed intracortical microstimulation over a period of six months.
The patient reported locations and perceptual qualities of the sensations elicited by microstimulation. The patient did not experience pain or “pins and needles” from any of the stimulus trains. Overall, 93% of the stimulus trains were reported as “possibly natural.”
Results from this study might be used to engineer upper-limb neuroprostheses which provide somatosensory feedback.

Simulation of rat CA1 region

(Bezaire, Raikov, Burk, Vyas, & Soltesz, 2016)

Detailed computational models of 338,740 neurons (including pyramidal cells and various types of interneurons) were equipped with connectivity patterns based on data from the biological CA1 region. External inputs were also estimated using biological data and incorporated into the simulation. It is important to note that these connectivity patterns described the typical convergence and divergence of neurites to and from particular cell types rather than explicitly representing the exact connections found in the biological rat.
Each neuron was simulated using a multicompartmental Hodgkin-Huxley-type model with its morphological structure based on biological data from the given cell type. Furthermore, different cell types received different numbers of presynaptic terminals at specified distances from the soma. In total, over five billion synapses were present within the CA1 model.
The simulation was implemented on several different supercomputers. Due to the model’s complexity, a four second simulation took about four hours to complete.
As with the biological CA1 region, the simulation gave rise to gamma oscillations and theta oscillations as well as other biologically consistent phenomena. In addition, parvalbumin-expressing interneurons and neurogliaform cells were identified as drivers of the theta oscillations, demonstrating the utility of detailed neuronal simulations for uncovering biological insights.

ca1 simulation

UltraTracer enhances existing neuronal tracing software

(Peng et al., 2017)

UltraTracer is an algorithm that can improve the efficiency of existing neuronal tracing software for handling large datasets while maintaining accuracy.
Datasets with hundreds of billions of voxels were utilized to test UltraTracer. Ten existing tracing algorithms were augmented.
For most of the existing algorithms, the performance improvements were around 3-6 times, though a few showed improvements of 10-30 times. Even when using computers with smaller memory, UltraTracer was consistently able to enhance conventional software.
UltraTracer was made opensource and is available as a plugin for the Vaa3D tracing software suite.

Whole-brain electron microscopy in larval zebrafish

(Hildebrand et al., 2017)

Serial electron microscopy facilitated imaging of the entire brain of a larval zebrafish at 5.5 days post-fertilization.
Neuronal tracing software (a modified version of the CATMAID software) was used to reconstruct all the myelinated axons found in the larval zebrafish brain.
The reconstructed dataset included 2,589 myelinated axon segments along with some of the associated soma and dendrites. It should be noted that only 834 of the myelinated axons were successfully traced back to their cell bodies.

Hippocampal prosthesis in monkeys

(S. A. Deadwyler et al., 2017)

Theodore Berger continued developing his cognitive prosthesis and tested it in Rhesus Macaques.
As with the rats, monkeys with the implant showed substantially improved performance on memory tasks.

The $100 billion Softbank Vision Fund

(Lomas, 2017)

Masayoshi Son, the CEO of Softbank (a Japanese telecommunications corporation), announced a plan to raise $100 billion in venture capital to invest in artificial intelligence. This plan involved partnering with multiple large companies in order to raise this enormous amount of capital.
By the end of 2017, the Vision Fund successfully reached its $100 billion goal. Masayoshi Son has since announced further plans to continue raising money with a new goal of over $800 billion.
Masayoshi Son’s reason for these massive investments is the Technological Singularity. He agrees with Kurzweil that the Singularity will likely occur at around 2045 and he hopes to help bring the Singularity to fruition. Though Son is aware of the risks posed by artificial superintelligence, he feels that superintelligent AI’s potential to tackle some of humanity’s greatest challenges (such as climate change and the threat of nuclear war) outweighs those risks.

Bryan Johnson launches Kernel

(Regalado, 2017)

Entrepreneur Bryan Johnson invested $100 million to start Kernel, a neurotechnology company.
Kernel plans to develop implants that allow for recording and stimulation of large numbers of neurons at once. The company’s initial goal is to develop treatments for mental illnesses and neurodegenerative diseases. Its long-term goal is to enhance human intelligence.
Kernel originally partnered with Theodore Berger and intended to utilize his hippocampal prosthesis. Unfortunately, Berger and Kernel parted ways after about six months because Berger’s vision was reportedly too long-range to support a financially viable company (at least for now).
Kernel was originally a company called Kendall Research Systems. This company was started by a former member of the Boyden lab. In total, four members of Kernel’s team are former Boyden lab members.

Elon Musk launches NeuraLink

(Etherington, 2017)

Elon Musk (CEO of Tesla, SpaceX, and a number of other successful companies) initiated a neuroengineering venture called NeuraLink.
NeuraLink will begin by developing brain-computer interfaces (BCIs) for clinical applications, but the ultimate goal of the company is to enhance human cognitive abilities in order to keep up with artificial intelligence.
Though many of the details around NeuraLink’s research are not yet open to the public, it has been rumored that injectable electronics similar to Lieber’s neural lace might be involved.

Facebook announces effort to build brain-computer interfaces

(Constine, 2017)

Facebook revealed research on constructing non-invasive brain-computer interfaces (BCIs) at a company-run conference in 2017. The initiative is run by Regina Dugan, Facebook’s head of R&D at division building 8.
Facebook’s researchers are working on a non-invasive BCI which may eventually enable users to type one hundred words per minute with their thoughts alone. This effort builds on past investigations which have been used to help paralyzed patients.
The building 8 group is also developing a wearable device for “skin hearing.” Using just a series of vibrating actuators which mimic the cochlea, test subjects have so far been able to recognize up to nine words. Facebook intends to vastly expand this device’s capabilities.

DARPA funds research to develop improved brain-computer interfaces

(Hatmaker, 2017)

The U.S. government agency DARPA awarded $65 million in total funding to six research groups.
The recipients of this grant included five academic laboratories (headed by Arto Nurmikko, Ken Shepard, Jose-Alain Sahel and Serge Picaud, Vicent Pieribone, and Ehud Isacoff) and one small company called Paradromics Inc.
DARPA’s goal for this initiative is to develop a nickel-sized bidirectional brain-computer interface (BCI) which can record from and stimulate up to one million individual neurons at once.

Human Brain Project analyzes brain computations using algebraic topology

(Reimann et al., 2017)

Investigators at the Human Brain Project utilized algebraic topology to analyze the reconstructed ~ 31,000 neuron cortical microcircuit from their earlier work.
The analysis involved representing the cortical network as a digraph, finding directed cliques (complete directed subgraphs belonging to a digraph), and determining the net directionality of information flow (by computing the sum of the squares of the differences between in-degree and out-degree for all the neurons in a clique). In algebraic topology, directed cliques of n neurons are called directed simplices of dimension n-1.
Vast numbers of high-dimensional directed cliques were found in the cortical microcircuit (as compared to null models and other controls). Spike correlations between pairs of neurons within a clique were found to increase with the clique’s dimension and with the proximity of the neurons to the clique’s sink. Furthermore, topological metrics allowed insights into the flow of neural information among multiple cliques.
Experimental patch-clamp data supported the significance of the findings. In addition, similar patterns were found within the elegans connectome, suggesting that the results may generalize to nervous systems across species.

hbp algebraic topology

Early testing of hippocampal prosthesis algorithm in humans

(Song, She, Hampson, Deadwyler, & Berger, 2017)

Dong Song (who was working alongside Berger) tested the MIMO algorithm on human epilepsy patients using implanted recording and stimulation electrodes. The full hippocampal prosthesis was not implanted, but the electrodes acted similarly, though in a temporary capacity. Although only two patients were tested in this study, many trials were performed to compensate for the small sample size.
Hippocampal spike trains from individual cells in CA1 and CA3 were recorded from the patients during a delayed match-to-sample task. The patients were shown various images while neural activity data were recorded by the electrodes and processed by the MIMO model. The patients were then asked to recall which image they had been shown previously by picking it from a group of “distractor” images. Memories encoded by the MIMO model were used to stimulate hippocampal cells during the recall phase.
In comparison to controls in which the same two epilepsy patients were not assisted by the algorithm and stimulation, the experimental trials demonstrated a significant increase in successful pattern matching.

Brain imaging factory in China

(Cyranoski, 2017)

Qingming Luo started the HUST-Suzhou Institute for Brainsmatics, a brain imaging “factory.” Each of the numerous machines in Luo’s facility performs automated processing and imaging of tissue samples. The devices make ultrathin slices of brain tissue using diamond blades, treat the samples with fluorescent stains or other contrast-enhancing chemicals, and image then using fluorescence microscopy.
The institute has already demonstrated its potential by mapping the morphology of a previously unknown neuron which “wraps around” the entire mouse brain.

china brain mapping image

Automated patch-clamp robot for in vivo neural recording

(Suk et al., 2017)

Ed Boyden and colleagues developed a robotic system to automate patch-clamp recordings from individual neurons. The robot was tested in vivo using mice and achieved a data collection yield similar to that of skilled human experimenters.
By continuously imaging neural tissue using two-photon microscopy, the robot can adapt to a target cell’s movement and shift the pipette to compensate. This adaptation is facilitated by a novel algorithm called an imagepatching algorithm. As the pipette approaches its target, the algorithm adjusts the pipette’s trajectory based on the real-time two-photon microscopy.
The robot can be used in vivo so long as the target cells express a fluorescent marker or otherwise fluoresce corresponding to their size and position.

automated patch clamp system

Genome editing in the mammalian brain

(Nishiyama, Mikuni, & Yasuda, 2017)

Precise genome editing in the brain has historically been challenging because most neurons are postmitotic (non-dividing) and the postmitotic state prevents homology-directed repair (HDR) from occurring. HDR is a mechanism of DNA repair which allows for targeted insertions of DNA fragments with overhangs homologous to the region of interest (by contrast, non-homologous end-joining is highly unpredictable).
Nishiyama, Mikuni, and Yasuda developed a technique which allows genome editing in postmitotic mammalian neurons using adeno-associated viruses (AAVs) and CRISPR-Cas9.
The AAVs delivered ssDNA sequences encoding a single guide RNA (sgRNA) and an insert. Inserts encoding a hemagglutinin tag (HA) and inserts encoding EGFP were both tested. Cas9 was encoded endogenously by transgenic host cells and in transgenic host animals.
The technique achieved precise genome editing in vitro and in vivo with a low rate of off-target effects. Inserts did not cause deletion of nearby endogenous sequences for 98.1% of infected neurons.

Neuropixels probe

(Jun et al., 2017)

Jun and colleagues created the Neuropixels probe to facilitate simultaneous recording from hundreds of individual neurons with high spatiotemporal resolution. Previous extracellular probes were only able to record from a few dozen individual neurons.
The Neuropixels recording shank is one centimeter long and includes 384 recording channels. Due to the small size of the accompanying apparatus (a 6×9 mm base and a data transmission cable), it enables high-throughput recording in freely moving animals. Because the shank is quite long, Neuropixels can record from multiple brain regions at once.
Voltage signals are processed directly on the base of the Neuropixels apparatus, allowing for noise-free data transmission along the cable for further analysis.

neuropixels

EEG-based facial image reconstruction

(Nemrodov, Niemeier, Patel, & Nestor, 2018)

EEG data associated with viewing images of faces was collected and used to determine the neural correlates of facial processing. In this way, the images were computationally reconstructed in a fashion resembling “mind reading.”
It should be noted that the images reconstructed using data taken from multiple people were more accurate than the images reconstructed using single individuals. Nonetheless, the single individual data still yielded statistically significant accuracy.
In addition to reconstructing the images themselves, the process gave insights on the cognitive steps involved in perceiving faces.

eeg reconstructions of faces

Near-infrared light and upconversion nanoparticles for optogenetic stimulation

(S. Chen et al., 2018)

Upconversion nanoparticles absorb two or more low-energy photons and emit a higher energy photon. For instance, multiple near-infrared photons can be converted into a single visible spectrum photon.
Shuo Chen and colleagues injected upconversion nanoparticles into the brains of mice and used them to convert externally applied near-infrared (NIR) light into visible light within the brain tissue. In this way, optogenetic stimulation was performed without the need for surgical implantation of fiber optics or similarly invasive procedures.
The authors demonstrated stimulation via upconversion of NIR to blue light (to activate ChR2) and inhibition via upconversion of NIR to green light (to activate a rhodopsin called Arch).
As a proof-of-concept, this technology was used to alter the behavior of the mice by activating hippocampally-encoded fear memories.

upconversion nanoparticles and nir

Map of all neuronal cell bodies within mouse brain

(Murakami et al., 2018)

Ueda, Murakami, and colleagues combined methods from expansion microscopy and CLARITY to develop a protocol called CUBIC-X which both expands and clears entire brains. Light-sheet fluorescence microscopy was used to image the treated brains and a novel algorithm was developed to detect individual nuclei.
Although expansion microscopy causes some increased tissue transparency on its own, CUBIC-X greatly improved this property in the enlarged tissues, facilitating more detailed whole-brain imaging.
Using CUBIC-X, the spatial locations of all the cell bodies (but not dendrites, axons, or synapses) within the mouse brain were mapped. This process was performed upon several adult mouse brains as well as several developing mouse brains to allow for comparative analysis.
The authors made the spatial atlas publicly available in order to facilitate global cooperation towards annotating connectivity among the neural cell bodies within the atlas.

cubic-x

Clinical testing of hippocampal prosthesis algorithm in humans

(Hampson et al., 2018)

Further clinical tests of Berger’s hippocampal prosthesis were performed. Twenty-one patients took part in the experiments. Seventeen patients underwent CA3 recording so as to facilitate training and optimization of the MIMO model. Eight patients received CA1 stimulation so as to improve their memories.
Electrodes with the ability to record from single neurons (10-24 single-neuron recording sites) and via EEG (4-6 EEG recording sites) were implanted such that recording and stimulation could occur at CA3 and CA1 respectively.
Patients performed behavioral memory tasks. Both short-term and long-term memory showed an average improvement of 35% across the patients who underwent stimulation.

Precise optogenetic manipulation of fifty neurons

(Mardinly et al., 2018)

Mardinly and colleagues engineered a novel excitatory optogenetic ion channel called ST-ChroME and a novel inhibitory optogenetic ion channel called IRES-ST-eGtACR1. The channels were localized to the somas of host neurons and generated stronger photocurrents over shorter timescales than previously existing opsins, allowing for powerful and precise optogenetic stimulation and inhibition.
3D-SHOT is an optical technique in which light is tuned by a device called a spatial light modulator along with several other optical components. Using 3D-SHOT, light was precisely projected upon targeted neurons within a volume of 550×550×100 μm³.
By combining novel optogenetic ion channels and the 3D-SHOT technique, complex patterns of neural activity were created in vivo with high spatial and temporal precision.
Simultaneously, calcium imaging allowed measurement of the induced neural activity. More custom optoelectronic components helped avoid optical crosstalk of the fluorescent calcium markers with the photostimulating laser.

Whole-brain Drosophila connectome data acquired via serial electron microscopy

(Zheng et al., 2018)

Zheng, Bock, and colleagues collected serial electron microscopy data on the entire adult Drosophila connectome, providing the data necessary to reconstruct a complete structural map of the fly’s brain at the resolution of individual synapses, dendritic spines, and axonal processes.
The data are in the form of 7050 transmission electron microscopy images (187500 x 87500 pixels and 16 GB per image), each representing a 40nm-thin slice of the fly’s brain. In total the dataset requires 106 TB of storage.
Although much of the the data still must be processed to reconstruct a 3-dimensional map of the Drosophila brain, the authors did create 3-dimensional reconstructions of selected areas in the olfactory pathway of the fly. In doing so, they discovered a new cell type as well as several other previously unrealized insights about the organization of Drosophila’s olfactory biology.

Human telepathy using BrainNet

(Jiang et al., 2018)

EEG recordings were taken from two individuals (termed senders) while they played a Tetris-like game. Next, the recordings were converted into transcranial magnetic stimulation signals that acted to provide a third individual (called a receiver) with the necessary information to make decisions in the game without seeing the screen. The occipital cortex was stimulated. Fifteen people (five groups of three) took part in the study.
To convey their information, the senders were told to focus upon either a higher or a lower intensity light corresponding to commands within the game (the two lights were placed on different sides of the computer screen). In the receiver’s mind, this translated to perceiving a flash of light. The receiver was able to distinguish the intensities and implement the correct command within the game.
Using only the telepathically provided stimulation, the receiver made the correct game-playing decisions 81% of the time.

Transcriptomic cell type classification across mouse neocortex

(Tasic et al., 2018)

Single-cell RNA sequencing was used to characterize gene expression across 23,822 cells from the primary visual cortex and the anterior lateral motor cortex of mice.
Using dimensionality reduction and clustering methods, the resulting data were used to classify the neurons into 133 transcriptomic cell types.
Injections of adeno associated viruses (engineered to express fluorescent markers) facilitated retrograde tracing of neuronal projections within a subset of the sequenced cells. In this way, correspondences between projection patterns and transcriptomic identities were established.

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Company	Category	Description and Key Facts
Ablynx	Services	Nanobodies as therapeutics and as laboratory reagents.
Aera Therapeutics	Biomed	Developing protein nanoparticle delivery vehicles (originally the “selective endogenous encapsidation for cellular delivery” or SEND platform) for gene therapy which are based on proteins from endogenous virus-like particles encoded by the human genome. Also developing proprietary gene editing proteins of compact size to overcome packaging limits. Co-founded by Feng Zhang. Raised $193M in a February 2023 funding round.
AgeX Therapeutics	Biomed	Treating aging using stem cell therapies, induced tissue regeneration, related methods.
Aldevron	Services	Provides manufacturing and development services such as large-scale plasmid DNA synthesis, mRNA production, gene editing production, and antibody manufacturing. In 2025, worked with Integrated DNA Technologies to manufacture a personalized (N of 1) gene editing therapy for an infant with (otherwise untreatable) urea cycle disorder consisting of a lipid nanoparticle, custom gRNA, and an mRNA encoding a base editor. Manufacturing took 6 months, three times faster than the standard timeline. As of May 2025, the treatment was successful.
Allonnia	Ecotech	Engineering microorganisms and enzymes to degrade environmental pollutants. Funded by the Ferment Consortium of Ginkgo Bioworks.
Alora	Ecotech	Engineering salt-tolerant rice via CRISPR for ocean agriculture to feed the world. Formerly known as Agrisea. Early stage: raised a $1.4M seed round as of September 2022.
Altos Labs	Biomed	Developing cellular rejuvenation technologies to reverse age-related diseases and aging. Has raised over $3B from funders such as Jeff Bezos, Yuri Milner, and others (the most funding of any biotechnology company as of June 2024). Steve Horvath is one of the principal investigators working at Altos Labs. Main scientific advisor is Nobel Laureate Shinya Yamanaka.
Apertura Therapeutics	Biomed	Has developed TfR1-binding AAV capsids which efficiently cross the blood-brain-barrier while avoiding excessive liver transduction. Based on research published in Science by Huang et al. wherein mice expressing humanized TfR1 were used. Has engineered CD59-binding AAV which can cross the blood-brain-barrier, target brain tissue, and target muscle tissue. Founded by Ben Deverman, director of vector engineering at the Broad Institute. Leveraging cutting-edge machine learning tools to engineer AAV capsids simultaneously optimized for immune evasion, manufacturability, and tissue targeting. Collaborating with Dr. Sonia Vallabh at the Broad Institute to support her efforts to cure the prion disease fatal familial insomnia (which she herself will probably develop due to family genetics). Announced licensing deal with the Rett Syndrome Research Trust (RSRT) towards developing AAV-based treatments for Rett syndrome. Announced licensing deals with Galibra Neuroscience (for treating GABA-imbalance disorders) and Emugen Therapeutics (for treating neurodegenerative disorders) in August 2025. Launched with a $67M series A during 2022.
Aptah Biosciences	Biomed	Developing a rationally designed single-stranded DNA (lead compound APT20TTMG) that crosses the blood-brain-barrier, restores cellular RNA integrity, and corrects multiple proteins to facilitate brain rejuvenation and combat aging. APT20TTMG binds to pre-mRNA and facilitates proper U1 snRNP assembly to globally decrease cleavage of pre-mRNAs, decrease abnormal RNA splicing, decrease expression of inappropriately truncated proteins, and restore functionality of regulatory miRNAs. George Church and Aubrey de Grey are on the scientific advisory board.
Arena Bioworks	Biomed	Ended its operations as of November 2025 and is now defunct. Not a company but a biomedical research institute that employs principal investigators to lead basic research into the mechanisms of human disease, to develop therapies, and then to create spinoff companies that can translate those therapies to the clinic. Emphasizes translation by providing its investigators with the support and infrastructure to do so. Relies solely on private funding, thus its investigators do not need to apply for grants and can focus on the research. CRISPR pioneer Keith Joung is one of the first principal investigators at Arena. Co-founder and CEO is Stuart Schreiber, who also co-founded the Broad Institute. Launched with $500M in private funding. Located in Cambridge near MIT and Harvard.
Asimov	Biotech	Developing computer aided design tools for synthetic biology, making host cell lines for viral vector and biologics manufacturing, constructing genetic parts database. One of the co-founders is Christopher Voigt. James Collins is on the scientific advisory board.
Atomic AI	Bio-AI	Has developed AI tools for RNA 3D structure prediction as well as wet lab assays for evaluation. Their large language model ATOM-1 uses chemical mapping data to improve RNA optimization, predicting structural and functional properties of RNAs. Their foundational RNA structural prediction technology was published in Science during 2021. Leveraging their tools to develop therapeutic RNA-targeted small molecules and RNA-based medicines such as mRNA vaccines, siRNAs, and circular RNAs.
Aukera	Biomed	Developing protein vault delivery vectors for delivery of peptides, small molecules, and possibly nucleic acids. Their vault formulation is reportedly stable for years at room temperature.
Beam Therapeutics	Biomed	Developing base editor technologies towards therapeutic applications. David Liu and Feng Zhang are among the co-founders.
Bexorg	Neurotech	Has developed instrumentation for maintaining the cellular functions (but not the consciousness) of whole human brains from deceased donors. Their machinery perfuses the brains with an artificial blood-like substance and continuously measures substances going into and out of the brains. This allows automatic adjustment of oxygen and nutrient levels as well as measurement of the responses of the brains to potential therapies. To prevent consciousness, the brains are kept in a low-energy state where the neurons do not exhibit electrical activity. As an additional measure of caution, anesthetics are included in the perfusate. They collect -omics data from experiments on the brains, using these data to create a map of how the brains respond to potential therapeutics over time. Their data are fed into AI software to create predictive models for how therapies interact with human brains. Aims to improve success rates in CNS clinical trials through their data and models of human brain responses. Spun out from Nenad Sestan’s laboratory at Yale University. Has raised $42.5M as of October 2025.
BigHat Biosciences	Bio-AI	Has developed a high-speed closed-loop pipeline (known as Milliner) for antibody discovery, development, and optimization which leverages wet lab automation, advanced machine learning techniques, and synthetic biology. Milliner starts with preexisting antibodies, phage display, or generative AI to discover initial hits. It then rapidly produces antibodies and comprehensively characterizes them to obtain training data, before updating them with AI models that optimize the design. This cycle repeats in a loop until high-quality antibodies with desired characteristics are created. Also develops AI-optimized VHHs, camelids, BiTEs, scFvs, and fusions of different antibody-related components. In 2022, made strategic partnerships with Merck and Amgen as well as acquired a cell-free protein synthesis company called Frugi Biotechnology. Has several preclinical therapeutic programs in development (one of which is at IND-enabling stage) as of September 2025. Has raised over $100M in total as of September 2025.
Bioasis	Biomed	Has developed a peptide called xB³ that facilitates transcytosis across the blood-brain barrier. Working towards applications in glioblastomas, brain metastases, and neurodegenerative diseases.
Biogen	Biomed	Large pharmaceutical company focusing on developing treatments for neurological diseases. Has made moves towards developing gene therapy pipelines for treating neurological diseases, though the company has experienced some setbacks in this space (i.e. failed clinical trials).
BioMarin Pharmaceutical	Biomed	Enzyme replacement therapies for rare diseases. During April 2021, announced a collaboration with the Allen Institute to develop AAV gene therapies for rare diseases of the brain.
Bionaut Labs	Biomed	Microrobotics as a new paradigm for drug delivery.
BioViva	Biomed	Developing gene therapies to treat aging, offers tests for determining biological age. Elizabeth Parrish (the company’s CEO) tested an experimental gene therapy on herself and reports positive results, though she did not intend for this information to go public. George Church and Aubrey de Grey are on the scientific advisory board. Anders Sandberg is the company’s ethics advisor.
Blackrock Neurotech	Neurotech	Owns commercial rights to the Utah Array, one of the best known and most widely used neural electrode array technologies. The Utah Array was first implanted in humans during 2004 and has been used in clinical studies since then. Licenses the Utah Array to academics, companies, and clinicians. Developing brain-computer interfaces for control of prosthetic limbs, control of computer functions, writing text via computer, and restoration of senses (touch, vision, and hearing). Sells devices for human studies, non-human primate research, and rodent research. Has restored sensory or motor function to over 40 human patients through their studies. Their devices have remained functioning in patients for a total of 30,000+ days (adding up how long in each patient). In 2021, received FDA Breakthrough Device Designation for their MoveAgain medical device, which facilitates control of cursors and keyboards, mobile devices, wheelchairs and prosthetic devices. During 2024, received a large infusion of funding in the form of $200M worth of cryptocurrency cash (before that, they had only taken on about $10M in funding despite their longevity as a company). Is not at all affiliated with the well-known finance company Blackrock investments.
Calico Life Sciences	Biomed	A subsidiary of Alphabet Inc. (Google) which focuses on studying and treating aging. Partnered with Abbvie to develop drugs for age-related diseases. Has also established partnerships with the Broad Institute of MIT and Harvard and with the Buck Institute for Research on Aging, has published numerous peer-reviewed papers on the biology of aging.
Capsida Biotherapeutics	Biomed	Developing targeted AAV gene therapies for a variety of brain diseases. Has made blood-brain barrier crossing AAVs that are liver untargeted and brain targeted. Founded by Viviana Gradinaru.
Capsigen	Biomed	Engineering superior AAV gene therapy vectors through a proprietary method called Transcription-Dependent Directed Evolution (TRADE^TM). Have developed greatly improved neurotrophic AAVs. Entered into a partnership with Biogen during May of 2021 to develop AAV gene therapies that treat various brain and neuromuscular disorders.
Caribou Biosciences	Biomed	Developing allogenic CAR-T and CAR-NK therapies using a Cas12a chRDNA (CRISPR hybrid RNA-DNA) genome-editing technology which enables multiplex gene edits, higher specificity, and less off-target editing. As of June 2023, has two CAR-T therapies for hematologic diseases in phase I clinical trials as well as a portfolio of other therapies at earlier stages of development. Jennifer Doudna is a co-founder and is on the scientific advisory board. As of June 2023, has raised $167.7M in funding.
Cathedral Therapeutics	Biomed	Encapsulating AAVs inside of protein vaults as a way of shielding from preexisting anti-AAV immunity found in up to 60% of patients, a platform technology to increase access to gene therapy and improve the efficacy of genetic treatments. Based on early data, vaultAAVs might also enhance AAV transduction efficiency by about 5-fold, which could enable treatments at lower doses and thus make AAV gene therapy safer and less expensive. My company, which I co-founded with David Curiel.
CATALOG	Biotech	Building a DNA-based platform for massive digital data storage and computation.
Celero Systems	Biomed	Developing ingestible pills which can diagnose, monitor, and treat diseases by sending data to external devices (e.g. cell phones). Their HEALTH-Dx^TM pill can monitor respiratory and cardiac rhythms to diagnose sleep apnea. Their RESCUE-Rx^TM pill can automatically administer rescue medication in the case of an opioid overdose. Robert Langer is an advisor and one of the co-founders.
Cirsium Biosciences	Biomanufacturing	Developing a platform for manufacturing clinical-grade AAVs at higher yields which uses plants. They deliver plant-specific helper plasmids into producer plants using a vector (possibly A. tumefaciens), produce the AAVs inside the plant tissues, and purify the AAVs. Have demonstrated 70% reduction in manufacturing lead times compared to traditional methods. Produces up to 1015 vg/kg AAVs and is highly scalable, lowering costs compared to traditional methods. Safer than traditional methods since they leverage plants designed for resistance to contamination with human pathogens. Received (up to) $61M in ARPA-H funding as of October 2024.
Coastal Carbon	Ecotech	Aggregating massive amounts of satellite imagery data as well as non-intrusive underwater sensors to train foundation models and measure seaweed biomass, facilitating access to blue carbon for seaweed farmers. This strategy could accelerate the development of seaweed farming towards carbon capture. As of September 2023, raised $1.6M to develop the non-intrusive underwater sensors that can capture data to enhance the accuracy of their models.
Code Biotherapeutics	Biomed	Has developed 3DNA, a multivalent DNA nanostructure (not DNA origami) which both carries therapeutic transgenes and can be linked to antibodies or peptides to facilitate cell-targeted delivery of said transgenes. Focusing on Duchenne Muscular Dystrophy while also in very early stages of exploring lung, pancreas, and liver diseases. Has raised $85M as of June 2023.
Cognito Therapeutics	Neurotech	Developing a noninvasive wearable visual and audio stimulation device to evoke gamma waves in the brain, slowing cognitive decline of Alzheimer’s patients. Based on studies from Ed Boyden’s and Li-Huei Tsai’s labs at MIT. Co-founded by Ed Boyden and Li-Huei Tsai. As of September 2024, has completed a phase II clinical trial and demonstrated up to 77% reduction in cognitive decline over a period of 6 months with patients using the device.
Cognigenics	Biomed	Developing inhalable AAVs to deliver CRISPR gene therapy for treating anxiety, depression, and mental impairment. Has demonstrated successes in mouse models for treating anxiety as of June 2023. Plans to start clinical trials in 2024 and claims that they may bring the product to market as early as 2025. Leveraging contract research organizations (CROs) and contract manufacturing organizations (CMOs) to accelerate their research and development. First raised initial funding in 2020 for early preclinical work from early angel investors and then received $950K during 2022 from Fifth Set Ventures and Lionheart Ventures for further preclinical studies and beyond.
Constellation Bio	Biomed	Developing molecularly precise probiotics that actually work. First target is to develop precision medicine probiotics for lowering cholesterol. Pre-seed stage as of October 2025, funded by angel investors. As of October 2025, the company is collecting fecal samples along with some data about cardiovascular health from volunteers as part of their R&D. Leveraging observational human research to bypass much of the red tape often associated with early-stage therapeutic products. Founded by Stephen Skolnick, who announced the company in a Substack post.
Colossal	Ecotech	Centered on moonshot projects that are using advanced CRISPR methods to bring back the Wooly Mammoth, the Thylacine (Tazmanian Tiger), and other extinct animals. Aims to reintroduce lost biodiversity and thus repair ecosystems. Will develop biomedical technologies such as artificial wombs in conjunction with its de-extinction research, providing additional benefits to humanity and acting as a way to bring in funding. Cofounded by George Church, Ben Lamm, and Andrew Busey. As of January 2025, received a $200M series C funding round (for a total of $435M funds raised) at a $10.2B valuation.
Composite Programmable Therapeutics	Biomed	Has developed DNA origami shells to multivalently capture viruses and trigger their clearance by the immune system. Co-founded by Hendrik Dietz. As of June 2023, also planning to develop new gene therapy vectors based on DNA origami as well as a biomanufacturing platform for producing large quantities of ssDNA. Has raised $29M as of September 2024.
Concerto Biosciences	Biotech	Has developed a high-throughput assay device (kChip) which displays millions of microbial communities with different combinations of microorganisms. Across these microbial communities, pathogen suppression, metabolite production or degradation, robustness to environment, and other metrics are tracked. Data from kChip assays are used to train kAI to predict microbial behavior in different community contexts, which allows identification of combinations of microorganisms that work together to achieve useful functions. They are leveraging kChip and kAI to develop multistrain probiotics for dermatology applications including treatment of vaginal yeast infections, general skin health, and treatment of atopic dermatitis. As of this writing (October 2025), a phase 1b clinical trial has been completed for the probiotic formulation aimed at treating atopic dermatitis. Has raised $25.5M as of October 2025.
Convergent Research	Services	Not a company but a nonprofit organization which incubates, finds philanthropic donors for, and supports Focused Research Organizations (FROs). For more information on FROs, see this open access article in Nature. Adam Marblestone is CEO and a co-founder.
Cortical Labs	Neurotech	Developing hybrid bioelectronic devices which incorporate cultured biological neurons to perform computational tasks. These devices are power efficient, scalable, robust to physical damage, and have the potential for fluid adaptation to many different computational problems.
Cradle	Neurotech	Aiming to develop reversible whole-body cryopreservation for humans. They have so far shown that electrophysiological activity can be restored in a cryopreserved and rewarmed slice of rat cerebellar tissue. Has raised $48M as of June 2024. Laura Deming and Hunter Davis are the co-founders.
Creative Biolabs	Services	Custom services for antibody engineering, membrane protein production and characterization, bioconjugation, gene therapy development, viral vector engineering, cell therapy development, molecular dynamics simulations, drug development consulting, and more.
Cultivarium	Biotech	Developing molecular techniques, hardware platforms, and software tools to accelerate adoption of non-model microorganisms for biotechnology. Cultivarium is a focused research organization (FRO), so it possesses a distinct funding approach and different goals compared to traditional startups. For more information, see this open access article describing FROs in Nature.
Dalan Animal Health	Ecotech	Has developed the world’s first bee vaccine (made using inactivated bacteria), which protects hives against American Foulbrood disease, a devastating infection caused by the bacterium Paenibacillus larvae that spreads rapidly and leaves persistent spores. Sells their vaccine for beekeepers to mix with queen candy or in the form of vaccinated queens. American Foulbrood disease harms ecosystems and costs the U.S. food industry over $400M in lost revenue. Antibiotics used to control American Foulbrood disease can lead to resistance and can negatively affect the health of the bees; the vaccine does not lead to antibiotic resistance or harm the bees. Also developing a number of other vaccines for various honeybee infectious diseases (e.g. a vaccine against deformed wing virus is in clinical development as of December 2024) as well as one for diseases in shrimp. Raised about $10M in total funding as of June 2023.
Deep	Ecotech	Developing modular undersea habitats that scientists will live inside of for extended periods of time during marine research missions. Also offers advanced manufacturing services for customers seeking large metal parts. Funded with £100M+ by a mysterious anonymous donor (as of September 2025). UK-based company.
DoriVac	Biomed	Developing DNA origami cancer vaccines which facilitate cross presentation of antigens and are also applicable to infectious diseases. Raised $100K by winning the 2022 Alnylam BioVenture Challenge. Early stage as of June 2023. Their technology was developed by William Shih and Yang Zeng at the Wyss Institute.
Dyno Therapeutics	Biomed	Using deep learning to improve properties of AAV capsids as a platform technology for gene therapy. George Church is one of the co-founders.
E11 Bio	Neurotech	Building moonshot technologies involving superior molecular barcoding, spatial -omics, and viral circuit tracing to help neuroscientists map the brain. Has a long-term goal of mapping brains at the one-hundred billion neuron scale. E11 Bio is a focused research organization (FRO), so it possesses a distinct funding approach and different goals compared to traditional startups. For more information, see this open access article describing FROs in Nature.
Editas Medicine	Biomed	CRISPR-based gene therapy. George Church, David Liu, Jennifer Doudna, Feng Zhang, and J. Keith Joung are the co-founders.
eGenesis	Biomed	Developing safer xenotransplants by using multiplexed CRISPR gene editing to inactivate all of the porcine endogenous retroviruses and to address the numerous mechanisms of immune-mediated rejection. Working on gene edited porcine kidneys, livers, and hearts for xenotransplantation. George Church is a co-founder. Has raised a total of $481M in funding as of September 2024.
Eikon Therapeutics	Biomed	Superior drug discovery platform which leverages high-throughput automated super-resolution microscopy for tracking single protein movements in living cells. Eric Betzig is one of the advisors.
Emerald Cloud Lab	Services	Remote automated laboratory as a service for researchers. Has a large array of automated equipment for synthetic biology and genetic engineering, physical and biophysical chemistry, structural biology, biochemistry, analytical chemistry, etc. Provides a software interface for users to instruct the automated equipment.
Entos	Biomed	Developing lipid nanoparticles with transmembrane fusogenic proteins to facilitate delivery of DNA, RNA, and CRISPR cargos. Neutral lipid formulation (not ionizable) gives lower toxicity while the fusogenic proteins facilitate delivery efficacy. As of June 2024, Entos is involved in oncology therapeutics, antivirals, gene editing therapies, immunotherapies, DNA vaccines, and senolytics. Has partnered with Oisin Biotechnologies (see later in this list) to develop a new senolytic therapy.
Eve Bio	Biomed	Mapping the “pharmome” with the goal of identifying all of the off-target effects of clinically approved small-molecule drugs. Leveraging high-throughput screening assays with 2,000 FDA-approved drugs on reporter cells, measuring the effects on up to 1,000 gene products per drug. Many of their assays use reporter cell lines engineered to emit a quantifiable optical signal when a test drug stimulates a specific gene product (a different cell line for each gene product). Releasing their data and assay designs to the public to support pharmacological safety profiling, drug repurposing, biomedical AI training, polypharmacology (finding drugs that act at multiple targets), chemical toxicology profiling, and future automated laboratory processes. Eve Bio is a focused research organization (FRO), so it possesses a distinct funding approach and different goals compared to traditional startups. For more information, see this open access article describing FROs in Nature.
EvolutionaryScale	Bio-AI	Has developed an open-source AI frontier model for biology (called ESM3) which can create a wide variety of proteins with desired functions through natural language prompting. ESM3 can create new proteins that diverge greatly from naturally occurring proteins including a variant of GFP with only 58% sequence similarity to the closest known naturally occurring type of GFP (calculated as the equivalent of simulating 500 million years of evolution). Has plans to develop plastic-degrading and carbon capture proteins using their models. An enormous amount of compute was used to train ESM3, it has 98 billion parameters, and it can be fine tuned by experimental results in a fashion analogous to RLHF (reinforcement learning with human feedback). ESM3 can reason across protein sequence, structure, and function, making it extremely generalizable. Even more compute resources and data for training could create new models with even greater generative capabilities and new models that operate across biological scales from individual molecules to whole cells. Patrick Hsu is one of their investors and is listed as an author on the ESM3 paper in the journal Science. Led by CEO Alexander Rives, former head of Meta’s AI protein team. Raised a seed round of $142M as of June 2024.
Evox Therapeutics	Biomed	Developing exosomes loaded with AAV as a delivery system for gene therapy, shielding AAVs from immune factors and targeting them to specific tissues. Also exploring other exosome cargos such as RNAs, CRISPR-Cas proteins, and therapeutic proteins. Preclinical stage as of June 2023.
Fauna Bio	Biomed	Has developed a platform called Convergence^TM AI which uses data from the Zoonomia Consortium, including genome alignments and protein-coding alignments of hundreds of mammalian species. Convergence^TM AI identifies protective genomic signatures in disease-resilient mammals such as hibernators (e.g. 13-lined ground squirrels) and maps these results to human cell models so that validation experiments can be performed. It also predicts compounds which can mimic the protective genomic phenotypes upon application to human cells. Working on preclinical development of drugs for cardiopulmonary and retinal indications as of October 2025. In January 2020, announced a collaboration with Novo Nordisk to discover new treatments for obesity. In December 2023, announced a partnership with Eli Lilly for preclinical drug discovery in obesity. This partnership renders Fauna Bio eligible to receive up to $494 million in preclinical, clinical, and commercial milestone payments as well as royalties on potential product sales. In addition to past funding, has raised a $40M series A as of March 2025.
Fieldstone Bio	Ecotech	Developing microbial biosensors which synthesize hyperspectral reporter molecules through engineered metabolism in response to desired signals on the ground (e.g. contaminants in soil). The hyperspectral reporters can be imaged from above using flying drones equipped with special cameras, enabling rapid surveying of chemical properties across large amounts of land. Applying AI software to automate analysis of images taken by drones. Application areas include contaminant detection, agriculture, national security, and mining. Their foundational technology is based on published research by Chemla and Levin et al. from Christopher Voigt’s laboratory at MIT.
Forest Neurotech	Neurotech	Developing a minimally invasive ultrasonic brain-computer interface implant that can access any part of the brain to understand and treat a wide range of neurological disorders. Will employ both ultrasonic neuroimaging and neuromodulation using Ultrasound-on-Chip technology from their partner Butterfly Network. Sumner Norman is CEO and a co-founder. Launched in 2023 with $14M in philanthropic funding from Convergent Research, has since raised additional funding. Has signed $20M contract to pay Butterfly Network for facilitating partnership and licensing of the Ultrasound-on-Chip technology. Forest Neurotech is a focused research organization (FRO), so it possesses a distinct funding approach and different goals compared to traditional startups. For more information, see this open access article describing FROs in Nature.
Form Bio	Services	Developing AI-powered computational services for characterization and prediction of the properties of engineered AAVs (e.g. simulation and analysis of bioreactor setups for AAV production, prediction of mRNA expression, immunotoxicity prediction, generative in silico AAV candidate optimization) as well as for analyzing data from AAV production. Spun off by another startup company (see earlier in this list) called Colossal. Some of its advisors include George Church, Christopher Mason, and Peter Diamandis.
Frontier Bio	Biotech	Has developed tissue engineered systems including Blood Vessel Mimics (already in use for medical device testing, a neurovascular-unit-on-a-chip for studying the blood-brain-barrier in health and disease, and vascularized organoids for aiding drug development and disease modeling. Has raised $1.1M from investors and an SBIR grant as of July 2023.
Future House	Bio-AI	Not a company but a research nonprofit organization funded through philanthropist Eric Schmidt, also seeking other funding. They plan to spend $20M ramping up during 2024. Has a 10-year mission to create “AI scientists”, semiautonomous AI systems that may dramatically accelerate the pace of biological research through not only laboratory automation, but also through cognitive automation of literature research, protocol writing, generating hypotheses, discerning patterns in data, etc. Founder and CEO is Sam Rodriques, a principal investigator at the Crick Institute.
Gameto	Biomed	Developing women’s reproductive health technologies, starting with Fertilo. Fertilo consists of lines of ovarian support cells that secrete hormones to mature eggs in a dish, replacing hormonal injections and shortening the IVF process from 14 days to 3 days. Eggs can be frozen or fertilized after Fertilo is used. Raised $73M in total funding as of December 2024. In December 2024, announced birth of first human baby who came from eggs matured using the Fertilo technology.
GATTAquant	Services	DNA origami imaging probes, fluorescence microscopy reagents. First commercial application of DNA origami.
Generate Biomedicines	Bio-AI	Generative artificial intelligence to create novel de novo protein therapeutics with desired protein-protein interactions, enhanced enzymatic activities, and invisibility to the immune system. Frances Arnold is on the board of directors. Has raised $420M as of July 2023.
Generation Bio	Biomed	Developing gene therapies for rare and prevalent genetic diseases using close-ended DNA and cell-targeted lipid nanoparticle platform using a scalable enzymatic synthesis strategy to produce the DNA in large quantities. Preclinical stage as of June 2023. Has raised over $536M as of June 2023. Established a strategic partnership with Moderna in March 2023.
Gensaic	Biomed	Developing M13 phage-derived particles displaying targeting molecules as a novel gene therapy vector, utilizing a high-throughput directed evolution platform to improve these phage-derived particles. Redosable since M13 phages are a part of the human virome. Tissue targets for their phage-derived particles include liver, lung, and central nervous system. As of June 2023, has raised $3.5M (grant from Cystic Fibrosis Foundation).
GenScript	Services	Services in artificial DNA synthesis, synthetic biology, antibodies, cell therapies, enzyme engineering, etc.
Ginkgo Bioworks	Services	Synthetic biology, biomanufacturing, microorganism design, enzyme engineering, etc. Acquired Gen9 in 2017.
Grove Biopharma	Biomed	Has developed proteomimetic peptide brush polymers (“bionic biologics” as they call the molecules) which act as therapeutics targeting protein-protein interactions. Their peptide brush polymers are designed to penetrate cell membranes and thus can work on intracellular targets. Their peptide brush polymers have longer half lives in vivo than traditional peptides. Has demonstrated the utility of peptide brush polymers against several different cancer and neurodegenerative disease targets in preclinical models. Raised a $30M series A as of April 2025.
HelixNano	Biomed	Developing an mRNA-based SARS-CoV-2 vaccine which might protect from all possible variants of the virus. Pivoted from original plan of developing cancer vaccines using the same technology. Co-founded by Hannu Rajaniemi, who is also a successful science fiction author. George Church is an advisor.
Humble Bee Bio	Ecotech	Identified a species of solitary bee which produces bioplastic to protect their nests and has leveraged the genetic blueprint from this bee to develop an environmentally friendly alternative to traditional plastics.
ImmuneAge Bio	Biomed	Developing ways of regenerating hematopoietic stem cells (HSCs) to treat the aging immune system and thus prevent ailments like cancer, brain aging, infections, and cardiovascular disease. Has developed a way of expanding numbers of human HSCs 1000-fold, which allows them to run high-throughput combinatorial drug screening assays for in vivo and ex vivo HSC rejuvenation. As of January 2025, working on an orally available small molecule (IA-101) which acts on mitophagy and mitochondrial biogenesis and has top indications of vaccine response, preventing respiratory infections, and mitigating post-chemotherapy immunosenescence.
Immunai	Bio-AI	Combining multi-omic single cell profiling technologies and machine learning to comprehensively map the immune system and thereby enable greatly improved immunotherapies as well as accelerate clinical trials and avoid costly failures.
Impossible Foods	Ecotech	Uses synthetic biology and biochemical engineering to develop plant-based substitutes for meat products. Their signature product is the Impossible Burger. They also make a product which mimics sausages. One notable strategy employed by Impossible Foods is production of leghemoglobin in yeast. This compound gives a meaty flavor when added to their food products. They also add other plant-based compounds to mimic the fats found in animal meat.
Imprint	Biotech	Developing experimental and computational tools to decode immunological memory in B and T cells with the aim of uncovering the causes of chronic diseases such as autoimmune conditions, long COVID, psychiatric disorders, and dementias. Hopes to pave the way for new treatments and diagnostics by uncovering the mechanisms of chronic diseases. Imprint a focused research organization (FRO), so it possesses a distinct funding approach and different goals compared to traditional startups. For more information, see this open access article describing FROs in Nature.
Inait	Bio-AI	Aiming to develop AGI by building on work from the Blue Brain Project and Human Brain Project. Founded by Henry Markram, the pioneer behind the European Union’s (somewhat controversial) Blue Brain Project and Human Brain Project. Combines biomimetic spiking neural net (SNN) AI architectures, a brain-like learning rule discovered during Henry Markram’s studies on SNNs, and contemporary AI technologies like LLMs, CNNs, and GNNs. Goal is to use biomimetic approaches to overcome limitations found in traditional advanced AI systems, Working on architectures which possess sensory-like systems to learn from complex digital environments and to adapt and function intelligently within said environments. Has partnered with Microsoft as of March 2025. Has raised $300M according to its website.
Insilico Medicine	Bio-AI	Leveraging artificial intelligence to facilitate every step of pharmaceutical development. Has developed software to discover and prioritize novel drug targets, generate novel molecules, and design and predict clinical trials. Alex Zhavoronkov is CEO, Executive Director, and Chairman of the Board. One of the company’s lead pharmaceuticals (TNIK) represents the first AI-designed drug to reach phase II clinical trials. Has raised over $400M in funding as of June 2024.
Intellia Therapeutics	Biomed	Developing therapies which employ CRISPR gene editing technology. Has conducted some successful clinical trials using CRISPR gene therapy to treat transthyretin amyloidosis (as of February 2022, this is not yet FDA approved though). Also working on CRISPR therapeutics for engineering T cells towards targeting acute myeloid leukemia. Partnered with Regeneron, Novartis, and others. Jennifer Doudna was one of the co-founders.
Kernel	Neurotech	Neurotechnology, noninvasive brain-computer interfaces, invasive neural prostheses. Some noninvasive products anticipated to be released during 2021. Founded by Bryan Johnson who personally invested $54M. Raised an additional $53M from outside investors. Early goal is to help treat brain disease, has ambitions to enable human enhancement.
Landmark Bio	Services	Provides services for clients in cell and gene therapy development including therapeutic discovery research, process development, analytical development, quality control, GMP manufacturing, and consulting. Emerged from a public-private partnership founded by MIT, Harvard, FUJIFILM Diosynth Biotechnologies, Cytiva, and Alexandria Real Estate Equities. Their mission is to accelerate biomanufacturing of cell and gene therapies as well as to serve as a forum for biomanufacturing workforce development in Massachusetts and beyond.
Laronde	Biomed	Developing therapies which utilize circular RNAs (Laronde calls these “endless RNAs”) as expression vehicles for proteins. Such circular RNAs are much more stable and less immunogenic than linear RNAs.
Ligandal	Biomed	Peptide nanoparticles for targeted CRISPR-Cas gene therapy delivery, immunotherapy, hematological gene therapy, aging treatments. Founded by Andre Watson.
Living Carbon	Ecotech	Developing genetically modified plants (including trees) with enhanced growth, carbon capture efficiency, and bioremediation properties. Has raised over $36M and has planted over 170,000 genetically modified trees as of August 2023.
Loyal	Biomed	Developing anti-aging therapeutics for dogs including LOY-001, LOY-002, and LOY-003. LOY-001 and LOY-002 corrects for the overexpression of insulin-like growth factor 1 (IGF-1) and growth hormone (GH) found post-maturity in large dogs, they are expected to be available in 2027. LOY-002 corrects metabolic dysfunction in senior dogs, is expected to be available in 2025. As of December 2024, working on a clinical trial for LOY-002 with over 1000 senior dogs enrolled across the USA. Founder and CEO is Celine Halioua. Has raised over $125M total funding as of March 2024. Loyal’s research may pave the way for human anti-aging therapies in the future.
LyGenesis	Biomed	Allogenic cell therapy that uses host lymph nodes as bioreactors to grow ectopic replacement organs. Has developed a method for generating ectopic livers via patient lymph nodes that is in early clinical trials as of September 2022.
Mammoth Biosciences	Biomed	CRISPR-based diagnostics. Jennifer Doudna is one of the co-founders.
ManifoldBio	Bio-AI	System for barcoding protein therapeutics to enable high-throughput design and testing in complex environments, machine learning to optimize drug design. George Church is one of the co-founders.
Marblis	Ecotech	Sustainable biomaterials company with flagship product Marblis Urchinite^TM, a marble-like material made from purple sea urchins, a highly overpopulated species off the coast of California which has taken over due to rising ocean temperatures and loss of predators. Marblis Urchinite^TMcan be used as a building material for countertops, wall coverings, furniture, decor, flooring, etc. Partners with marine conservation organizations, researches ways to alleviate plastic pollution, to restore kelp ecosystems, and to leverage market-driven solutions as well as runs educational initiatives on sustainable ocean innovation. Has a biomaterials laboratory called Primitives which offers custom biomaterials R&D services and has already developed Marblis Urchinite^TM as well as seaweed-based biosensors and compostable packaging materials.
Markov Biosciences	Bio-AI	Developing deep learning tools that learn the dynamics of cellular systems by taking in a vast amount of data from genomics, transcriptomics, and more. Leveraging cutting-edge mechanistic interpretability tools to find mechanistic insights from their AI-derived simulations of cellular processes. Their mechanistic interpretability system is implemented by probing the simulations with questions in natural language, facilitating actionable insights from in silico experiments.
Medtronic	Biomed	World’s largest medical device company by revenue as of 2024 rankings, employs over 90,000 people. An American-Irish company with legal and executive headquarters in Ireland and operational headquarters in Minnesota. Operates primarily in the USA, but has some level of operation in over 150 countries. Has developed wearable and implantable pacemakers, the implantable cardioverter defibrillator, the world’s smallest pacemaker, and the world’s smallest spinal cord stimulator, an automated insulin pump, implantable drug delivery systems, and more.
Microdrop Technologies	Services	Sells instruments that can rapidly and accurately dispense liquid droplets in amounts as small as 20 picoliters using piezo-driven inkjet printing technology, also sells accurate nanoliter to microliter dispensing systems as well as instruments to automate the dispensing systems.
Micro-X	Biomed	Small, light, and fast proprietary x-ray imaging technology based on novel electronically controlled carbon nanotube emitters. Products are applied in portable medical imaging and in security. There are over 380 of their medical x-ray devices used across 35 countries. Their medical x-ray products have been used extensively in the field on Ukraine’s frontlines in the ongoing Ukraine-Russia war.
Moderna	Biomed	Biomedical technologies which utilize mRNA inside of lipid nanoparticles; application areas include drug discovery, drug development, and vaccines. Major player in COVID-19 pandemic since it was one of the first companies which developed and distributed SARS-CoV-2 vaccines to the world.
Motif Neurotech	Neurotech	Developing a small device implanted in skull bone which can perform transcranial magnetic stimulation (TMS) to treat depression and other mental health disorders, users wear a baseball cap with coils to activate the device. Unlike traditional TMS, this device does not require numerous visits to a clinic with access to bulky equipment, vastly improving accessibility. Has raised $100K as of June 2023. Jacob Robinson from Rice University is co-founder.
Nanite Bio	Bio-AI	Employing a high-throughput AI platform to predict properties of polymers and to design nanomaterials which serve as efficacious gene delivery vehicles, synthesizes and tests in vitro thousands of distinct polymer nanoparticles over a few days, uses multiplexed in vivo screening to test many polymer nanoparticles at once in animal models. Has raised $8M in funding as of June 2023.
Nautilus Biotechnology	Services	Developing a high-throughput single-molecule proteomics platform which integrates many novel techniques to decipher protein networks and thereby help accelerate basic science, new therapeutics, and new diagnostics.
Neurable	Neurotech	Developing a non-invasive brain-computer interface based on headphones that use electroencephalography to record brain signals, allowing people to control devices like phones with their minds. As of September 2022, the company appears fairly far along in its product development process and is likely to release their headphones within a year or so.
Neuralink	Neurotech	High-bandwidth brain-machine interfaces, surgical robots which implant the interfaces in a manner resembling a sewing machine. Early goal is to help treat brain disease, has ambitions to enable human enhancement. Founded by Elon Musk and others, highly publicized by Elon Musk. Has done testing on rats, pigs, monkeys, and other animals as of April 2021.
NewLimit	Biomed	Extending human longevity through epigenetic reprogramming, starting with restoring youthful function in the liver and the immune system. Has raised $40M as of May 2023. Co-founded by Coinbase CEO Brian Armstrong.
Nudge	Neurotech	Developing whole-brain focused ultrasound devices which achieve millimeter precision. Has already developed a helmet-like phased array device which can be used along with an MRI machine, allowing visualization of the effects of the ultrasound. Also has developed an MRI-based acoustic radiation force imaging technique to visualize the ultrasound focus in the brain. Has developed powerful simulation and imaging algorithm software to provide control over their device’s interactions with the brain. Running studies on patients with essential tremor, tinnitus, substance use disorders, and chronic pain (though as of September 2025, these studies are aimed at device feasibility rather than treatment). Will run studies on healthy volunteers in the future to study ways that ultrasound can influence the brain. Announced a $100M series A led by Thrive Capital and Greenoaks in July 2025.
Nvelop Therapeutics	Biomed	Developing delivery vehicles for tissue-specific targeting and gene editing; based on lentivirus-like particles with fused gene editing proteins instead of DNA inside of the envelope (as seen in publications from David Liu’s academic laboratory). Co-founded by David Liu and Keith Joung. Launched with $100M of funding as of April 2024.
Oisin Biotechnologies	Biomed	Developing senolytics which target senescent cells by triggering apoptosis only when certain genes are expressed. Has received investment from the SENS Research Foundation, the Methuselah Foundation, and the Methuselah Fund.
Olden Labs	Services	Developing technologies to automate mouse research, has released their first product: DOME cages, which use AI on 24/7 video of housed mice to track the movement of multiple mice with 99% accuracy over long time periods. DOME cages also automatically feed mice, calculate numerous behavioral metrics (e.g. total distance traveled, sleep time, average acceleration, food and water intake, number of aggressions, etc.), evaluate behavior-based health metrics, provide automated emergency alerts when problems arise, and are compatible with existing rack systems. Michael Florea is CEO and one of the co-founders.
Openwater	Neurotech	Portable medical imaging technologies which employ novel optoelectronics, lasers, and holographic systems. Wearable imaging technologies which could be 1,000x cheaper than MRI and achieve similar or better results. Has speculated that their technology might eventually allow telepathic communication. Founded by Mary Lou Jepsen.
Orchid Health	Biomed	Performs whole-genome sequencing on embryos to screen for neurodevelopmental disorders, birth defects, and chromosomal abnormalities as well as for genetic predispositions to cancers and ailments of the brain, heart, and more. Helps patients ensure that their children have a healthy future and gives them the option to not move forward with the pregnancy if the embryo may lead to an unhealthy person.
Organovo	Biomed	3D tissue bioprinting for in vivo clinical applications, in vitro tissue models for disease modeling and toxicology. Long-term goal is to print entire human organs for transplants.
Oviva Therapeutics	Biomed	Therapies for ovarian aging to aiming extend women’s healthspan and longevity. Developing a treatment to improve ovarian longevity that uses recombinant Anti-Müllerian Hormone (AMH), a first-in-class therapeutic which may delay menopause and thus exert beneficial effects on health. Daisy Robinton is a co-founder and the CEO. Raised a $11.5M seed round in May 2022.
Oxford Nanopore Technologies	Biotech	Portable nanopore sequencing devices, high-throughput desktop nanopore sequencing devices, sample preparation kits. The company states that they have the first and only nanopore DNA and RNA sequencing platform as of May 2021.
Oxgene	Biomanufacturing	Provides AAV manufacturing kits and services leveraging tetracycline enabled self-silencing adenovirus (TESSA^TM) technology to greatly enhance yields. The TESSA technique increases AAV yields by around 40-fold relative to traditional methods, increases overall infectivity of the virus particles, and is well-suited to GMP-quality production. Provides self-inactivating (SIN) lentiviral plasmids for lentivirus production with optimized safety and translation efficiency; this can increase viral yields by up to 10-fold compared to traditional methods. Provides stable lentiviral packaging and producer cell lines (based on HEK293) which facilitate consistent production of high-titer lentivirus after transfection of a viral genomic plasmid carrying a gene of interest or after stable integration of a gene of interest respectively. The lentiviral packaging and producer cell lines can be grown without animal serum in the media.
Oxitec	Ecotech	Genetically modified male insects which curb the reproduction of populations of their species in the wild, acting as a precise and environmentally friendly way of controlling dangerous pests that spread disease or destroy crops. After years of battles with activists and regulatory bodies, the company will release 750 million genetically modified mosquitos in the Florida Keys (the first time this has been done in the U.S.) with the goal of reducing rates of illnesses such as yellow fever and dengue.
Panacea Longevity	Biomed	Enhancing longevity and health using a fasting-mimetic metabolite supplementation. Early stage as of May 2021.
Panluminate	Services	Offers expansion microscopy (ExM) as a service as well as related tissue labeling (e.g. Unclearing, chromatin labels for ExM, etc.) and imaging services, can expand tissues up to 25x using their pan-ExM technology. CEO Ons M’Saad developed pan-ExM and some of Panluminate’s related technologies while working in Joerg Bewersdorf’s laboratory at Yale.
Paradromics	Neurotech	Developing surgically implanted brain-computer interface called Connexus which uses hairlike intracortical electrodes to record from 1684 channels, aims to restore communication abilities to people with severe motor impairments (e.g. amyotrophic lateral sclerosis). Interface is scalable to possibly add even more channels for future applications. Has raised a total of $88.7M as of December 2024.
Pioneer Labs	Ecotech	Not a startup company but a nonprofit research organization with a startup-like approach. Developing engineered microorganisms that may be able to grow on Mars with the future goal of terraforming, combining various types of extremophiles that individually have some of the abilities necessary for survival on Mars. Shorter term goal of green manufacturing in resource-constrained environments. CEO is Erika DeBenedictis, formerly a principal investigator at the Crick Institute. Funded by the Astera Institute as well as supported by another nonprofit founded by Erika DeBenedictis called Align to Innovate.
Precision Neuroscience	Neurotech	Developing a thin-film microelectrode array (called the “Layer 7 Cortical Interface”) which conforms to the surface of the brain and collects high-resolution data from 1024 microelectrodes. Layer 7 Cortical interface can be implanted with minimally invasive and reversible surgery, facilitates recording and stimulation, and is designed to allow paralyzed people to control computers with their thoughts. Aiming to treat conditions such as spinal cord injury, stroke, ALS, and traumatic brain injury Started clinical trials in 2023 and has (as of April 2025) tested the device in 37 patients, for which it was implanted temporarily to aid in situations like surgical removal of brain tumors. One of the co-founders is Benjamin Rapoport, who previously was part of the founding team at Neuralink. Has raised $155M as of December 2024, including series A, B, and C rounds.
Prime Medicine	Biomed	Developing CRISPR Prime editing technology as a novel therapeutic modality. David Liu and Andrew Anzalone are co-founders.
Profluent Bio	Bio-AI	AI platform for designing de novo proteins such as enzymes, gene editors, antibodies, and more. Has released the first freely available AI-generated gene editor called OpenCRISPR-1, which has similar structure to Cas proteins, yet its sequence differs by over 400 mutations compared to Cas9 and over 200 mutations compared to any known Cas protein. Has raised a total of $44M in funding as of March 2024.
Proteinea	Ecotech	Mass-produced insect larvae as an affordable way of manufacturing recombinant proteins. Early stage as of May 2021.
ReCode Therapeutics	Biomed	Has developed selective organ targeting (SORT) lipid nanoparticles, which include the four components of traditional lipid nanoparticles plus a fifth biochemically distinct lipid to facilitate bypassing of the liver and targeting of other organs such as lung and spleen. As of July 2023, has reached early-stage clinical trials for treating primary ciliary dyskinesia with inhalable SORT lipid nanoparticles that carry mRNA, is just starting early-stage clinical trials for treating cystic fibrosis with inhalable SORT lipid nanoparticles that carry mRNA, and has begun discovery-stage work on several other treatments. Has raised a total of $422M as of July 2023. Co-founded by Daniel Siegwart, a professor at the University of Texas.
Recursion Pharmaceuticals	Bio-AI	High-throughput platform for drug discovery which leverages AI and multimodal automated screening tools to achieve a cycle of homing in on useful drug molecules, narrowing the search space recursively. Has found some molecules which are now in clinical trials as of June 2023.
Rejuvenate Bio	Biomed	Developing anti-aging gene therapy using liver-directed AAVs encoding FGF21, a protein facilitates global regulation of a network of genes and helps reverse multiple conditions such as age-related obesity, diabetes, heart failure, and renal failure. Lead indication (desmoplakin arrhythmogenic cardiomyopathy) is at IND-enabling study stage as of January 2025, also at preclinical stage for other indications. Running a clinical trial for cardioprotective gene therapy to treat dogs with mitral valve disease as of January 2025. George Church is a co-founder. Has raised over $14M in funding as of January 2025.
Renewal Bio	Biomed	Developing a method that acts as an artificial womb and facilitates ex vivo production of human embryos similar to those found in a pregnancy around day 40 to 50. Have demonstrated successful proof-of-principle for making human embryos ex vivo. Aims to use the embryos as “3D bioprinters” to make tissues and organs for transplantation. The embryos may produce immune cells that could be transplanted into an older person to rejuvenate her/his immune system and facilitate longevity. The embryos may produce gonad tissues that could be transplanted into women to restore fertility and improve health. Strictly not aiming to create embryos that could develop further due to ethical issues. Likely will be able to genetically engineer the embryos to prevent formation of a head, mitigating ethical concerns. Based in Israel. Has published several high-profile scientific papers (two in Nature and one in Cell).
Repair Biotechnologies	Biomed	Developing a cholesterol degrading platform therapy which can reverse atherosclerosis. The CEO, who is known as Reason, is outspoken about the need to combat aging. Has preclinical proof-of-concept as of May 2021.
Resilience	Biomanufacturing	New manufacturing platforms to service partners for development and scaling of gene therapies, cell therapies, vaccines, protein therapies, and more. Received $800M in funding during 2020.
Retro Biosciences	Biomed	Longevity company with the goal of adding 10 years to the healthy human lifespan. Developing treatments for aging in the areas of hematopoietic stem cell reprogramming, autophagy enhancement, microglia therapeutics, tissue reprogramming, and T cell reprogramming. Sam Altman invested $180M into Retro Biosciences in 2023.
Ring Therapeutics	Biomed	Developing anellovirus as a minimally toxic and redosable alternative to existing gene therapy viral vectors. Anellovirus is a commensal human virus. Employing a platform called Anelloscope for screening of anellovirus sequences from human tissue, this then leads into to design of improved anellovirus variants.
Sanmai	Neurotech	Developing transcranial focused ultrasound devices (noninvasive) for neuromodulation to treat mental illnesses. Has published a pilot study (2023) showing that 60% of people with treatment-resistant anxiety experienced a statistically significant reduction in their feelings of anxiety. Has published a pilot study (2020) showing that 70% of people with treatment-resistant depression experienced a statistically significant improvement in certain forms of mood. As of 2025, in the process of performing a clinical trial with Acacia Mental Health clinic to determine if multiple sessions extend anxiety reduction effect. Raised a $12M series A in June 2025 from Reid Hoffman (LinkedIn co-founder and wealthy individual).
Sarepta Therapeutics	Biomed	A large medical biotechnology company with 4 FDA-approved therapies and 40 investigational therapies under-development (as of September 2025). Their FDA-approved therapies include three antisense oligonucleotides (made with phosphorodiamidate morpholino oligomer backbones) as well as the AAV gene therapy Elevidys, all medicines for treating Duchenne muscular dystrophy. The investigational therapies are aimed at treating Duchenne muscular dystrophy, limb-girdle muscular dystrophies, Charcot-Marie-Tooth disease, and some CNS-related disorders. The cost of Elevidys is $3.2M per patient (one-time treatment). Elevidys has endured significant public controversy due to several patient deaths (acute liver failure) in 2025, which led to a hold on the therapy as requested by the FDA. The hold on Elevidys was lifted by the FDA in July 2025, but concerns remain. Additionally, the European Medicines Agency has recommended against marketing Elevidys in the European Union.
Science	Neurotech	Developing a device-therapy combination to restore sight in people who have lost photoreceptors but retain retinal ganglion cells. Leveraging optogenetic gene therapy to give retinal ganglion cells the ability to respond to light as well as an implantable device that fits over the retina and stimulates the modified retinal ganglion cells with appropriate wavelengths to reproduce vision. Has an in-house foundry which can provide custom electronics fabrication as a service to interested parties. Also developing a new type of brain-computer interface which uses an external device containing living neurons that interface with the brain tissue, are activated via optogenetic stimulation in the external device, and are recorded by electrodes in the external device.
Sherlock Biosciences	Biomed	CRISPR-based diagnostics. Feng Zhang is one of the co-founders.
Siren Biotechnology	Biomed	Developing AAVs encoding cytokines to induce the immune system to attack solid tumors. Planning a first clinical program which will use cytokine-encoding AAVs to treat gliomas via local delivery, taking advantage of the brain’s immune-privileged status to avoid anti-AAV immunity. A low dose of AAVs is injected directly into tumors, expresses cytokines which kill the cancer cells as well as attract the innate immune system (e.g. macrophages, natural killer cells) to further eradicate the cancer. Nicole Paulk (formerly a UCSF professor) is the CEO, founder, and president. Has raised $25.6M as of January 2025.
Somalogic	Biotech	Proteomics platform called SomaScan for protein biomarker discovery which aids researchers in the development of new diagnostics. SomaScan is an aptamer-based platform which can simultaneously measure 7,000 protein biomarkers. Founded by Larry Gold, who is the inventor of SELEX.
SpiNNcloud	Bio-AI	Developing neuromorphic supercomputers so that AI can take advantage of biologically-inspired hardware architectures. Has built SpiNNaker and SpiNNaker2 high-performance computing clusters using their neuromorphic chips; these systems are highly scalable and energy efficient. The original SpiNNaker system was developed as part of the Human Brain Project; both systems are well-suited to running biologically realistic neuroscience simulations in real time.
SpyBiotech	Biomed	Developing a vaccine against human cytomegalovirus using virus-like particles equipped with their SpyTag-SpyCatcher molecular glue technology. As of June 2024, is in the process of a phase I clinical trial for their vaccine against human cytomegalovirus. Has licensed the SpyTag-SpyCatcher technology to a variety of research groups working on vaccines for cancer, chronic diseases, viral diseases, bacterial diseases, parasite diseases, and veterinary diseases. Mark Howarth, who originally developed the SpyTag-SpyCatcher technology in his academic lab, is a co-founder.
Strateos	Services	Offers R&D services through remotely controlled automated laboratories. Has extensive automated equipment for research in drug discovery, synthetic biology, imaging, cell and gene therapy, etc.
Synchron	Neurotech	Endovascular brain-computer interfaces as a minimally invasive approach for neural prosthetics, neuromodulation, and neurodiagnostics. Has developed the strentrode, an endovascular electrode array that can record or stimulate neurons from within blood vessels. As of September 2022, a technology called brain.io (that employs stentrodes) is in early clinical trials and gives paralyzed patients the ability to control digital devices.
Synthego	Services	CRISPR genome engineering services, custom cell lines, custom screening libraries, CRISPR reagents and kits, aiding both academic researchers and clinical drug developers.
Systemic Bio	Biotech	Develops vascularized organ models in hydrogels as tools for accelerating and improving preclinical drug testing.
Syzygy Plasmonics	Ecotech	Developing a photocatalytic reactor system which leverages a nanoparticle-based plasmonic photocatalyst. The photocatalyst consists of a larger light-harvesting plasmonic nanoparticle decorated with smaller catalytic nanoparticles. Their first product will be a clean hydrogen fuel production system which does not rely on petroleum. More of a chemical engineering company than a biotechnology company, but their technology may eventually have applications in biology.
Tahoe Therapeutics	Bio-AI	Developing AI virtual cell models to help find drugs for treating cancer. Working with data from perturbative interactions between single cells and drugs as well as data from drug-patient interactions. Has built an open-source foundation model (Tahoe-100M) which was trained using 100M single cell data points and 60,000 drug-patient interactions. Working on larger models to continue towards the goal of finding clinical leads to translate. Has raised a $30M series A (as of August 2025) to build a model mapping between 1B single-cell datapoints and 1M drug-patient interactions.
Tektonyx Bio	Biotech	Developing new protein therapeutics using genetically recoded bacteria with expanded genetic alphabets which include noncanonical amino acids. Has several journal publications from 2015 to 2021.
Tessera Therapeutics	Biomed	Developing gene writing technology for therapeutics. Characterizing a database of over 100,000 candidate mobile genetic elements to use in their technologies; using these to develop a toolkit for single nucleotide edits, correcting pathogenic alleles, replacing whole exons, and introducing whole genes. Leveraging target primed reverse transcription (TPRT) to engineer the genome, this is done with an RNA template and a gene writer protein, these components come from retrotransposon systems. TPRT gene writers bind and nick DNA before using reverse transcription to write into the genome (no double strand breaks). Also developing DNA gene writers for stably integrating large pieces of DNA into the genome; these can be delivered with lower doses of AAVs compared to traditional gene therapies. Has developed proprietary lipid nanoparticles for delivery of template RNAs along with RNAs encoding the gene writers to the liver, hematopoietic stem cells, and T cells. Seeking to address monogenic diseases, provide genetic treatments for prevalent diseases, and develop both in vivo and ex vivo cancer treatments. Has raised over $500M in total funding as of April 2022, more recently (December 2024) completed an agreement with the Bill and Melinda Gates Foundation to receive an additional amount of up to $50M.
Terrain Biosciences	Services	Leverages next-generation AI to design libraries of optimal RNA sequences (improved manufacturability, stability, expression quality, immunogenicity, durability, and targetability) for customers, has a rapid manufacturing pipeline to produce the RNAs. Aids customers in designing lead RNAs at early stages of development, helps via high-quality manufacturing for later (clinical) development. Co-founded by Patrick Hsu, Jonathan Gootenberg, and Omar Abudayyeh. Raised $9M in seed funding as of February 2025.
The Far Out Initiative	Biotech	Public benefit corporation developing technologies to mitigate biological suffering as inspired by philosopher David Pearce’s Hedonistic Imperative manifesto. Investigating cases of pain insensitivity where people experience very little or no pain while still having an instinctive capacity to avoid actions which may cause bodily harm; aiming to use the genetics of such people to develop a gene therapy that confers similar benefits. Working on germline engineering of farm animals and feed animals to minimize their capacity for suffering. Carefully evaluates the ethics of its proposed technologies and similar emerging technologies in order to hopefully move the world towards less suffering overall without accidentally exacerbating mistreatment of animals, etc. Early stage as of January 2025.
Tidal	Ecotech	Provides autonomous underwater robotic camera system equipped with AI computer vision technology along with environmental sensors which help fish farmers keep track of the growth, behaviors, and health of their fish and to monitor the water’s salinity, temperature, etc. The systems can furthermore facilitate real-time biomass monitoring, sea lice detection, autonomous feeding, and thus inform the decision making of fish farmers. Much of the data collected by the computer vision system occurs on timescales of milliseconds, faster than the human eye can track. Has expanded use of their technology beyond Norway to customers across the globe. Also working to leverage its systems towards ways of protecting the Earth’s oceans. Started out as a project at Alphabet’s X Moonshot Factory.
Tilibit Nanosystems	Services	Service which gives researchers predesigned and custom DNA origami nanostructures, including ones with chemical modifications. Founded by Hendrik Dietz, who was CEO from 2012-2014. He is now a scientific advisor.
Topas Therapeutics	Biomed	Developing Topas Particle Conjugates (TPCs), which consist of nanoparticles linked to immunogenic epitopes involved in selected autoimmune diseases; TPCs target liver sinusoidal endothelial cells (LSECs) and induce antigen-specific immune tolerance, thus treating specific autoimmune conditions. Targeting LSECs with TPCs results in antigen-specific tolerance via induction of regulatory T cells. As of January 2025, has shown positive results from a phase 2a trial for treating celiac disease. Has also advanced a treatment for the rare disease pemphigus vulgaris to phase 2 clinical trials. Has raised a total of $70M as of January 2025.
TreeCo	Ecotech	Developing CRISPR gene editing technology to create enhanced trees with improved characteristics for applications in timber, pulp and paper, and biofuels as well as for sustainability. For the sustainability applications, they are working on improved frost tolerance, drought tolerance, and disease resistance.
Turbine AI	Bio-AI	Predictive computational models of cancer cells, the “Simulated Cell^TM” platform, performing in silico experiments to test millions of drugs. Has partnered with Bayer, AstraZeneca, and others for drug development efforts.
Twist Bioscience	Biomanufacturing	Artificial DNA synthesis services. Synthetic biology towards insulin manufacturing in yeast, scalable spider silk manufacturing, combating malaria, and DNA data storage. Emily Leproust is a co-founder.
Vault Pharma	Biomed	Protein vault nanocompartments as a drug delivery platform to treat cancers and other diseases, protein vaults as a vaccine platform. Co-founded by Leonard Rome.
VectorBuilder	Services	Services in vector cloning, virus packaging, library construction, cell lines, etc.
Verve Therapeutics	Biomed	Developing CRISPR base editing therapies to turn off key genes (e.g. PCSK9 and ANGPTL3) involved in atherosclerotic plaque formation and thus to combat cardiovascular disease. The delivery mechanism involves lipid nanoparticles carrying gRNA and mRNA encoding a base editor protein. Has potential to save tens of millions of lives due to the status of heart disease as one of the most common causes of death. Early clinical trials began in July 2022.
Virica Biotech	Biomanufacturing	Helps in biomanufacturing of viral vectors through utilizing Viral Sensitizers, a library of small molecules which inhibit cellular antiviral defenses and thus increase yields of viruses from producer cells by around 5-10x. Provides custom services in aiding client biomanufacturing process development by incorporating Viral Sensitizers. Has raised $1.1M as of July 2023.
Xaira Therapeutics	Bio-AI	Leveraging machine learning data generation to develop a drug discovery platform and therapeutic products. Has received $1B of funding as of April 2024, though was recently announced and is still ramping up. David Baker is a co-founder. Led by Marc Tessier-Lavigne, former CSO of Genentech. Staff includes the scientists who developed RFdiffusion and RFantibody in David Baker’s lab.
YourChoice Therapeutics	Biomed	Developing a daily non-hormonal male birth control pill which is thus far (i) 99% effective and 100% reversible in mice and (ii) after 2 weeks decreases sperm count in primates to a level below fertility threshold as defined by NIH Contraceptive Development Program chief. Has completed a phase 1a clinical trial in human patients to evaluate safety and pharmacokinetics as reported by a 2025 publication. Their drug blocks spermatogenesis by inhibiting sperm progenitor cell division and by inhibiting release of mature sperm from the seminiferous tubules. Raised a $15M series A as of July 2022.
Zetta.ai	Neurotech	Advancing connectomics via computational reconstructions of neuronal wiring diagrams from image data. Offers a wide variety of automatic image reconstruction services to neuroscience laboratories. Created the automated AI reconstruction software behind reconstruction of the cubic millimeter of mouse cortex from MICrONS as well as reconstruction of the adult Drosophila brain from FlyWire. Working closely with BRAIN CONNECTs, a ten-year effort with the US BRAIN Initiative aiming to map a whole mouse brain.
Zymergen	Ecotech	Synthetic biology, metabolic engineering, biomanufacturing of materials and compounds as a substitute for chemical engineering practices.
4D Molecular Therapeutics	Biomed	Using high-throughput screening and recombination methods to develop novel AAV serotypes that evade immune responses and that target and transduce specific organs. Clinical trials for several new AAV vectors that treat pulmonary, cardiac, and eye diseases are ongoing as of September 2022
10x Genomics	Services	Spatial transcriptomics, genomics, proteomics, immune cell profiling, etc. Acquired ReadCoor and Cartana in 2020.
64x Bio	Biotech	High-throughput screening and computational design of new mammalian cell lines for manufacturing gene and cell therapies. George Church and Pamela Silver are among the co-founders.