Last Updated: 16-May-2024

What I'm reading:

7-May-2024

Structure-Based Vaccine Antigen Design

• https://doi.org/10.1146%2Fannurev-med-121217-094234

Principals and practical applications of structure-based vaccine design

• https://doi.org/10.1016%2Fj.coi.2022.102209

31-Oct-2023

Synthetic viruses: a new opportunity to

understand and prevent viral disease

• https://doi.org/10.1038/nbt.1593

Synthetic virology: engineering viruses for gene delivery

• https://doi.org/10.1002%2Fwnan.1287

25-Oct-2023

BAC-VAC, a novel generation of (DNA) vaccines: A bacterial artificial chromosome (BAC) containing a replication-competent, packaging-defective virus genome induces protective immunity against herpes simplex virus 1

• https://doi.org/10.1073/pnas.96.22.12697

• I'm surprised this technology has not been developed more since this publication, a search of PubMed for the term "BAC VAC" results in only 20 hits. This seems like an innovative, creative method by which live-attenuated vaccines may be delivered with greater manufacturing convenience and flexibility. I contend that this technology could be revolutionary to the field of live-attenuated vaccines. Of course, as a virologist, I prefer the use of recombinant viruses packaged as live-attenuated vaccines because of their tremendous efficacy and longevity of protective immunity (plus it's fun to make viruses!).

Engineered antibody cytokine chimera synergizes with DNA-launched nanoparticle vaccines to potentiate melanoma suppression in vivo

• https://doi.org/10.3389/fimmu.2023.1072810

25-Sep-2023

Alternative splicing of its 5' UTR limits CD20 mRNA translation and enables resistance to CD20-directed immunotherapies

• https://doi.org/10.1182/blood.2023020400

3-Sep-2023

Recombinant, live-attenuated tetravalent dengue virus vaccine formulations induce a balanced, broad, and protective neutralizing antibody response against each of the four serotypes in rhesus monkeys

• https://doi.org/10.1128/jvi.79.9.5516-5528.2005

A live, attenuated dengue virus type 1 vaccine candidate with a 30-nucleotide deletion in the 3' untranslated region is highly attenuated and immunogenic in monkeys

• https://doi.org/10.1128/jvi.77.2.1653-1657.2003

23-Aug-2023

Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM

• https://doi.org/10.1038/s41467-021-25087-4

• Woah, what a cool technique

17-Aug-2023

The journey to a respiratory syncytial virus vaccine

• https://doi.org/10.1016/j.anai.2020.03.017

10-Aug-2023

Search-and-replace genome editing without double-strand breaks or donor DNA

• https://doi.org/10.1038/s41586-019-1711-4

Phage-assisted evolution and protein engineering yield compact, efficient prime editors

• https://doi.org/10.1016/j.cell.2023.07.039

Engineered pegRNAs improve prime editing efficiency

• https://doi.org/10.1038/s41587-021-01039-7

Designing and executing prime editing experiments in mammalian cells

• https://doi.org/10.1038/s41596-022-00724-4

PrimeDesign software for rapid and simplified design of prime editing guide RNAs

• https://doi.org/10.1038/s41467-021-21337-7

8-Aug-2023

Ecological dynamics of emerging bat virus spillover

• http://dx.doi.org/10.1098/rspb.2014.212

Hendra and Nipah viruses: different and dangerous

• https://doi.org/10.1038/nrmicro1323

What I'm reading:

16-Apr-2023

Mass Spectrometry-Based Structural Virology

• https://dx.doi.org/10.1021/acs.analchem.0c04339 

9-Apr-2023

Fourier transform ion cyclotron resonance mass spectrometry: A primer

• https://doi.org/10.1002/(SICI)1098-2787(1998)17:1%3C1::AID-MAS1%3E3.0.CO;2-K 

5-Apr-2023

Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography

• https://doi.org/10.1021/acs.analchem.2c04114

Ribosome Collisions Trigger General Stress Responses to Regulate Cell Fate

• https://doi.org/10.1016/j.cell.2020.06.006

Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria

• https://doi.org/10.1038/s41586-022-04416-7

• What a beautiful set of structures! The fact that the tRNAs, mRNA, and SmrB can all be resolved really allows for a tremendous amount of biological information to be extracted from data like these. I look forward to reading more studies like this in the future that capture molecular machines in-process.

Live-cell imaging reveals kinetic determinants of quality control triggered by ribosome stalling

• https://doi.org/10.1016/j.molcel.2021.01.029 

2-Apr-2023

The molecular basis of eukaryotic transcription

• https://doi.org/10.1073/pnas.0704138104 

Structural insights into RNA polymerases of negative-sense RNA viruses

• https://doi.org/10.1038/s41579-020-00501-8 

20-Mar-2023

A protocol for capturing RNA-sensing innate immune receptors in multiple conformations by single-particle cryo-EM

• https://doi.org/10.1016/j.xpro.2023.102166 

The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands

• https://doi.org/10.1016/j.molcel.2022.09.029 

23-Feb-2023

A bat MERS-like coronavirus circulates in pangolins and utilizes human DPP4 and host proteases for cell entry

• https://doi.org/10.1016/j.cell.2023.01.019 

15-Feb-2023

The Integrated Stress Response Methods and Protocols

• https://doi.org/10.1007/978-1-0716-1975-9 

10-Feb-2023

Evaluating data integrity in ribosome footprinting datasets through modelled polysome profiles

• https://doi.org/10.1093/nar/gkac705 

2-Feb-2023

Structural insights into the activity regulation of full-length non-structural protein 1 from SARS-CoV-2

• https://doi.org/10.1016/j.str.2022.12.006 

18-Dec-2022

Discovery and structure of a widespread bacterial ABC transporter specific for ergothioneine

• https://doi.org/10.1038/s41467-022-35277-3 

11-Dec-2022

In Situ Tagged nsp15 Reveals Interactions with Coronavirus Replication/Transcription Complex- Associated Proteins

• https://doi.org/10.1128/mbio.02320-16

27-Nov-2022

Spatial and Temporal Resolution of Global Protein Synthesis during HSV Infection Using Bioorthogonal Precursors and Click Chemistry

• https://doi.org/10.1371/journal.ppat.1005927 

21-Nov-2022

N-Terminal Modification of Gly-His-Tagged Proteins with Azidogluconolactone

• https://doi.org/10.1002/cbic.202100381

25-Sep-2022

HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry

• https://doi.org/10.1038/s41467-018-06591-6

25-Sep-2022

Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome

• https://doi.org/10.1038/s41594-021-00653-y 

12-Sep-2022

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

• https://doi.org/10.1038/nprot.2012.086 

9-Aug-2022

The mechanism of RNA capping by SARS-CoV-2

• doi: https://doi.org/10.1038/s41586-022-05185-z

22-Jun-2022

Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2

• doi: 10.1126/science.abc8665

• What a groundbreaking article. It would be really interesting to repeat this study in the context of true virus infection. This may reveal other viral proteins (especially nucleocapsid) that bind the interact with the ribosome-nsp1 complex. It would be fascinating if one could capture the viral genomic (or sub-genomic) RNA, nsp1, ribosome complex to better understand the function of nsp1. I think it's possible that coronaviruses utilize a unique translation initiation mechanism that may involve nsp1, N, the structured 5'UTR of coronaviral mRNAs, and perhaps host factors such as eIF4H1. Ribosome profiling (Ribo-seq) and polysome profiling would provide valuable information, too, and would be convenient given that preparation of ribosomes for structural studies (as I suggest above) could also be used for Ribo-seq. I would also be interested to understand the role of eIF2a and phosphorylation of eIF2a in coronavirus translation initiation.

11-Apr-2022

A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity

• https://doi.org/10.1126/science.1225829 

7-Mar-2022

Functional Transcriptional Regulatory Sequence (TRS) RNA Binding and Helix Destabilizing Determinants of Murine Hepatitis Virus (MHV) Nucleocapsid (N) Protein 

• doi: https://doi.org/10.1074/jbc.M111.287763

16-Feb-2022

The murine coronavirus nucleocapsid gene is a determinant of virulence

• https://doi.org/10.1128/jvi.01758-09 

1-Nov-2021

A Contemporary View of Coronavirus Transcription

• https://doi.org/10.1128/jvi.01358-06 

Everything You Always Wanted to Know About Rabies Virus (But Were Afraid to Ask)

• https://doi.org/10.1146/annurev-virology-100114-055157

How the Spread of Disease Juiced the Lore of Vampires Into Pandemic Proportions

• https://news.virginia.edu/content/how-spread-disease-juiced-lore-vampires-pandemic-proportions 

More ‘Disease’ Than ‘Dracula’—How the Vampire Myth Was Born

• https://getpocket.com/explore/item/more-disease-than-dracula-how-the-vampire-myth-was-born 

Quoth the Raven: It Was Actually Rabies

• https://cvm.missouri.edu/quoth-the-raven-it-was-actually-rabies/ 

Themes

• Live-attenuated vaccines

• RNA-protein complexes

• Structural analysis of ribosomes

• Structural virology

• Molecular virology

• Synthetic biology

• Innovative vaccine technology

• Immunotherapy

• Gene therapy

• Physical (wave-based) brain interactions

• Intelligence & reconnaissance