Chetan Srinath @quick_ben

Our preprint describing the moonlighting functions of SEC13 in NMD and regulation of the UPR is out now in bioRxiv biorxiv.org/cgi/content/sh…

📢'The World Is Your Oyster' is for those who are born in global north countries--don't experience visa bureaucracy & emotional burden that non-white global south scholars do. Citizenship is a privilege that we need to recognize in the academe. 1/n nature.com/articles/d4158…

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A postdoc position is available in our lab @mrc_hgu to study regulation and physiological relevance of the Nonsense-mediated decay (NMD) pathway in vivo, using cells in culture and transgenic mice models. See details at elxw.fa.em3.oraclecloud.com/hcmUI/Candidat…

Happy to see that our work on developing a #GeneTherapy that can support cardiomyocyte regeneration has been published in @CircAHA. Congrats to everyone @TenayaThera, I'm excited to see how this can help people with #HeartDisease in the future.

Circulation @CircAHA

3 years ago

#OriginalResearch: A combination of cardiac reprogramming genes delivered via a novel AAV can support myocardial cell regeneration and improve function in rats following MI. @TenayaThera #AHAjournals ahajournals.org/doi/10.1161/CI…

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We’ve just published a review article on mRNA quality control mechanisms @embojournal, led by Laura Monaghan and Dasa Longman @mrc_hgu embopress.org/doi/full/10.15…

1/10📢Thrilled to announce our new preprint! In this work, we describe a new method called TREX for unbiased discovery of proteins that directly bind to a given region of an RNA of interest. And all this is from living cells under endogenous settings! #RNA biorxiv.org/content/10.110…

Legal immigration is *impossible* for nearly all immigrants wishing to immigrate to the U.S. legally. You can’t just “get in line.” That’s a fiction perpetuated by those who want to keep immigration illegal. My latest report explains why. Here’s the summary in 1 pic... 🧵

An important paper on the genetic architecture of South Asians is published by a fantastic team of industry and academic researchers. I recommend you read the paper to learn about all the interesting findings. But here are some general thoughts. I am not involved in this study, but I was looking forward to seeing this work published since it was preprinted. In any paper on South Asian genetics, you will read about two major population phenomena—endogamy and consanguinity—that have sculpted the genomes of South Asians over hundreds to thousands of years resulting in the unique genetic architecture that we see today. Endogamy and consanguinity are practices of non-random mating. Endogamy is marrying within a closed community (typically, individuals of a particular caste), and consanguinity is marrying within close relatives (i.e., cousin marriages). Non-random mating means a shuffling of similar chromosomes which will reduce genetic diversity in the subsequent generations, but at the same time let some deleterious variants drift to higher frequencies. Medical researchers interested in sequencing South Asian populations are typically into identifying such drifted variants and studying their phenotypic associations. But there are challenges. When investing in sequencing inbred populations, there is a trade-off. You’ll identify more deleterious (and protective) variants at higher frequencies but overall you’ll identify fewer variants, compared to sequencing an outbred population of similar sample size. Many of the drifted variants of interest can be captured by genotyping and imputation (using a custom imputation panel built from a subsample) without the necessity for sequencing, a strategy that Iceland and Finland have been sticking with so far. But countries like India are different in a way that they are not single founder populations but rather a pool of thousands of founder populations (i.e., endogamy producing founder-like effects), each with its own unique set of drifted variants. In the current study, the authors analyze whole genome sequences of >5000 individuals from India, Pakistan and Bangladesh and report that there are more loss of function variants (pLoFs) in South Asians than in Europeans, with ~61% of the pLoFs being unique to South Asians. But what is more interesting is a substantial number of these South Asian-specific pLoFs are not shared across the subgroups (Indians, Pakistanis and Bengalis), suggesting that each of the subgroups contributes unique sets of pLOFs through independent genetic drifts. This will be the case as one zooms into the subgroups. Each of thousands of small endogamous communities that together form South Asia would have experienced genetic drifts independently resulting in their own private set of drifted pLoFs. This intra-population genetic diversity is what will make it extremely challenging to build a single cohort such as the UK Biobank in South Asia that will be representative of the entire population. As large-scale efforts to sequence South Asian populations are underway, I am curious to see how researchers tackle this challenge. nature.com/articles/s4146…

Had a blast hanging out with some wonderful scientists at #RNA23!

Thiago Britto-Borges @tbrittoborges

3 years ago

Science and laughter with the future of RNA #RNA23

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A Postdoc position available in our lab @mrc_hgu to study DExH/D RNA helicases and GPATCH proteins in pre-mRNA splicing with relevance to Colorectal cancer (CRC), in collaboration with Malcolm Dunlop elxw.fa.em3.oraclecloud.com/hcmUI/Candidat… Application deadline, 21st February 2023

Apply by January 9 2023 for our #PhD programme in Human Genetics, Genomics and Disease. Join us in Edinburgh to develop your research career and tackle key problems in understanding how our DNA affects health and disease @EdinUni_IGC ed.ac.uk/mrc-human-gene…

Our latest paper describing a dual role for the DExH/D RNA helicase DHX34 in NMD and pre-mRNA splicing is now @RNAJournal @mrc_hgu @nelehug @michaela_raab @DasaDLongman, Stuart Aitken and collaborators @QMBCI @fitzig02 @kevin_rouault @hanarmes@anariomachin

RNA @RNAJournal

4 years ago

DExH/D RNA helicase DHX34 acts in both pre-mRNA splicing and nonsense-mediated decay (NMD). These functions could act on different RNAs, but for a subset, DHX34 may couple splicing and NMD. Mutations in DHX34 are implicated in blood disorders (AML/MDS) bit.ly/3bS0JlB

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Were two separate, major lines of Alzheimer’s research tainted by image fabrication, with far-reaching implications for the field? I take a deep look for @ScienceMagazine science.org/content/articl… 🧵 1/11

I'm excited to be back in the lab, and looking forward to working with Dasa Longman and @JavierFCaceres1 on NMD!

Javier F Caceres @JavierFCaceres1

4 years ago

We are very happy to welcome to our lab new PhD student Chetan Srinath @quick_ben. He will be working on some cool projects on NMD regulation.

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Welcome to the @Nasdaq family, Tenaya Therapeutics! 🎉 Now trading: $TNYA Learn more about the #TenayaTherapeuticsIPO: tenayatherapeutics.com

Downgrading the concern on B.1.617, the poorly named "double mutant" —98% effectiveness of mRNA vaccine in an Israeli outbreak @CT_Bergstrom —Lab studies: minimal immune evasion, expected full protection from vaccine @GuptaR_lab

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Gupta Lab @GuptaR_lab

5 years ago

Here is the REALLY IMPORTANT part. The combination of the two mutations gives a value of 4, in other words the two mutations DO NOT confer substantial antibody evasion and we can stop using the term 'Double Mutant'.

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A few thoughts on the B.1.617 variant, first seen in India in late 2020, recently seen in >100 cases in the UK, and very much in the news here. TLDR: we should watch carefully, but I don't think any of our best lines of evidence on variants are yet cause for concern. 🧵

“You should always hang your bananas instead of keeping them flat in a bowl because that makes them think that they are still on the tree and thus they ripen slowly” is a beautiful way to explain it

Once Upon a Time: an RNA vaccine! How does the #vaccine work, and what happens if the #coronavirus tries to attack a vaccinated person? @helsinkiuni @HelsinkiOne @LifeSciHelsinki PDF: bit.ly/coronavacc #COVID19 #COVID19Vaccine #SARSCoV2

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