Ishan Bhatt

Having a PhD means you can find the word “unfortunately” in an email faster that the search function

Why academic writing deserves to be beautiful The refusal to write beautifully is often justified in the name of neutrality, of detachment, of discipline.

www.thedailystar.net/books-litera...

Reimagining PhD supervision through allyship, creativity and decolonising practice How a creative, person-centred and decolonising approach to PhD supervision can transform outcomes for postgraduate researchers from diverse and non-traditional backgrounds

Rethinking #PhD supervision: creative, person-centred and decolonising approaches can transform outcomes for diverse researchers: www.timeshighereducation.com/campus/reima... #Academia #HigherEd #AcademicChatter #AcademicSky

“As recognized for over a century, faculty should be able to engage as individual citizens in extramural speech. Faculty should exercise these rights responsibly and professionally, but when they fail to do so, it is not the role of the government or the university to sanction them.”

Making yogurt with the ant holobiont uncovers bacteria, acids, and enzymes for food fermentation Entomology; Food microbiology

Tired of endlessly scrolling through 'news' was pleasantly greeted by "had a slight tangy taste with mild herbaceousness and pronounced flavors of grass-fed fat" (D. Zilber). Super cool work! www.cell.com/iscience/ful...

Sometimes, the locals are in charge but sometimes, the immigrants are in charge. On foreign DNA in bacteria 🤣😍

Oof, alongside the LLM suspicion is another aspect that isn't talked about enough- the widening rift between mol/mechanistic biol and evolutionary perspectives implicit in network-based/ shared backbone approaches!

How I confronted my growing cynicism about academia—and rekindled my sense of purpose “Maintaining hope doesn’t mean ignoring hardships or naïvely expecting things to work out,” this professor writes

www.science.org/content/arti...

Gene flow can reveal ghost lineages Abstract. Ghost species, encompassing extinct, unknown, and unsampled taxa, vastly outnumber those typically included in phylogenetic analyses. This hidden

Here, the potential of horizontal gene transfer detection methods were explored, based on phylogenies, to detect & quantify ghost diversity. What did they find? Read the full paper to find out (2/2)👇🧪🌍
doi.org/10.1093/evol...
@bastien-boussau.bsky.social
@damdevienne.bsky.social

Multilevel regulation of c-di-GMP biosynthesis by cAMP signaling increases Shigella sonnei fitness and pathogenicity in response to bile salts Intestinal pathogens employ different mechanisms to facilitate their infection and colonization in the intestines. Wang et al. demonstrate that Shigella sonnei elevates intracellular levels of cAMP by...

Multilevel regulation of c-di-GMP biosynthesis by cAMP signaling increases Shigella sonnei fitness and pathogenicity in response to bile salts

in @cp-cellreports.bsky.social

www.cell.com/cell-reports...

Applying evolutionary theory to understand host–microbiome evolution - Nature Ecology & Evolution This Perspective discusses how well-established theoretical models of evolution can be adapted to study and generate testable predictions about the evolutionary dynamics of host–microbiota association...

Source: Nature
search.app/7kUKP

Identification of PilD mutants reveals the iterative social evolution in Pseudomonas aeruginosa | Applied and Environmental Microbiology P. aeruginosa is a leading cause of opportunistic acute and chronic infections in humans, in which its pathogenicity is intricately intertwined with its evolutionary trajectory and the emergence of ge...

Identification of PilD mutants reveals the iterative social evolution in Pseudomonas aeruginosa

#ApplEnvironMicrobiol

journals.asm.org/doi/10.1128/...

Gene co-occurrence and its association with phage infectivity in bacterial pangenomes | Philosophical Transactions of the Royal Society B: Biological Sciences Phages infect bacteria and have recently re-emerged as a promising strategy to combat bacterial infections. However, there is a lack of methods to predict whether and why a particular phage can or can...

Gene co-occurrence and its association with phage infectivity in bacterial pangenomes

Phil. Trans. R. Soc. B by @annecmg.bsky.social et al
with @fbaumdicker.bsky.social

royalsocietypublishing.org/doi/10.1098/...

How do microbes become permanent partners? 🌊🔬🦠 Check out our new study published in Current Biology showing how cyanobacterial genomes evolve step-by-step into endosymbionts of diatoms. www.sciencedirect.com/science/arti...
@currentbiology.bsky.social @mehrshmali.bsky.social

Prokaryotic Circadian Systems: Cyanobacteria and Beyond

#AnnuRevMicrobiol from Susan Golden
with @partchlab.bsky.social

#chronobiology

www.annualreviews.org/content/jour...

The Interaction Between the Nematode Caenorhabditis elegans and Its Coexisting Fungal Microbiome Member Barnettozyma californica Barnettozyma californica is a member of the fungal microbiome of the model nematode Caenorhabditis elegans and can serve as food for worms. When combined with E. coli, this fungus can increase popula....

The Interaction Between the Nematode Caenorhabditis elegans and Its Coexisting Fungal Microbiome Member Barnettozyma californica

#EnvironMicrobiol from @michaelhabig.bsky.social
with @schulenburglab.bsky.social
@crc1182.bsky.social

enviromicro-journals.onlinelibrary.wiley.com/doi/full/10....

My generation had to deal with datasets where Excel had autocorrected gene names to dates. Future generations are going to have to deal with the hallucinations of slopbots.

Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis | PNAS Endosymbiotic gene transfer (EGT) and import of host-encoded proteins have been considered hallmarks of organelles necessary for stable integration...

www.pnas.org/doi/10.1073/... Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis #protistsonsky

Our review on the last decade+ of hybrid incompatibility research is now out! www.sciencedirect.com/science/arti...

Original thread here: bsky.app/profile/moll...

Protein Structure Informed Bacteriophage Genome Annotation with Phold Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n

www.biorxiv.org/content/10.1...

Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium Cells require highly polymorphic receptors to perform accurate self/non-self recognition. In the amoeba Dicytostelium discoideum, polymorphic TgrB1 & TgrC1 proteins are used to bind sister cells and e...

I'm excited to announce our new biorxiv preprint, wherein we investigate the evolution of the weirdest genetic locus I've ever seen! Behold the tgr genes of the social amoeba, which mediate self/non-self discrimination during facultative multicellularity 🐅 🧵 1/
www.biorxiv.org/content/10.1...

Congratulations all!

The combination of active partitioning and toxin-antitoxin systems is most advantageous for low-copy plasmid fitness - Nature Communications Effe et al. evaluate how specific plasmid traits influence plasmid fitness; they provide mechanistic insight into the persistence of large conjugative plasmids, including those that disseminate antibi...

Happy to finally share this! Read here about the best strategy the the persistence of low-copy plasmids. @mariosanter.bsky.social @iwangtoknow.bsky.social doi.org/10.1038/s414...

Having an organized space reduces visual cues and can help ADHD'ers reduce overwhelm. However, putting everything away has consequences for our memory.

This means it's much more important to be intentional about how we use our space rather than to be organized for organization's sake

Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication www.biorxiv.org/content/10.1... #jcampubs

As a transitioning semi-degreed heathen, I have to say that academia is incomprehensibly heirarchical and harrowingly inaccessible. That is what breaks my heart and motivates me at the same time. This should be more a table discussion than a random tweet!

The cost of biological research is large.

Why?

Have we had a hard convo about salary expectations, supplier pricing transparency, licensing red tape, and lack of communal tools yet?

Its easy to parrot "research is expensive" and avoid asking why. Not all biotech is pharma...

Late due to vacation, but
📢 New preprint out, presenting a new approach to reduce compositional heterogeneity in alignments. A passion project led by the amazing @stephkoe.bsky.social

👀 Check out this great explanation thread below 👇

Just a thought: what if we stopped measuring the economy by the state of the stock market and started measuring it based The Biggest Economic Lies We’re Told | Robert Reich

Just a thought: what if we stopped measuring the economy by the state of the stock market and started measuring it based on how many people are housed and clothed and fed? https://youtu.be/tFjoDq0HfFw?si=vtbE2QNmXskvutjF

Question: if you are sequencing genomes with linear plasmids, how are they closed?