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Items tagged with: Preprint

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New #ISEPpapers #preprint! Viral infection to the raphidophycean alga #Heterosigma akashiwo affects both intracellular organic matter composition and dynamics of a coastal prokaryotic community biorxiv.org/content/10.1101/20…

#protists #algae #viruses #microbes #biology

Viral infection to the raphidophycean alga Heterosigma akashiwo affects both intracellular organic matter composition and dynamics of a coastal prokaryotic community

Marine microalgae play a crucial role in marine ecosystem by supplying dissolved organic matter to heterotrophic prokaryotes, which mediate the microbial loop.
bioRxiv
#biology #protists #preprint #viruses #microbes #algae #iseppapers #heterosigma

#protists #preprint #genomics #microbes #algae #iseppapers #parasites #prototheca @bioRxiv

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New #ISEPpapers #preprint! Comprehensive analysis of the microbial consortium in the culture of flagellate #Monocercomonoides exilis biorxiv.org/content/10.1101/20… #protists #microbes #mitochondria #bacteria #biorxiv @biorxivpreprint

"Monocercomonoides exilis is the only known amitochondriate eukaryote, making it an excellent model for studying the implications of mitochondrial reduction from a cellular and evolutionary point of view."

Comprehensive analysis of the microbial consortium in the culture of flagellate Monocercomonoides exilis

Monocercomonoides exilis is the only known amitochondriate eukaryote, making it an excellent model for studying the implications of mitochondrial reduction from a cellular and evolutionary point of view. Although M.
bioRxiv
#bacteria #protists #preprint #mitochondria #microbes #biorxiv #iseppapers #monocercomonoides @bioRxiv

Tools
"Here, we engineered tobacco rattle virus to carry the compact RNA-guided TnpB enzyme ISYmu1 and its guide RNA. This innovation allowed transgene-free editing of #Arabidopsis thaliana in a single step, with edits inherited in the subsequent generation. "
#Preprint
biorxiv.org/content/10.1101/20…

Viral delivery of an RNA-guided genome editor for transgene-free plant germline editing

Genome editing is transforming plant biology by enabling precise DNA modifications. However, delivery of editing systems into plants remains challenging, often requiring slow, genotype-specific methods such as tissue culture or transformation.
bioRxiv
#preprint #Arabidopsis

A #preprint detective story
"Our two laboratories encountered independently sudden-onset, major impediments to such research. Spore suspensions and vegetative cells no longer plated effectively on minimal media. By systematically analyzing multiple different media components from multiple different suppliers, we identified the source of the problem"
biorxiv.org/content/10.1101/20…

Laboratory horror stories: Poison in the agars

The fission yeast Schizosaccharomyces pombe is a single-celled eukaryote that can be cultured as a haploid or as a diploid.
bioRxiv
#preprint

'Both genomes had been analysed before, but the fragmented assemblies had scaffold sizes comparable to the length of long reads prior to assembly. Our new assemblies illustrate how long-read technologies allow for a much better representation of species genomes. We are now able to conduct more accurate downstream assays based on more complete gene and transposable element predictions.'
#Preprint #Evolution #Genomics

biorxiv.org/content/10.1101/20…

Revisiting genomes of non-model species with long reads yields new insights into their biology and evolution

High-quality genomes obtained using long-read data allow not only for a better understanding of heterozygosity levels, repeat content, and more accurate gene annotation, and prediction when compared to those obtained with short-read technologies, but…
bioRxiv
#Evolution #preprint #genomics

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New #ISEPpapers #preprint! Encyclopaedia of #DNApolymerases localized in #organelles: Evolutionary contribution of diverse #bacteria including the proto-#mitochondrion biorxiv.org/content/10.1101/20… #eukaryogenesis #evolution #microbes

Encyclopaedia of DNA polymerases localized in organelles: Evolutionary contribution of diverse bacteria including the proto-mitochondrion

DNA polymerases (DNAPs) synthesize DNA from deoxyribonucleotides in a semi-conservative manner and serve as the core of DNA replication and repair machineries.
bioRxiv
#Evolution #bacteria #preprint #microbes #mitochondrion #iseppapers #dnapolymerases #organelles #Eukaryogenesis

#microbiology #preprint

'To address this critical knowledge gap, we conducted a comprehensive cross-species analysis of transcriptomic data from over 6000 blood samples from macaques and humans infected with one of 31 viruses, including #Lassa, #Ebola, #Marburg, #Zika, and #dengue.'
#Immunology #Virology #preprint

biorxiv.org/content/10.1101/20…

Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans

Viral pandemics and epidemics pose a significant global threat, with emerging and re-emerging viruses responsible for four pandemics in the 21st century alone.
bioRxiv
#preprint #immunology #virology #dengue #Lassa #ebola #marburg #zika

We have a new preprint online! A great collab with the Tresch lab in Cologne. We found that mRNA 🧬 export out of the nucleus is surprisingly slow and and a rate limiting step for mRNA metabolism. Take a look: biorxiv.org/content/10.1101/20…
#ScienceMastodon #RNA #mRNA #preprint #mpinat

Nuclear export is a limiting factor in eukaryotic mRNA metabolism

The eukaryotic mRNA life cycle includes transcription, nuclear mRNA export and degradation. To quantify all these processes simultaneously, we perform thiol-linked alkylation after metabolic labeling of RNA with 4-thiouridine (4sU), followed by seque…
bioRxiv
#ScienceMastodon #preprint #RNA #mrna #MPINAT

An antibacterial peptide encoded in the mitochondrial genome (#preprint).
#immunology #InnateImmunity

"We demonstrate that MOTS-c (mitochondrial open reading frame from the twelve S rRNA type-c) is a mitochondrial-encoded amphipathic and cationic peptide with direct antibacterial and immunomodulatory functions, consistent with the peptide chemistry and functions of known HDPs."

biorxiv.org/content/10.1101/20…

The Human Mitochondrial Genome Encodes for an Interferon-Responsive Host Defense Peptide

The mitochondrial DNA (mtDNA) can trigger immune responses and directly entrap pathogens, but it is not known to encode for active immune factors. The immune system is traditionally thought to be exclusively nuclear-encoded.
bioRxiv
#preprint #immunology #innateimmunity

(I realize that some of these suggestions would best be used simulatenously, e.g., #newPaper and #preprint have obviously different content. What I am searching for is a common tag for *threads* explaining research articles, not only posts announcing a new publication 🙂.
I had to drop one tag bc of the 5-option limit in polls, and I went for #mastoPrint as it was my own suggestion.)

Some further thoughts:
One could combine these tags in a standardized way with research field names, e.g. #newNeuroPaper, #neuroPreprint, or #neuroPaperThread.
Also, please remember to use #camelCase or #CamelCase notation in these tags for screenreader accessibility!

Tagging some people who responded to my first post (sorry for bothering you!):
@mwt @toddhorowitz @achterbrain @PessoaBrain @elduvelle @Brendanjones @gdiak @EricLawton @annettamallon @UlrikeHahn @ryneches @x1l3f @nyates314 @bsweber @ArneBab @tfardet @emergentnexus @DrAnneCarpenter @f @harcel @MarkHanson @Iris

#preprint #camelcase #newpaper #mastoprint #newneuropaper #neuropreprint #neuropaperthread @ArneBab @Tanguy Fardet @Jascha Achterberg @Brendan Jones @MAHanson @Iris van Rooij 💭 @Dr. Ruchira S. Datta @Bryan S. Weber @El Duvelle @Ulrike Hahn @MWT @Dr Annetta Mallon @Russell Neches @Felix Reutter @Eric Lawton @toddhorowitz @PessoaBrain @gdiak @nyates314 @DrAnneCarpenter @f @harcel

Hi #science #research #mastodon community! A few days ago, a post of mine recieved a lot of attention. Thanks for the engagement and the very interesting suggestions! neuromatch.social/@LeonDLotter…

On #Twitter, I loved the common practice of writing threads explaining new #preprints and #papers in an understandable way.
I uttered my concern that through the chronological timeline here people might miss interesting science. A solution would be to agree on names for hashtags and/or a.gup.pe groups to ease tracking these "paper threads".

Following tags were named more then once: #newPaper #paperThread #preprint #researchPaper #mastoPrint #tootPrint.
Also, there was #tootorial, but that might be a slightly different category?

I heard people like participation - so let's do a poll! What's your favourite tag for threads explaining research articles? 📊​ Multiple choices possible!

#twitterMigration #scienceTwitter #scientist @academicchatter @neuroscience @cognition @psychology @phdstudents

Leon Lotter (@LeonDLotter@neuromatch.social)

On #scienceTwitter, my favourite thing was reading and, on rare occasions, writing "paper/preprint threads". From the researchers I followed and through the #Twitter algorithm, this became my most important source for new #research.
Neuromatch Social

  • #newPaper (26%, 67 votes)
  • #paperThread (37%, 93 votes)
  • #preprint (27%, 68 votes)
  • #researchPaper (34%, 85 votes)
  • #tootPrint (9%, 23 votes)
250 voters. Poll end: 3 years ago

#mastodon #science #Research #Twitter #twittermigration #sciencetwitter #preprint #scientist #preprints #papers #newpaper #paperthread #researchpaper #mastoprint #tootprint #tootorial @u/cognition @u/academicchatter @u/psychology @u/phdstudents @u/neuroscience

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New #preprint alert! What are the core symbionts of lichens? TLDR: we analyzed >400 lichen metagenomes from around the world and found that 4 bacterial groups are as frequent in lichens as the alga, one of the two main partners in the symbiosis. 🧵 1/11 biorxiv.org/content/10.1101/20…

Evidence for a core set of microbial lichen symbionts from a global survey of metagenomes

Lichens are the archetypal symbiosis and the one for which the term was coined. Although application of shotgun sequencing techniques has shown that many lichen symbioses can harbour more symbionts than the canonically recognized fungus and photobion…
bioRxiv
#preprint

#preprint #viruses #marine #Giant @Frank Aylward

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Happy to announce this #preprint , the culmination of last 10 years. 🥳

We find that #antimicrobialpeptides are evolved to control specific #microbiome #bacteria. This example is a textbook case of host #immune #evolution being shaped by the microbiome 🦠 which depends on host #ecology.

Thanks for comments! Bit of an experiment: we are posting pre-submit to get feedback 🙂.

biorxiv.org/content/10.1101/20…
#immunity #Drosophila #EvolutionaryBiology #inflammation #NFkB

Single innate immune effectors control ecological microbiome bacteria across evolutionary timescales

Antimicrobial peptides are host-encoded antibiotics that combat invading microbes and help shape the microbiome in plants and animals.
bioRxiv
#ecology #Evolution #bacteria #preprint #antimicrobialpeptides #microbiome #immune #immunity #drosophila #evolutionarybiology #inflammation #nfkb

#frugalinnovation #synbio #preprint @drew endy

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