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Items tagged with: Preprint
New #ISEPpapers #preprint! Viral infection to the raphidophycean alga #Heterosigma akashiwo affects both intracellular organic matter composition and dynamics of a coastal prokaryotic community https://www.biorxiv.org/content/10.1101/2024.10.07.616994v1
#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
New #ISEPpapers #preprint! Comprehensive analysis of the microbial consortium in the culture of flagellate #Monocercomonoides exilis https://www.biorxiv.org/content/10.1101/2024.02.02.578639v2 #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
"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
https://www.biorxiv.org/content/10.1101/2024.07.17.603964v1
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
"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"
https://www.biorxiv.org/content/10.1101/2024.06.06.597796v1
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
Small but mitey: long-read assembly of a streamlined mite genome from contaminated host plant sequencing data
Technological advances have propelled DNA sequencing of non-model organisms, making sequencing more accessible and cost effective, which has also increased the availability of raw data in public repositories.bioRxiv
Chimeric origin of eukaryotes from Asgard archaea and ancestral giant viruses
The details surrounding the evolution of complex cells remain some of the most enduring mysteries in biology.bioRxiv
The Ribosomal Operon Database (ROD): A full-length rDNA operon database extracted from genome assemblies
Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the ITS region.bioRxiv
MotifScope: a multi-sample motif discovery and visualization tool for tandem repeats
Tandem repeats (TRs) constitute a significant portion of the human genome, exhibiting high levels of polymorphism due to variations in size and motif composition.bioRxiv
Universal signatures of transposable element compartmentalization across eukaryotic genes
The evolutionary mechanisms shaping the origins of genome architecture remain poorly understood but can now be assessed with unprecedented power due to the abundance of genome assemblies spanning phylogenetic diversity.bioRxiv
Systematic identification of cargo-carrying genetic elements reveals new dimensions of eukaryotic diversity
Cargo-carrying mobile elements (CCEs) are genetic entities that transpose diverse protein coding sequences. Although common in bacteria, we know little about the biology of eukaryotic CCEs because no appropriate tools exist for their annotation.bioRxiv
Polinton-like Viruses Associated with Entomopoxviruses Provide Insight into Replicon Evolution
Polinton-like viruses (PLVs) are a diverse group of small integrative dsDNA viruses that infect diverse eukaryotic hosts. Many PLVs are hypothesized to parasitize viruses in the phylum Nucleocytoviricota for their own propagation and spread.bioRxiv
'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
https://www.biorxiv.org/content/10.1101/2023.10.06.561169v1
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
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
Phage-plasmids promote genetic exchanges between phages and plasmids and create novel ones.
Phages and plasmids have key roles in bacterial evolution and are usually very different. Yet, they must recombine, since they sometimes carry nearly identical accessory genes.bioRxiv
New preprint on inter-plasmid competition via type IV-A3 CRISPR systems. Something to think about.
https://www.biorxiv.org/content/10.1101/2023.06.23.546257v1
Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans
Type IV-A CRISPR-Cas systems are primarily encoded on plasmids and form multi-subunit ribonucleoprotein complexes with unknown biological functions.bioRxiv
'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
https://www.biorxiv.org/content/10.1101/2023.06.22.546003v1?med=mas
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
#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
#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."
https://www.biorxiv.org/content/10.1101/2023.03.02.530691v1
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
Community diversity affects functionality and species sorting during propagation of a natural microbial community
The influence of community diversity on community function has long been a central question in ecology. Particularly, the dynamics over time of this relationship as a function of levels of diversity remains unclear.bioRxiv
Repeatability of adaptation in sunflowers: genomic regions harbouring inversions also drive adaptation in species lacking an inversion
Local adaptation commonly involves alleles of large effect, which experience fitness advantages when in positive linkage disequilibrium (LD).bioRxiv
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
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)
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
Assessing the biogeography of marine giant viruses in four oceanic transects
Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems.bioRxiv
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 🙂.
https://www.biorxiv.org/content/10.1101/2022.12.23.521774v2.full
#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
Content warning: This paper made me think about who is served directly by current modes of synthetic biology research, we could be unlocking the potential for home brewers to make a variety of valuable builk/fine chemicals but we're not
