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Mastodon: AboutGet the appKeyboard shortcutsView source codev4.4.0-nightly.2025-04-15

#preprint

1 post1 participant0 posts today
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conscientious objector🇨🇭🪂

Studie zeigt langfristige Immun- und Stoffwechselschäden nach einer #Corona Infektion.

Die University of California San Francisco, NIH und das Frederick National Cancer Laboratory zeigen, dass COVID-19 zu erheblichen und dauerhaften Veränderungen des Immun- und Stoffwechselsystems betroffener Personen führen kann.

Das heißt neben #LongCovid leider auch #Krebs.

Auch 2025 solltet Ihr besser kein #Corona bekommen.

polybio.org/polybio-supported-

Forscher und Mitarbeiter des Long-term Impact of Infection with Novel Coronavirus (LIINC)-Programms der UCSF stehen am Freitag, den 8. August 2024, im Zuckerberg San Francisco General Hospital in San Francisco. (Foto: Noah Berger)
#Covid#preprint
Public
preLights

Bring bacteria back! 🦠 The influence of microbial manipulation on sugar kelp development.

Jasmine Talevi covers work from Jungsoo Park & team (#ParfreyLab) that highlights the fundamental role microbiomes play across diverse biological systems. #preprint

#preLight ⬇️ 👀
prelights.biologists.com/highl

preLightsAn experimental test of the influence of microbial manipulation on sugar kelp (Saccharina latissima) supports the core influences host function hypothesis - preLightsBring bacteria back: The influence of microbial manipulation on sugar kelp development
#biology#ecology#kelp
Public
petersuber

I like this idea for a #LettersToTheEditor #preprint server.
link.springer.com/article/10.1

"Such a preprint server would offer three major benefits…: format-free ease of swift communication, increased author visibility and accountability, and avoiding the homelessness of unpublished [letters]."

PS: I've sent letters to journals that had policies not to publish them, but without saying so anywhere. Once I sent a letter to a new journal that had never received or published one and needed time to think about it. Right now #SocialMedia takes up this slack and does a pretty good job. But posting letters as preprints would give authors more space, prevent even published letters from languishing behind #paywalls, and offer better opportunities for #PIDs, #metadata, and #discoverability.

SpringerLinkReinventing the Letter to the Editor in Science: A Dedicated Preprint Server - Publishing Research QuarterlyAlthough letters to the editor (LTEs, or Correspondence) have a wide range of communicative functions within science, they also present several drawbacks, three of which we highlight: editorial ambiguity, technological limitations and skewed perceptions about their format. An assessment of Scopus (September 16, 2023) indicated that letters account for 1.7% to 3.2% per year, relative to articles and reviews, suggesting that the LTE field is undeveloped. We argue that the creation of a new preprint server, which we name CoArXiv or LettersArXiv, would allow LTEs—with timely and valuable knowledge and insight—to be posted in much the same way as other preprints, and would be one way to overcome needed reform of LTE-publishing culture, ultimately expanding the range of science communication channels for multidisciplinary research. We consider that such a preprint server would offer three major benefits for scientific research: format-free ease of swift communication, increased author visibility and accountability, and avoiding the homelessness of unpublished LTEs.
#ScholComm
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preLights

Listen to your gut – lessons from the brain. 🧠

Dang M. Nguyen & team (#BilboLab) demonstrate how prenatal environmental stressors disrupt gut immune cells, impair synaptic pruning in the gut + contribute to neurodevelopmental issues. #preprint

Another great #preLight by Jeny Jose ⬇️ 👀

prelights.biologists.com/highl

preLightsPrenatal exposure to environmental stressors alters gut macrophage development and gastrointestinal function of male offspring - preLights’Listen to your gut’ – lessons from the brain. How prenatal environmental stressors disrupt gut immune cells, impair synaptic pruning in the gut and contribute to neurodevelopmental issues
#biology#immunology#neuroscience
Public
Amelia Cervera 🧬

30S-seq redefines the bacterial Ribosome Binding Site.

#Ribosomes #30Ssubunit #ShineDalgarnoMotif #TranslationInitiation #Ecoli #Preprint

biorxiv.org/content/10.1101/20

bioRxiv · 30S-seq redefines the bacterial Ribosome Binding SiteThe translation initiation step is rate limiting for the efficiency of gene expression in all organisms. However, the mechanism of ribosome recruitment to mRNA start sites strikingly differs between eukaryotes and prokaryotes. The eukaryotic small (40S) ribosomal subunit binds 5' end caps and scans for the start codon while the bacterial small (30S) subunit directly binds to the Shine-Dalgarno (SD) motif close to the initiation site. Pioneer studies have shown rare 30S loading events further upstream within 5' untranslated regions (5'UTRs), at ribosome standby sites (1-3). Together with the frequent occurrence of long bacterial mRNA 5'UTRs and degenerated SD sequences, this indicates that the 30S subunit might bind upstream of the SD more commonly than currently thought. We therefore developed 30S-seq to map 30S-mRNA interactions in a bacterial transcriptome (Escherichia coli), inspired by translation complex profile sequencing (TCP-seq) previously used in eukaryotes (4,5). Our results provide new and unsuspected insights into the behaviour of 30S and 70S complexes during the canonical translation initiation process. Notably, 30S subunits are recruited upstream of the start codon, primed to receive the SD released by the departing 70S ribosome. Remarkably, we also find hundreds of non-canonical 30S binding sites within mRNA 5'UTRs, sometimes over 100 nucleotides upstream of the start region. We validated several of these upstream ribosome binding sites, and demonstrated their strong impact on gene expression. Thus, even in bacteria, ribosomes frequently bind mRNAs outside of the start region to initiate translation, challenging the classic ribosome binding site model. ### Competing Interest Statement The authors have declared no competing interest.
Public
LucCogZest

Now on ResearchGate: A free #preprint of an article describing the theory behind the #cognitiveShuffle is available on ResearchGate. It's called the somnolent information processing theory. It will be in the upcoming #CambridgeUniversityPress book on sleep theories edited by Daniel Kay:
researchgate.net/publication/3 #sleep #insomnia

Public
Bibliolater 📚 📜 🖋

🔴 **Long-term hunter-gatherer continuity in the Rhine-Meuse region was disrupted by local formation of expansive Bell Beaker groups**

“_We document an exception to this pattern in the wider Rhine-Meuse area in communities in the wetlands, riverine areas, and coastal areas of the western and central Netherlands, Belgium and western Germany, where we assembled genome-wide data for 109 people 8500-1700 BCE. Here, a distinctive population with high hunter-gatherer ancestry (∼50%) persisted up to three thousand years later than in continental European regions, reflecting limited incorporation of females of Early European Farmer ancestry into local communities._”

Olalde, I. et al. (2025) 'Long-term hunter-gatherer continuity in the Rhine-Meuse region was disrupted by local formation of expansive Bell Beaker groups,' bioRxiv (Cold Spring Harbor Laboratory) [Preprint]. doi.org/10.1101/2025.03.24.644.

#Preprint #Science #Biology #Genetics #Archaeology #Archaeodons #Anthropology #Europe @archaeodons

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Nick Byrd, Ph.D.

🔔 In Religious Studies: Analytic #Atheism & Analytic Apostasy...

Steve Stich, Justin Sytsma, and I studied >70k people across the globe.

Apostates were more reflective thinkers.

That explained links between reflection and #religion.

#Preprint + audio: byrdnick.com/archives/28471/up

The final typeset version is also freely available (#openAccess) via #CambridgeUP; doi.org/10.1017/S0034412525000

Pages from the accepted manuscript (Byrd, Stich, and Sytsma 2025).
Nick Byrd, Ph.D. · Why do atheists tend to do better on critical thinking tests?Apostates seem to score better than others. And they tend to be atheists. So "analytic atheism" seems to be explained by analytic APOSTASY.
#psychology#psychometrics#cogSci
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Dr Micha Campbell

One month left to provide feedback on our preprint "Rainfall recharge thresholds decrease after an intense fire over a near-surface cave at Wombeyan, Australia."

We are keen for some constructive feedback to improve the paper :)

egusphere.copernicus.org/prepr

#hydrology #KarstHydrology #Groundwater #preprint

@Andbaker

egusphere.copernicus.orgRainfall recharge thresholds decrease after an intense fire over a near-surface cave at Wombeyan, AustraliaAbstract. Quantifying the amount of rainfall needed to generate groundwater recharge is important for the sustainable management of groundwater resources. Here, we quantify rainfall recharge thresholds using drip loggers situated in a near-surface cave: Wildman’s cave at Wombeyan, southeast Australia. In just over two years of monitoring, 42 potential recharge events were identified in the cave, approximately 4 m below land surface which comprises a 30° slope with 37 % bare rock. Recharge events occurred within 48 hours of rainfall. Using daily precipitation data, the median 48 h rainfall needed to generate recharge was 19.8 mm, without clear seasonal variability. An intense experimental fire experiment was conducted 18 months into the monitoring period: the median 48 h rainfall needed to generate recharge was 22.1 mm before the fire (n=22) and 16.4 mm after the fire (n=20), with the decrease in rainfall recharge most noticeable starting three months after the fire.. Rainfall recharge thresholds and number of potential recharge events at Wildman’s Cave are consistent with those published from other caves in water-limited Australia. At Wildman’s Cave, we infer that soil water storage, combined with the generation of overland flow over bare limestone surfaces is the pathway for water movement to the subsurface via fractures and that these determine the rainfall recharge threshold. Immediately after the fire, surface ash deposits initially retard overland flow, and after ash removal from the land surface, soil loss and damage decrease the available soil water storage capacity, leading to more efficient infiltration and a decreased rainfall recharge threshold.
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Amelia Cervera 🧬

Relaxed DNA substrate specificity of transposases involved in programmed genome rearrangement.

#Transposons #Tc1Mariner #TelomereBearingElements #Oxytricha_trifallax #Transposase #Genomics #Preprint

biorxiv.org/content/10.1101/20

bioRxiv · Relaxed DNA substrate specificity of transposases involved in programmed genome rearrangementDuring post-zygotic development, the ciliate Oxytricha trifallax undergoes massive programmed genome rearrangement that involves over 225,000 DNA cleavage and joining events. An Oxytricha family of Tc1/mariner transposons, known as Telomere-Bearing Elements (TBEs), encodes a transposase that has been implicated in rearrangement, but its high copy number (>34,000 paralogs) has precluded genetic strategies to investigate its DNA recognition properties directly in Oxytricha. Here, we developed a heterologous strategy to assay TBE transposase expression and activity in E. coli, revealing highly promiscuous DNA cleavage properties. Systematic ChIP-seq experiments allowed us to define the DNA binding specificities of multiple distinct transposase subfamilies, which exhibited a binding and cleavage preference for short, degenerate sequence motifs that resemble features present within the TBE transposon ends. The relaxed sequence preference is striking for autonomous transposases, which typically recognize their end sequences with strict specificity to avoid compromising host fitness. Finally, we developed a custom antibody to investigate TBE transposases in their native environment and found that they precisely localize to the developing nucleus exclusively during the rearrangement process. Collectively, this work establishes a robust heterologous workflow for the biochemical investigation of enzymes that have been repurposed for large-scale genome rearrangements. ### Competing Interest Statement M.W.G.W. is a co-founder of Can9 Bioengineering. S.H.S. is a co-founder and scientific advisor to Dahlia Biosciences, a scientific advisor to CrisprBits and Prime Medicine, and an equity holder in Dahlia Biosciences and CrisprBits.
Public
Maabur

Can cells break the laws of thermodynamics?
Our preprint investigates the current scientific controversy. Using our nanosensor, we addressed unexpected artifacts and measured temperature with record accuracy inside cells.
researchsquare.com/article/rs-
The remarkable work from P. Maurer's lab also independently reports similar artifacts.
arxiv.org/abs/2503.20816
#quantumsensing #nanodiamond #NVcentre #arxiv #thermodynamics #nanothermometry #nanotechnology #research #quantum #science #preprint

www.researchsquare.comInvestigating intracellular heating rates with millikelvin nanothermometryNanothermometry within living cells is an important endeavour in physics,as the mechanisms of heat diffusion in such complex and dynamic environments remain poorly understood. In biology, nanothermometry may offer new insights into cellular biology and open new avenues for drug-discovery. Previou...
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