bluuebunny/crossref_metadata_2025_split huggingface dataset:
Planarian CREB-binding protein (CBP) gene family regulates stem cell maintenance and differentiation
Authors: Fraguas Susanna , Cárcel Sheila , Vivancos Coral , Molina Ma Dolores , Ginés Jordi , Mazariegos Judith , Sekaran Thileepan , Bartscherer Kerstin , Romero Rafael , Cebrià Francesc 
Published: September 2020

ABSTRACTThe regulation of stem cells plasticity and differentiation is still an open question in developmental biology. CBP (CREB-binding protein)/p300 is a conserved gene family which functions as a transcriptional co-activator and shows an important role in a wide range of cellular processes, such as cell death, DNA damage response and tumorigenesis. Moreover, CBPs have an acetyl transferase activity that is relevant as histone and non-histone acetylation results in changes in chromatin architecture and protein activity that affects gene expression. Many studies have shown the conserved functions of CBP/p300 on stem cell proliferation and differentiation. The planarianSchmidtea mediterraneais an excellent model to studyin vivothe molecular mechanism underlying stem cell differentiation during regeneration. We have identified five differentSmed-cbpgenes inS. mediterraneathat show different expression patterns. Functional analyses indicate thatSmed-cbp-2seems to be essential for stem cell maintenance and cell survival. On the other hand, the silencing ofSmed-cbp-3results in the growth of apparently normal blastemas; however, these remain largely depigmented and undifferentiated.Smed-cbp-3silencing affects the differentiation of several cell lineages including neural, epidermal, digestive and excretory cell types. Finally, we have analyzed the predicted interactomes of CBP-2 and CBP-3 as an initial step to better understand their function on planarian stem cell biology.
Structure and dynamics of the quaternaryhunchbackmRNA translation repression complex
Authors: Macošek Jakub , Simon Bernd , Linse Johanna-Barbara , Winter Sophie , Foot Jaelle , Perez Kathryn , Rettel Mandy , Ivanović Miloš T. , Masiewicz Pawel , Murciano Brice , Savitski Mikhail M. , Hub Jochen S. , Gabel Frank , Hennig Janosch 
Published: September 2020

ABSTRACTA key regulatory process duringDrosophiladevelopment is the localized suppression of thehunchbackmRNA translation at the posterior, which gives rise to ahunchbackgradient governing the formation of the anterior-posterior body axis. The suppression of the RNA is achieved by a concerted action of Brain Tumour (Brat), Pumilio (Pum) and Nanos. Each protein is necessary for properDrosophiladevelopment. The RNA contacts have been elucidated for the proteins individually in several atomic-resolution structures. However, the interplay of all three proteins in the RNA suppression remains a long-standing open question. We characterize the quaternary complex of the RNA-binding domains of Brat, Pum and Nanos withhunchbackmRNA by combining NMR spectroscopy, SANS/SAXS, XL/MS with MD simulations and ITC assays. The quaternaryhunchbackmRNA suppression complex is flexible with the unoccupied nucleotides of the RNA functioning as a flexible linker between the Brat and Pum-Nanos moieties of the complex. Moreover, Brat and Pum with Nanos bind the RNA completely independently. In accordance with previous studies, showing that Brat can suppresshunchbackmRNA independently and is distributed uniformly throughout the embryo, this suggests thathunchbackmRNA suppression by Brat is functionally separate from the suppression by Pumilio and Nanos.
Analysis of SARS-CoV-2 genomes from across Africa reveals potentially clinically relevant mutations
Authors: Longjohn Modeline N. , Egbule Olivia S. , Danso Samuel O. , Akujuru Eugene E. , Ibubeleye Victor T. , Oweredaba Christabel I. , Ogharanduku Theodora , Manu Alexander , Iweriebor Benson C. 
Published: September 2020

AbstractSARS-CoV-2 is a betacoronavirus, the etiologic agent of the novel Coronavirus disease 2019 (COVID-19). The World Health Organization officially declared COVID-19 as a pandemic in March 2020 after the outbreak in Wuhan, China, in late 2019. Across the continents and specifically in Africa, all index cases were travel-related. Understanding how the virus’s transportation across continents and different climatic conditions affect the genetic composition and the consequent effects on transmissibility, infectivity, and virulence of the virus is critical. Thus, it is crucial to compare COVID-19 genome sequences from the African continent with sequences from selected COVID-19 hotspots/countries in Asia, Europe, North and South America and Oceania.To identify possible distinguishing mutations in the African SARS-CoV-2 genomes compared to those from these selected countries, we conductedin silicoanalyses and comparisons. Complete African SARS-CoV-2 genomes deposited in GISAID and NCBI databases as of June 2020 were downloaded and aligned with genomes from Wuhan, China and other SARS-CoV-2 hotspots. Using phylogenetic analysis and amino acid sequence alignments of the spike and replicase (NSP12) proteins, we searched for possible vaccine coverage targets or potential therapeutic agents. Identity plots for the alignments were created with BioEdit software and the phylogenetic analyses with the MEGA X software.Our results showed mutations in the spike and replicate proteins of the SARS-Cov-2 virus. Phylogenetic tree analyses demonstrated variability across the various regions/countries in Africa as there were different clades in the viral proteins. However, a substantial proportion of these mutations (90%) were similar to those described in all the other settings, including the Wuhan strain. There were, however, novel mutations in the genomes of the circulating strains of the virus in African. To the best of our knowledge, this is the first study reporting these findings from Africa. However, these findings’ implications on symptomatic or asymptomatic manifestations, progression to severe disease and case fatality for those affected, and the cross efficacy of vaccines developed from other settings when applied in Africa are unknown.
Inheritance of associative memories inC. elegansnematodes
Authors: Deshe Noa , Eliezer Yifat , Hoch Lihi , Itskovits Eyal , Ben-Ezra Shachaf , Zaslaver Alon 
Published: September 2020

SummaryThe notion that associative memories may be transmitted across generations is intriguing, yet controversial. Here, we trainedC. elegansnematodes to associate an odorant with stressful starvation conditions, and surprisingly, this associative memory was evident two generations down of the trained animals. The inherited memory endowed the progeny with a fitness advantage, as memory reactivation induced rapid protective stress responses that allowed the animals to prepare in advance for an impending adversity. Sperm, but not oocytes, transmitted the associative memory, and the inheritance required H3K9 and H3K36 methylations, the small RNA-binding Argonaute NRDE-3, and intact neuropeptide secretion. Remarkably, activation of a single chemosensory neuron sufficed to induce a serotonin-mediated systemic stress response in both the parental trained generation and in its progeny. These findings challenge long-held concepts by establishing that associative memories may indeed be transferred across generations.
High-throughput method to test antimicrobial gels against a multispecies oral biofilm
Authors: Chathoth Kanchana , Martin Bénédicte , Bonnaure-Mallet Martine , Baysse Christine 
Published: September 2020

ABSTRACTPeriodontitis, characterized by the damage of the periodontium can eventually lead to tooth loss. Moreover, severe forms of periodontitis are associated with several systemic disorders. The evolution of the disease is linked to the pathogenic switch of the oral microbiota comprising of commensal colonizers and anaerobic pathogens. Treatment with antimicrobial gels has the potential to help eradicate periodontal pathogens. Testing antibacterial gels againstin vitrobiofilm models is complicated. Recovery of detached and sessile bacteria fromin vitrobiofilms treated with gel formulations using conventional methods (microtiter plates, μ-slides, flow cells etc.,) may prove arduous. To overcome this challenge, we optimised a simple method using the principle of the Calgary Biofilm Device (CBD) for testing antimicrobial gels against multispecies oral biofilms. First, we established three-species oral biofilms consisting of two periodontal pathogens (Porphyromonas gingivalis,Treponema denticola) and a primary colonizer of the dental plaque (Streptococcus gordonii) on the surface of pegs. Next, a protocol to test gels against oral biofilms was implemented using commercially available gels with different active products. This method enables the analysis of the composition of biofilm and detached/planktonic cells to measure the effect of topical gel formulations/antibacterial gels for the treatment of periodontitis. However, the method is not restricted to oral biofilms and can be adapted for other biofilm-related studies.
Diversity and function of microbial lipases within the mammalian gut
Authors: Hitch Thomas C. A. , Masson Johannes M. , Streidl Theresa , Fischöder Thomas , Elling Lothar , Clavel Thomas 
Published: September 2020

AbstractBackgroundCurrent estimates suggest the majority of microbial proteins within the mammalian gut lack meaningful annotation. One such functional group are microbial lipases (EC:3.1.1.3), which can alter host access and utilisation of dietary fat. In this paper, we describe the diversity of lipolytic bacteria, includingin vitrocharacterisation of a new lipase.ResultsMetagenomic sequence-based network analysis identified that the majority of microbial lipases in the gut of three host species (human, mouse, pig) belong to two unique clusters. These clusters were characterized by the presence of two novel motifs, AHSKGG and TTxxTPH, which may play a key functional role due to co-localisation in the active site, as identified by structural modelling. Analysis of metagenomic assembled genomes (MAGs) indicated that the majority of lipase-positive species belong to the phylum Firmicutes, although all dominant phyla within the human gut were represented by positive species. Metabolic analysis of these genomes identified a high prevalence of glycerol rather than fatty acid metabolism. The occurrence of microbial lipases determined across ~800 metagenomic gut samples depended on dietary fat consumption, with lipase expression increased in lard fed compared to palm oil fed mice. A representative lipase encoded within the genome of the speciesClostridium symbiosumwas cloned and its characterization confirmed thein silicoprediction and provided detailed annotation to 373 proteins.ConclusionsMicrobial lipases within the gut represent a conserved group characterized by unique amino acid sequence motifs. While an increase in microbial lipase occurrence was positively associated with dietary fat intake, lipase-producing species seemed unable to metabolise the released fatty acids. In this paper, we provide a global analysis of the functional importance and diversity of microbial lipases within the intestine of mammals, which will improve the resolution of future sequence-based studies and open avenues for mechanistic experiments based on isolates.
Mental Chronometry of Speaking in Dialogue: Semantic Interference Turns into Facilitation
Authors: Kuhlen Anna K. , Rahman Rasha Abdel 
Published: September 2020

AbstractNumerous studies demonstrate that the production of words is delayed when speakers process in temporal proximity semantically related words. Yet the experimental settings underlying this effect are different from those under which we typically speak. This study demonstrates that semantic interference disappears, and can even turn into facilitation, when semantically related words are embedded in a meaningful communicative exchange. Experiment 1 and 3 (each N=32 university students) implemented a picture- word interference task in a game played between two participants: one named the distractor word and, after a stimulus-onset-asynchrony of -150ms or -650ms, the other named a semantically related or unrelated target picture. Semantic interference reappeared with identical experimental parameters in a single-person picture-word interference setting (Experiment 2, N=32). We conclude that the inhibitory context effects leading to semantic interference in single-subject settings are attenuated whereas facilitatory effects are enhanced in communicative settings.HighlightsIn isolated speakers processing semantically related words interferes with speakingYet we typically speak to communicate with othersThis study transfers picture-word interference to a communicative settingSemantically related words produced by a partner do not interfere with speaking
Decoding the Protein Composition of Whole Nucleosomes with Nuc-MS
Authors: Schachner Luis F. , Jooβ Kevin , Morgan Marc A. , Piunti Andrea , Meiners Matthew J. , Lee Alexander , Kafader Jared O. , Iwanaszko Marta , Cheek Marcus A. , Burg Jonathan M. , Howard Sarah A. , Keogh Michael-Christopher , Shilatifard Ali , Kelleher Neil L. 
Published: September 2020

AbstractNuc-MS characterizes histone modifications and variants directly from intact endogenous nucleosomes. Preserving whole nucleosome particles enables precise interrogation of their protein content, as for H3.3-containing nucleosomes which had 6-fold co-enrichment of variant H2A.Z over bulk chromatin. Nuc-MS, validated by ChIP-seq, showed co-occurrence of oncogenic H3.3K27M with euchromatic marks (e.g., H4K16ac and >15-fold enrichment of H3K79me2). By capturing the entire epigenetic landscape, Nuc-MS provides a new, quantitative readout of nucleosome-level biology.
Identification of colonisation and virulence determinants ofStreptococcus pneumoniaevia experimental evolution in mouse infection models
Authors: Green Angharad E , Howarth Deborah , Chaguza Chrispin , Echlin Haley , Langendonk R Frèdi , Munro Connor , Barton Thomas E , Hinton Jay CD , Bentley Stephen D , Rosch Jason W , Neill Daniel R 
Published: September 2020

AbstractStreptococcus pneumoniaeis a commensal of the human nasopharynx and a major cause of respiratory and invasive disease. Pneumococcus stimulates upper respiratory tract inflammation that promotes shedding from mucosal surfaces and transmission to new hosts. Colonisation and transmission are partially antagonistic processes. Adhesion to surfaces and evasion of host responses favours the former, whilst detachment, promoted by inflammation, is necessary for the latter. We sought to determine how adaptation and evolution of pneumococcus within its nasopharyngeal niche might progress when selective pressures associated with transmission were removed. This was achieved by serial passage of pneumococci in mouse models of nasopharyngeal carriage, manually transferring bacteria between mice. To assess the role of host environmental factors on pneumococcal evolution, we also performed analogous experimental evolution in a mouse pneumonia model, passaging pneumococci through lungs. Nasopharynx-passaged pneumococci became more effective colonisers, whilst those evolved within lungs showed reduced virulence. We observed selection of mutations in genes associated with cell wall biogenesis and metabolism in both nasopharynx and lung lineages, but identified prominent examples of parallel evolution that were niche specific. We focussed ongpsA, a gene in which the same single nucleotide polymorphism arose in two independently evolved nasopharynx-passaged lineages. We identified a single nucleotide change conferring resistance to oxidative stress and enhanced nasopharyngeal colonisation potential. We show thatgpsAis also a frequent target of mutation during human colonisation. These findings highlight the role played by the host environment in determining trajectories of bacterial evolution and the potential of experimental evolution in animal infection models for identification of novel pathogen virulence and colonisation factors.
Viral infection of algal blooms leaves a halogenated footprint on the dissolved organic matter in the ocean
Authors: Kuhlisch Constanze , Schleyer Guy , Shahaf Nir , Vincent Flora , Schatz Daniella , Vardi Assaf 
Published: September 2020

AbstractAlgal blooms are important hotspots of primary production in the ocean, forming the basis of the marine food web and fueling the pool of dissolved organic matter (DOM)1, which is the largest global inventory of reduced carbon and a market place for metabolic exchange in the ocean2. Marine viruses are key players in controlling algal bloom demise and act as major biogeochemical drivers of nutrient cycling and metabolic fluxes by shunting algal biomass from higher trophic levels to the DOM pool, a process termed the ‘viral shunt’3,4. Nevertheless, the metabolic composition of virus-induced DOM (vDOM) in the marine environment is unknown. To decode the metabolic footprint of the ‘viral shunt’, we induced a bloom of the ecologically important algaEmiliania huxleyiin the natural environment, and followed its succession using an untargeted exometabolomics approach. Here we show that algal bloom succession induces extensive and dynamic changes in the exometabolic landscape, especially during bloom demise. By correlating to a specific viral gene marker, we discovered a set of novel chlorine-iodine-containing metabolites that were induced by viral infection and copiously released during bloom demise. We further detected several of these chloro-iodo metabolites in virus-infected open ocean blooms ofE. huxleyi, supporting their use as sensitive biomarkers for virus-induced demise in the natural environment. Therefore, we propose halogenation to be a hallmark of theE. huxleyivDOM, providing insights into the profound metabolic consequences of viral infection for the marine DOM pool.
Effects of substrate availability on growth and metabolism in soil microbes: Insights from theoretical modeling of studies of the Warburg effect and substrate-induced respiration
Authors: Swain Anshuman , Fagan William F 
Published: September 2020

AbstractCarbon Use Efficiency (CUE) is a popular concept for measuring the efficiency of biomass production in different biological systems and, is frequently employed to understand effects of microbial processes on soil carbon dynamics. CUE in soil microbes is often measured through respiration-based studies, especially through the addition of a labile carbon substrate such as glucose. Therefore, exploring the response of microbial respiration to availability of labile substrates is crucial to understand microbial CUE in soils. In this work, we build upon a cellular model of the Warburg effect, where cells simultaneously utilize inefficient aerobic glycolysis/fermentation and efficient oxidative phosphorylation pathways for energy synthesis even at high oxygen availability, to predict microbial community response to various levels of substrate availability. We test our predictions systematically using a series of substrate-induced respiration (SIR) experiments to demonstrate prevalence of the Warburg effect in soil microbial communities. We further discuss the relevance of the underlying metabolic processes behind the Warburg effect in interpreting soil microbial CUE.
Terminal Modification, Sequence, and Length Determine Small RNA Stability in Animals
Authors: Gainetdinov Ildar , Colpan Cansu , Cecchini Katharine , Albosta Paul , Jouravleva Karina , Vega-Badillo Joel , Lee Yongjin , Özata Deniz M. , Zamore Phillip D. 
Published: September 2020

ABSTRACTIn animals, piRNAs, siRNAs, and miRNAs silence transposons, fight viral infections, and regulate gene expression. piRNA biogenesis concludes with 3′ terminal trimming and 2′-O-methylation. Both trimming and methylation influence piRNA stability. Here, we report that trimming and methylation protect mouse piRNAs from different decay mechanisms. In the absence of 2′-O-methylation, mouse piRNAs with extensive complementarity to long RNAs become unstable. In flies, 2′-O-methylation similarly protects both piRNAs and siRNAs from complementarity-dependent destabilization. Animal miRNAs are unmethylated, and complementarity-dependent destabilization helps explain differences in miRNA decay rates in both mice and flies. In contrast, trimming protects mouse piRNAs from a separate degradation pathway unaffected by target complementarity but sensitive to the 3′ terminal, untrimmed sequence. Because distinct sets of mouse piRNAs are protected by each of these mechanisms, loss of both trimming and 2′-O-methylation causes the piRNA pathway to collapse, demonstrating that these two small RNA modifications collaborate to stabilize piRNAs.Highlights2′-O-methylation protects mouse and fly piRNAs from complementarity-dependent decay2′-O-methylation protects fly siRNAs with extensive complementarity to long RNAsComplementarity to long RNAs predicts the half-life of fly and mouse miRNAsMouse pre-piRNA decay reflects both pre-piRNA sequence and PIWI protein identity
The risk of introducing SARS-CoV-2 to the UK via international travel in August 2020
Authors: Taylor Rachel A. , McCarthy Catherine , Patel Virag , Moir Ruth , Kelly Louise A , Snary Emma L 
Published: September 2020

AbstractInternational travel poses substantial risks for continued introduction of SARS-CoV-2. As of the 17th August 2020, travellers from 12 of the top 25 countries flying into the UK are required to self-isolate for 14 days. We estimate that 895 (CI: 834–958) infectious travellers arrive in a single week, of which 87% (779, CI: 722–837) originate from countries on the UK quarantine list. We compare alternative measures to the 14 day self-isolation (78.0% effective CI: 74.4–81.6) which could be more feasible long-term. A single RT-PCR taken upon arrival at the airport is 39.6% (CI: 35.2–43.7) effective, or equivalently, it would only detect 2 in 5 infectious passengers. Alternatively, testing four days after arrival is 64.3% (CI: 60.0–68.3) effective whereas a test at the airport plus additional test four days later is 68.9% (CI: 64.9–73.0) effective. Rapidly implementing control measures for travellers from risky countries is vital to protect public health; this methodology can be quickly updated to assess the impact of any further changes to international travel policy or disease occurrence.