bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genomics ofPocilloporacorals: insights from RAD-sequencing
Authors: Aurelle Didier , Pratlong Marine , Oury Nicolas , Haguenauer Anne , Gélin Pauline , Magalon Hélène , Adjeroud Mehdi , Romans Pascal , Vidal-Dupiol Jeremie , Claereboudt Michel , Noûs Camille , Reynes Lauric , Toulza Eve , Bonhomme François , Mitta Guillaume , Pontarotti Pierre 
Published: May 2021

AbstractScleractinian corals are of great ecological interest as ecosystem engineer species. Accordingly, there is a wealth of studies on their adaptive abilities facing climate change. Such studies should rely on precise species and population delimitation. Nevertheless species delimitation in corals can be hindered by the lack of adequate genetic markers, by hybridization, and by morphological plasticity. Here we applied RAD sequencing to the study of species delimitation and genetic structure in populations ofPocilloporaspp. from Oman and French Polynesia with the objectives to test primary species hypotheses based on mitochondrial DNA sequencing, and to study the genetic structure among sampling sites inside species. Regarding the varying levels of missing data observed among samples we tested different filtering strategy. The main genetic differentiation was observed between samples from Oman and French Polynesia, which also corresponded to different mitochondrial lineages and species hypotheses. In Oman, we did not observe any clear differentiation according to the main mitochondrial lineages considered here, nor between sampling sites. In French Polynesia where a single mitochondrial lineage was studied, we did not evidence any differentiation according to sampling sites. These results provide an additional example of the importance of using independent nuclear markers for the study of species delimitation. Our analyses also allowed the identification of clonal lineages in our samples, and to take them into account in our interpretations. We used simulations to study the impact of clonal reproduction on the distribution of statistics of genetic diversity and genetic structure among loci.
A universal pocket in Fatty acyl-AMP ligases ensures redirection of fatty acid pool away from Coenzyme A-based activation
Authors: Patil Gajanan S. , Kinatukara Priyadarshan , Mondal Sudipta , Shambhavi Sakshi , Patel Ketan D. , Pramanik Surabhi , Dubey Noopur , Narasimhan Subhash , Madduri Murali Krishna , Pal Biswajit , Gokhale Rajesh S. , Sankaranarayanan Rajan 
Published: May 2021

ABSTRACTFatty acyl-AMP ligases (FAALs) channelize fatty acids towards biosynthesis of virulent lipids in mycobacteria and other pharmaceutically or ecologically important polyketides and lipopeptides in other microbes. They do so by bypassing the ubiquitous coenzyme A-dependent activation and rely on the acyl carrier protein-tethered 4’-phosphopantetheine (holo-ACP). The molecular basis of how FAALs strictly reject chemically identical and abundant acceptors like coenzyme A (CoA) and acceptholo-ACP unlike other members of the ANL superfamily remains elusive. We show FAALs have plugged the promiscuous canonical CoA-binding pockets and utilize highly selective alternative binding sites. These alternative pockets can distinguish adenosine 3’, 5’-bisphosphate-containing CoA fromholo-ACP and thus FAALs can distinguish between CoA andholo-ACP. These exclusive features helped identify the omnipresence of FAAL-like proteins and their emergence in plants, fungi, and animals with unconventional domain organisations. The universal distribution of FAALs suggests they are parallelly evolved with FACLs for ensuring a CoA-independent activation and redirection of fatty acids towards lipidic metabolites.
The gut parasiteNosema ceranaeimpairs olfactory learning in bumblebees
Authors: Gómez-Moracho Tamara , Durand Tristan , Lihoreau Mathieu 
Published: May 2021

AbstractPollinators are exposed to numerous parasites and pathogens when foraging on flowers. These biological stressors may affect critical cognitive abilities required for foraging. Here, we tested whether exposure toNosema ceranae, one of the most widespread parasite of honey bees also found in wild pollinators, impacts cognition in bumblebees. We investigated different forms of olfactory learning and memory using conditioning of the proboscis extension reflex. Seven days after feeding parasite spores, bumblebees showed lower performance in absolute and differential learning, and reversal learning than controls. Long-term memory was also slightly reduced. The consistent effect ofN. ceranaeexposure across different types of olfactory learning indicates that its action was not specific to particular brain areas or neural processes. We discuss the potential mechanisms by whichN. ceranaeimpairs bumblebee cognition and the broader consequences for populations of pollinators.
Pivotal Roles for Ribonucleases inStreptococcus pneumoniaePathogenesis
Authors: Sinha Dhriti , Frick Jacob , Clemmons Kristen , Winkler Malcolm E. , De Lay Nicholas R. 
Published: May 2021

ABSTRACTRNases perform indispensable functions in regulating gene expression in many bacterial pathogens by processing and/or degrading RNAs. Despite the pivotal role of RNases in regulating bacterial virulence factors, the functions of RNases have not yet been studied in the major human respiratory pathogenStreptococcus pneumoniae(pneumococcus). Here, we sought to determine the impact of two conserved RNases, the endoribonuclease RNase Y and exoribonuclease polynucleotide phosphorylase (PNPase), on the physiology and virulence ofS. pneumoniaeserotype 2 strain D39. We report that RNase Y and PNPase are essential for pneumococcal pathogenesis as both deletion mutants showed strong attenuation of virulence in murine models of invasive pneumonia. Genome-wide transcriptomic analysis revealed that nearly 200 mRNA transcripts were significantly up-regulated, whereas the abundance of several pneumococcal sRNAs, including the Ccn (CiaRControlledNoncoding RNA) sRNAs, were altered in the Δrnymutant relative to the wild-type strain. Additionally, lack of RNase Y resulted in pleiotropic phenotypes that included defects in pneumococcal cell morphology and growthin vitro. In contrast, Δpnpmutants showed no growth defectin vitro, but differentially expressed a total of 40 transcripts including the tryptophan biosynthesis operon genes and numerous 5’-cis-acting regulatory RNAs, a majority of which were previously shown to impact pneumococcal disease progression in mice using the serotype 4 strain TIGR4. Altogether our data suggest that RNase Y exerts a global impact on pneumococcal physiology, while PNPase-mediates virulence phenotypes, likely through sRNA regulation.IMPORTANCEStreptococcus pneumoniaeis a notorious human pathogen that adapts to conditions in distinct host tissues and responds to host cell interactions by adjusting gene expression. Ribonucleases (RNases) are key players that modulate gene expression by mediating the turnover of regulatory and protein-coding transcripts. Here, we characterized two highly conserved RNases, RNase Y and PNPase, and evaluated their impact on the S. pneumoniaetranscriptome for the first time. We show that PNPase influences the levels of a narrow set of mRNAs, but a large number of regulatory RNAs primarily implicated in virulence control, whereas RNase Y has a more sweeping effect on gene expression, altering levels of transcripts involved in diverse cellular processes including cell division, metabolism, stress response, and virulence. This study further reveals that RNase Y regulates expression of genes governing competence by mediating the turnover ofCiaR-controlled-noncoding (Ccn) sRNAs.
Glioblastoma mutations impair ligand discrimination by EGFR
Authors: Hu Chun , Leche Carlos A. , Kiyatkin Anatoly , Stayrook Steven E. , Ferguson Kathryn M. , Lemmon Mark A. 
Published: May 2021

SUMMARYThe epidermal growth factor receptor (EGFR) is frequently mutated in human cancer, and is an important therapeutic target. EGFR inhibitors have been successful in lung cancer, where the intracellular tyrosine kinase domain is mutated, but not in glioblastoma multiforme (GBM) – where mutations (or deletions) occur exclusively in the EGFR extracellular region. Wild-type EGFR is known to elicit distinct signals in response to different growth factor ligands, exhibiting biased agonism. We recently showed that individual ligands stabilize distinct receptor dimer structures, which signal with different kinetics to specify outcome. EGF induces strong symmetric dimers that signal transiently to promote proliferation. Epiregulin (EREG) induces weak asymmetric dimers that generate sustained signaling and differentiation. Intriguingly, several GBM mutation hotspots coincide with residues that define the asymmetric and symmetric dimer structures. Here, we show that common extracellular GBM mutations prevent EGFR from distinguishing between EGF and EREG based on dimer structure and stability – allowing strong dimers to form with both ligands. Crystal structures show that the R84K mutation symmetrizes EREG-driven dimers, whereas the A265V mutation remodels key dimerization sites. Our results suggest that modulating EGFR’s biased agonism plays an important role in GBM, and suggest new approaches for ‘correcting’ aberrant EGFR signaling in cancer.
Comparison of unit resolution versus high-resolution accurate mass for parallel reaction monitoring
Authors: Heil Lilian R. , Remes Philip M. , MacCoss Michael J. 
Published: May 2021

AbstractParallel reaction monitoring (PRM) is an increasingly popular alternative to selected reaction monitoring (SRM) for targeted proteomics. PRM’s strengths over SRM are that it monitors all product ions in a single spectrum, thus eliminating the need to select interference-free product ions prior to data acquisition, and that it is most frequently performed on high-resolution instruments, such as quadrupole-orbitrap and quadrupole-time of flight instruments. Here, we show that the primary advantage of PRM is the ability to monitor all transitions in parallel, and that high-resolution data are not necessary to obtain high quality quantitative data. We run the same scheduled PRM assay, measuring 432 peptides from 126 plasma proteins, multiple times on a Orbitrap Eclipse Tribrid mass spectrometer, alternating separate liquid chromatography-tandem mass spectrometry runs between the high resolution Orbitrap and the unit resolution linear ion trap for PRM. We find that both mass analyzers have similar technical precision, and that the linear ion trap’s superior sensitivity gives it better lower limits of quantitation on over 62% of peptides in the assay.Abstract graphic
Transcriptomic and rRNA:rDNA signatures of environmental vs. entericEnterococcus faecalisisolates under oligotrophic freshwater conditions
Authors: Suttner Brittany , Kim Minjae , Johnston Eric R. , Orellana Luis H. , Ruiz-Perez Carlos A. , Rodriguez-R Luis M. , Hatt Janet K. , Brown Joe , Santo Domingo Jorge W. , Konstantinidis Konstantinos T. 
Published: May 2021

ABSTRACTThe use of enterococci as a fecal indicator bacterial group for public health risk assessment has been brought into question by recent studies showing that “naturalized” populations ofE. faecalisexist in the extraenteric environment in a viable but not culturable (VBNC) state. The extent to which these naturalized or VBNCE. faecaliscan confound water quality monitoring is unclear. To determine if strains isolated from different habitats display different survival strategies and responses, we compared the decay patterns of threeE. faecalisisolates from the natural environment (environmental strains) against three human gut isolates (enteric strains) in laboratory mesocosms that simulate an oligotrophic, aerobic freshwater environment. Our results showed similar overall decay rates between enteric and environmental isolates based on viable plate and qPCR counts. However, the enteric isolates exhibited a spike in rRNA:rDNA ratios between days 1 and 3 of the mesocosm incubations that was not observed in environmental isolates, which could indicate a different stress response. Nevertheless, there was no strong evidence of differential expression of genes thought to be related to habitat adaptation in the accompanying mesocosm metatranscriptomes when compared between environmental and enteric isolates. Overall, our results provide novel information on how rRNA levels may vary over different metabolic states (i.e., alive vs. VBNC) for this important indicator bacteria. We also observed some evidence for habitat adaptation inE. faecalis; however, this adaptation may not be substantial or consistent enough for integration in water quality monitoring.IMPORTANCEEnterococci are commonly used worldwide to monitor environmental fecal contamination and public health risk for waterborne diseases. However, some species within this group can enter an inactive, viable but not culturable (VBNC) state that make it difficult to accurately quantify during routine monitoring. Furthermore, lower-risk, environmental enterococci strains may also confound water quality estimates. We developed an rRNA:rDNA viability assay forE. faecalis(a predominant species within this fecal group) and tested it against both enteric and environmental isolates in freshwater mesocosms to assess whether this approach can serve as a more sensitive water quality monitoring tool. We were unable to reliably distinguish the different isolate types using this assay under the conditions tested here; thus, environmental strains should continue to be counted during routine water monitoring. However, this assay could be useful for distinguishing more recent (i.e., higher risk) fecal pollution because rRNA levels significantly decreased after one week in all isolates.
A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance
Authors: Bourassa Lori , Perchetti Garrett A. , Phung Quynh , Lin Michelle J. , Mills Margaret G. , Roychoudhury Pavitra , Harmon Kimberly G. , Reed Jonathan C. , Greninger Alexander L. 
Published: May 2021

AbstractMore than one year into a global pandemic, SARS-CoV-2 is now defined by a variety of rapidly evolving variant lineages. Several FDA authorized molecular diagnostic tests have been impacted by viral variation, while no reports of viral variation affecting antigen test performance have occurred to date. While determining the analytical sensitivity of the Quidel Sofia SARS Antigen FIA test (Sofia 2), we uncovered a high viral load specimen that repeatedly tested negative by this antigen test. Whole genome sequencing of the specimen uncovered two mutations, T205I and D399N, present in the nucleocapsid protein of the isolate. All six SARS-CoV-2 positive clinical specimens available in our laboratory with a D399N nucleocapsid mutation and CT < 31 were not detected by the Sofia 2 but detected by the Abbott BinaxNOW COVID-19 Ag Card, while clinical specimens with the T205I mutation were detected by both assays. Testing of recombinant SARS-CoV-2 nucleocapsid with these variants demonstrated an approximate 1000-fold loss in sensitivity for the Quidel Sofia SARS Antigen FIA test associated with the D399N mutation, while the BinaxNOW and Quidel Quickvue SARS Antigen tests were unaffected by the mutation. The D399N nucleocapsid mutation has been relatively uncommon to date, appearing in only 0.02% of genomes worldwide at time of writing. Our results demonstrate how routine pathogen genomics can be integrated into the clinical microbiology laboratory to investigate diagnostic edge cases, as well as the importance of profiling antigenic diversity outside of the spike protein for SARS-CoV-2 diagnostics.
Chronic Aryl Hydrocarbon Receptor Activity Phenocopies Smoking-induced Skeletal Muscle Impairment
Authors: Thome Trace , Miguez Kayla , Willms Alexander , de Souza Angela R. , Chandran Vijayendran , Burke Sarah S. , Goddard Yana , Baglole Carolyn , Anagnostou Maria-Eleni , Bourbeau Jean , Thomas Jagoe R. , Morais Jose , Taivassalo Tanja , Ryan Terence , Hepple Russell T. 
Published: May 2021

ABSTRACTBackgroundCOPD patients exhibit skeletal muscle atrophy, denervation, and reduced mitochondrial oxidative capacity. Whilst chronic tobacco smoke exposure is implicated in COPD muscle impairment, the mechanisms involved are ambiguous. The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that activates detoxifying pathways with numerous exogenous ligands, including tobacco smoke. Whereas transient AHR activation is adaptive, chronic activation can be toxic. On this basis, we tested the hypothesis that chronic smoke-induced AHR activation causes adverse muscle impact.MethodsWe used clinical patient muscle samples, andin vitro(C2C12 myotubes) andin vivomodels (mouse), to perform gene expression, mitochondrial function, muscle and neuromuscular junction morphology, and genetic manipulations (adeno-associated virus-mediated gene transfer).Results16 weeks tobacco smoke exposure in mice caused: muscle atrophy, neuromuscular junction degeneration, and reduced oxidative capacity. Similarly, smoke exposure reprogrammed the muscle transcriptome, with down-regulation of mitochondrial and neuromuscular junction genes. In mouse and human patient specimens, smoke exposure increased muscle AHR signaling. Mechanistically, experiments in cultured myotubes demonstrated that smoke condensate activated the AHR, caused mitochondrial impairments, and induced an AHR-dependent myotube atrophy. Finally, to isolate the role of AHR activity, expression of a constitutively active AHR mutant without smoke exposure caused atrophy and mitochondrial impairments in cultured myotubes, and muscle atrophy and neuromuscular junction degeneration in mice.ConclusionsThese results establish that chronic AHR activity, as occurs in smokers, phenocopies the atrophy, mitochondrial impairment and neuromuscular junction degeneration caused by chronic tobacco smoke exposure.
Relief of ParB autoinhibition by parS DNA catalysis and ParB recycling by CTP hydrolysis promote bacterial centromere assembly
Authors: Antar Hammam , Soh Young-Min , Zamuer Stefano , Bock Florian P. , Anchimiuk Anna , De Los Rios Paolo , Gruber Stephan 
Published: May 2021

AbstractThree-component ParABS systems are widely distributed factors for plasmid partitioning and chromosome segregation in bacteria. ParB protein acts as an adaptor between the 16 bp centromericparSDNA sequences and the DNA segregation ATPase ParA. It accumulates at high concentrations at and near aparSsite by assembling a partition complex. ParB dimers form a DNA sliding clamp whose closure atparSrequires CTP binding. The mechanism underlying ParB loading and the role of CTP hydrolysis however remain unclear. We show that CTP hydrolysis is dispensable for Smc recruitment toparSsites inBacillus subtilisbut is essential for chromosome segregation by ParABS in the absence of Smc. Our results suggest that CTP hydrolysis contributes to partition complex assembly via two mechanisms. It recycles off-target ParB clamps to allow for new attempts atparStargeting and it limits the extent of spreading fromparSby promoting DNA unloading. We also propose a model for howparSDNA catalyzes ParB clamp closure involving a steric clash between ParB protomers binding to opposingparShalf sites.
Engineered protein-small molecule conjugates empower selective enzyme inhibition
Authors: Lewis Andrew K. , Harthorn Abbigael , Johnson Sadie M. , Lobb Roy R. , Hackel Benjamin J. 
Published: May 2021

SummarySpecific, potent ligands drive precision medicine and fundamental biology. Proteins, peptides, and small molecules constitute effective ligand classes. Yet greater molecular diversity would aid the pursuit of ligands to elicit precise biological activity against challenging targets. We demonstrate a platform to discover protein-small molecule (PriSM) hybrids to combine unique pharmacophore activities and shapes with constrained, efficiently engineerable proteins. A fibronectin protein library was yeast displayed with a single cysteine coupled to acetazolamide via a maleimide-poly(ethylene glycol) linker. Magnetic and flow cytometric sorts enriched specific binders to carbonic anhydrase isoforms. Isolated PriSMs exhibited potent, specific inhibition of carbonic anhydrase isoforms with superior efficacy to acetazolamide or protein alone including an 80-fold specificity increase and 9-fold potency gain. PriSMs were engineered with multiple linker lengths, protein conjugation sites, and sequences against two different isoforms, which reveals platform flexibility and impacts of molecular designs. PriSMs advance the molecular diversity of efficiently engineerable ligands.
Mapping the Central and Peripheral Projections of Lung Innervating Sensory Neurons
Authors: Su Yujuan , Barr Justinn , Jaquish Abigail , Xu Jinhao , Verheyden Jamie M , Sun Xin 
Published: May 2021

AbstractWhile best known as the gas exchange organ, the lung is also critical for sensing and responding to the aerosol environment in part through interaction with the nervous system. The rich diversity of lung innervating neurons remains poorly understood. Here, we interrogated the cell body location, projection pattern and targets of lung-innervating sensory neurons. Retrograde tracing from the lung labeled neurons primarily in the vagal ganglia, in a spatially distributed population expressing markers includingVglut2, Trpv1, Tac1, Calb1orPiezo2. Centrally, they project to the nucleus of the solitary tract in the brainstem. Peripherally, they project along the branching airways and terminate on airway smooth muscles, vasculature including lymphatics, and selected alveoli. Notably, a discrete population of Calb1+ neurons preferentially innervate pulmonary neuroendocrine cells, a demonstrated airway sensor population. This comprehensive illustration of the properties of lung innervating sensory neurons serves as a foundation for understanding their function in lung.
Detecting natural selection in trait-trait coevolution
Authors: Jiang Daohan , Zhang Jianzhi 
Published: May 2021

ABSTRACTNo phenotypic trait evolves independently of all other traits, but the cause of trait-trait coevolution is poorly understood. While the coevolution could arise simply from pleiotropic mutations that simultaneously affect the traits concerned, it could also result from multivariate natural selection favoring certain trait relationships. To gain a general mechanistic understanding of trait-trait coevolution, we examine the evolution of 220 cell morphology traits across 16 natural strains of the yeastSaccharomyces cerevisiaeand the evolution of 24 wing morphology traits across 110 fly species of the family Drosophilidae, along with the variations of these traits among gene deletion or mutation accumulation lines (a.k.a. mutants). For numerous trait pairs, the phenotypic correlation among evolutionary lineages differs significantly from that among mutants. Specifically, we find hundreds of cases where the evolutionary correlation between traits is strengthened or reversed relative to the mutational correlation, which, according to our population genetic simulation, is likely caused by multivariate selection. Furthermore, we detect selection for enhanced modularity of the yeast traits analyzed. Together, these results demonstrate that trait-trait coevolution is shaped by natural selection and suggest that the pleiotropic structure of mutation is not optimal. Because the morphological traits analyzed here are chosen largely because of their measurability and thereby are not expected to be biased with regard to natural selection, our conclusion is likely general.