bluuebunny/crossref_metadata_2025_split huggingface dataset:
A nanobody-functionalized organic electrochemical transistor for the rapid detection of SARS-CoV-2 and MERS antigens at the physical limit
Authors: Guo Keying , Wustoni Shofarul , Koklu Anil , Díaz-Galicia Escarlet , Moser Maximilian , Hama Adel , Alqahtani Ahmed A. , Ahmad Adeel Nazir , Alhamlan Fatimah Saeed , McCulloch Iain , Arold Stefan T. , Grünberg Raik , Inal Sahika 
Published: November 2020

AbstractThe COVID-19 pandemic highlights the need for rapid protein detection and quantification at the single-molecule level in a format that is simple and robust enough for widespread point-of-care applications. We here introduce a modular nanobody-organic electrochemical transistor architecture that enables the fast and specific detection and quantification of single-molecule to nanomolar protein antigen concentrations in complex bodily fluids. The sensor combines a new solution-processable organic semiconductor material in the transistor channel with the high-density and orientation-controlled bioconjugation of nanobody fusion proteins on disposable gate electrodes. It provides results after a 10 minutes exposure to 5 µL of unprocessed samples, maintains high specificity and single-molecule sensitivity in human saliva or serum, and is rapidly reprogrammed towards any protein target for which nanobodies exist. We demonstrate the use of this highly modular platform for the detection of green fluorescent protein, SARS-CoV-1/2, and MERS-CoV spike proteins and validate the sensor for COVID-19 screening in unprocessed clinical nasopharyngeal swab and saliva samples.
Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: A Systematic Review and Meta-analysis
Authors: Lee Rose A. , Herigon Joshua C. , Benedetti Andrea , Pollock Nira R. , Denkinger Claudia M. 
Published: November 2020

ABSTRACTBackgroundNasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs.MethodsWe systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval October 1st, 2020) for comparative studies of alternative specimen types [saliva, oropharyngeal (OP), and nasal (NS) swabs] versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in sub-groups. The QUADAS 2 tool was used to assess bias.ResultsFrom 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives [NS (0.82, 95% CI: 0.73-0.90), OP (0.84, 95% CI: 0.57-1.0), saliva (0.88, 95% CI: 0.81 – 0.93)] than NP swabs, while combined OP/NS matched NP performance (0.97, 95% CI: 0.90-1.0). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield.ConclusionsNP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric vs. adult, late vs. early in disease course) and head-to head studies of sampling strategies are urgently needed.
Inhibition of SARS-CoV-2 main protease by allosteric drug-binding
Authors: Günther Sebastian , Reinke Patrick Y. A. , Fernández-García Yaiza , Lieske Julia , Lane Thomas J. , Ginn Helen M. , Koua Faisal H. M. , Ehrt Christiane , Ewert Wiebke , Oberthuer Dominik , Yefanov Oleksandr , Meier Susanne , Lorenzen Kristina , Krichel Boris , Kopicki Janine-Denise , Gelisio Luca , Brehm Wolfgang , Dunkel Ilona , Seychell Brandon , Gieseler Henry , Norton-Baker Brenna , Escudero-Pérez Beatriz , Domaracky Martin , Saouane Sofiane , Tolstikova Alexandra , White Thomas A. , Hänle Anna , Groessler Michael , Fleckenstein Holger , Trost Fabian , Galchenkova Marina , Gevorkov Yaroslav , Li Chufeng , Awel Salah , Peck Ariana , Barthelmess Miriam , Schlünzen Frank , Xavier P. Lourdu , Werner Nadine , Andaleeb Hina , Ullah Najeeb , Falke Sven , Srinivasan Vasundara , Franca Bruno Alves , Schwinzer Martin , Brognaro Hévila , Rogers Cromarte , Melo Diogo , Zaitseva-Kinneberg Joanna I. , Knoska Juraj , Peña Murillo Gisel E. , Mashhour Aida Rahmani , Guicking Filip , Hennicke Vincent , Fischer Pontus , Hakanpää Johanna , Meyer Jan , Gribbon Phil , Ellinger Bernhard , Kuzikov Maria , Wolf Markus , Beccari Andrea R. , Bourenkov Gleb , Stetten David von , Pompidor Guillaume , Bento Isabel , Panneerselvam Saravanan , Karpics Ivars , Schneider Thomas R. , Garcia Alai Maria Marta , Niebling Stephan , Günther Christian , Schmidt Christina , Schubert Robin , Han Huijong , Boger Juliane , Monteiro Diana C. F. , Zhang Linlin , Sun Xinyuanyuan , Pletzer-Zelgert Jonathan , Wollenhaupt Jan , Feiler Christian G. , Weiss Manfred S. , Schulz Eike-Christian , Mehrabi Pedram , Karničar Katarina , Usenik Aleksandra , Loboda Jure , Tidow Henning , Chari Ashwin , Hilgenfeld Rolf , Uetrecht Charlotte , Cox Russell , Zaliani Andrea , Beck Tobias , Rarey Matthias , Günther Stephan , Turk Dusan , Hinrichs Winfried , Chapman Henry N. , Pearson Arwen R. , Betzel Christian , Meents Alke 
Published: November 2020

AbstractThe coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous health problems and economical challenges for mankind. To date, no effective drug is available to directly treat the disease and prevent virus spreading. In a search for a drug against COVID-19, we have performed a massive X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for the virus replication and, thus, a potent drug target. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds binding to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and five non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.
Western KenyanAnopheles gambiae s.s.showing intense permethrin resistance harbor distinct microbiota
Authors: Omoke Diana , Kipsum Mathew , Otieno Samson , Esalimba Edward , Sheth Mili , Lenhart Audrey , Njeru Ezekiel Mugendi , Ochomo Eric , Dada Nsa 
Published: November 2020

AbstractBackgroundInsecticide resistance poses a growing challenge to malaria vector control in Kenya and around the world. Following evidence of associations between the mosquito microbiota and insecticide resistance, we comparatively characterized the microbiota ofAn. gambiae s.s. from Tulukuyi village, Bungoma, Kenya, with differing permethrin resistance profiles.MethodsUsing the CDC bottle bioassay, 133 2-3 day-old, virgin, non-blood fed female F1progeny of field-caughtAn. gambiae s.s. were exposed to five times (107.5μg/ml) the discriminating dose of permethrin. Post bioassay, 50 resistant and 50 susceptible mosquitoes were subsequently screened forkdrEast and West mutations, and individually processed for microbial analysis using high throughput sequencing targeting the universal bacterial and archaeal 16S rRNA gene.Results47% of the samples tested (n=133) were resistant, and of the 100 selected for further processing, 99% were positive forkdrEast and 1% forkdrWest. Overall, 84 bacterial taxa were detected across all mosquito samples, with 36 of these shared between resistant and susceptible mosquitoes. A total of 20 were unique to the resistant mosquitoes and 28 were unique to the susceptible mosquitoes. There were significant differences in bacterial composition between resistant and susceptible individuals (F=2.33, P=0.001), with presence ofSphingobacterium, LysinibacillusandStreptococcus(all known pyrethroid-degrading taxa), and the radiotolerantRubrobacter, being significantly associated with resistant mosquitoes. On the other hand, the presence ofMyxococcus, was significantly associated with susceptible mosquitoes.ConclusionThis is the first report of distinct microbiota inAn. gambiae s.s. associated with intense pyrethroid resistance. The findings highlight differentially abundant bacterial taxa between resistant and susceptible mosquitoes, and further suggest a microbe-mediated mechanism of insecticide resistance in mosquitoes. Our results also indicate fixation of thekdrEast mutation in this mosquito population, precluding further analysis of its associations with the mosquito microbiota, but presenting the hypothesis that any microbe-mediated mechanism of insecticide resistance would be likely of a metabolic nature. Overall, this study lays initial groundwork for understanding microbe-mediated mechanisms of insecticide resistance in African malaria vectors, and potentially identifying novel microbial markers of insecticide resistance that could supplement existing vector surveillance tools.
Molecular characterisation of, and antimicrobial resistance in,Clostridioides difficilefrom Thailand, 2017-2018
Authors: Imwattana Korakrit , Putsathit Papanin , Knight Daniel R , Kiratisin Pattarachai , Riley Thomas V 
Published: November 2020

AbstractBackgroundAntimicrobial resistance (AMR) plays an important role in the pathogenesis and spread ofClostridioides difficileinfection (CDI). Many antimicrobials, such as fluoroquinolones, have been associated with outbreaks of CDI globally.ObjectivesThis study aimed to characterise AMR among clinicalC. difficilestrains in Thailand, a country where the use of antimicrobials remains inadequately regulated.MethodsStool samples were screened fortcdBand positives were cultured.C. difficileisolates were characterised by toxin profiling and PCR ribotyping. Antimicrobial susceptibility testing was performed using an agar incorporation method, and whole-genome sequencing and AMR genotyping performed on a subset of strains.ResultsThere were 321C. difficilestrains isolated from 326 stool samples. The most common toxigenic ribotype (RT) was RT 017 (18%), followed by RTs 014 (12%) and 020 (7%). There was a high resistance prevalence (≥ 10%) to clindamycin, erythromycin, moxifloxacin and rifaximin, and resistance prevalence was greatest among RT 017 strains. AMR genotyping revealed a strong correlation between resistance genotype and phenotype for moxifloxacin and rifampicin. The presence oferm-class genes was associated with high-level clindamycin and erythromycin resistance. Point substitutions on the penicillin-binding proteins (PBP1 and PBP3) were not sufficient to confer meropenem resistance, however, a Y721S substitution in PBP3 was associated with a slight increase in meropenem MIC. No resistance to metronidazole, vancomycin or fidaxomicin was observed.ConclusionThere was a large proportion ofC. difficileRT 017 in Thailand and a high AMR prevalence among these strains. The concordance between AMR phenotype and genotype was strong.
Costs of choosiness can promote reproductive isolation in parapatry
Authors: Aubier Thomas G. , Joron Mathieu 
Published: November 2020

AbstractSpecies often replace each other spatially along contact zones, giving scope for parapatric speciation. In models of parapatric speciation driven by assortative mating, costs of female choosiness have so far be ignored. Yet, if females encounter only a limited number of males, those that are too choosy may remain unmated, and this should create direct sexual selection against choosiness. In our individual-based model of parapatric ecological speciation, disruptive viability selection leads to divergence of an ecological trait. Additionally, female choosiness (following a ‘matching mating rule’ based on the same ecological trait) can evolve at the risk of remaining unmated, and can limit gene flow between diverging populations. In line with previous litterature, out of the contact zone, the evolution of cost-free choosiness stops at intermediate values due to indirect selection against strong choosiness. Here we show that a weak cost of choosiness, by modifying genotypic frequencies on which viability selection acts, reduces this selection pressure, thus permitting the evolution of stronger choosiness than in the absence of costs. In strong contrast to sympatric models, costs of choosiness can therefore promote reproductive isolation in parapatry.
Unraveling Molecular Mechanisms of Low-Salinity Adaptation inFenneropenaeus chinensis: Insights from Gill Tissue Transcriptomics
Authors: Liu Jun , Liu Rongchen , Jiang Hui , Zhang Hai , Zheng Dianyuan , Zhang Daizhen 
Published: November 2020

AbstractThis study investigates the molecular responses of Chinese shrimp (Fenneropenaeus chinensis) to low salinity stress, employing RNA-seq and functional enrichment analyses. A total of 12,332 expressed genes were identified, with 227 differentially expressed genes (DEGs) detected, revealing intricate adaptive responses in gill tissues. Functional enrichment analysis highlighted DEGs associated with ion-transport regulation, bio-metabolism and detoxification (based on GO terms). The upregulation ofATP1A1,SLC26A2, andSTK39suggested a pivotal role of ion-transport regulation, emphasizing the importance of maintaining osmotic balance. In terms of bio-metabolism,ENPP6,GLS, andDMGDHexhibited significant upregulation, indicating adjustments in energy metabolism for low-salinity adaptation. Notably, the downregulation ofGSTO1andCTHraised questions about detoxification pathways, potentially reflecting adaptations or compromises in response to low salinity. Further correlation network analysis highlighted key genes likeGLS,STK39,SESN1, andSARDH, revealing intricate relationships among DEGs. RT-qPCR validation confirmed the consistency of gene expression patterns with RNA-seq results. In conclusion, this study provides a comprehensive understanding of the molecular mechanisms underlying Chinese shrimp responses to low salinity stress. The identified genes lay the groundwork for targeted interventions and strategies to enhance shrimp aquaculture system resilience amid changing salinity levels.
In vitroselection of a microbial consortium predictive of synergistic functioning along multiple ecosystem scales
Authors: Baas Peter , Bell Colin , Mancini Lauren , Lee Melanie , Wallenstein Matthew D. , Conant Richard T. 
Published: November 2020

AbstractSoil microbes form complex interactive networks throughout the soil and plant rhizosphere. These interactions can result in emergent properties for consortia that are not predictable from the phenotypes of constituents in isolation. We used a four-species consortium to assess the capacity of individual microbial species versus different consortia permutations of the four species to contribute to increased P-solubilization using soil incubations and plant growth experiments. We found that as different combinations of bacterial species were assembled into differing consortia, they demonstrated differing abilities to stimulate soil P cycling and plant growth. The combination of all four microbes in the consortia were much more effective at solubilizing P and stimulating plant growth than any of the individual bacterial species alone. This suggests thatin vivofunctionally synergistic soil microbial consortia can be adept at performing specific ecosystem functionsin situ. Improving our understanding of the mechanisms that facilitate synergistic functioning examined in this study is important for maximizing future food production and agroecosystem sustainability.
Subunit-dependent and independent rules of AMPA receptor trafficking during long-term depression in hippocampal neurons
Authors: Matsuda Shinji , Yuzaki Michisuke 
Published: November 2020

ABSTRACTLong-term potentiation (LTP) and depression (LTD) of excitatory neurotransmission are believed to be the neuronal basis of learning and memory. Both processes are primarily mediated by neuronal activity-induced transport of postsynaptic AMPA-type glutamate receptors (AMPARs). While AMPAR subunits and their specific phosphorylation sites mediate differential AMPAR trafficking, LTP and LTD could also occur in a subunit-independent manner. Thus, it remains unclear whether and how, certain AMPAR subunits with phosphorylation sites are preferentially recruited to or removed from synapses during LTP and LTD. Here, we show that phosphorylation of the membrane-proximal region (MPR), which only occurs in GluA1 AMPAR subunits, mediates the subunit-dependent endosomal transport of AMPARs during LTD. AP-2 and AP-3, adaptor protein complexes necessary for clathrin-mediated endocytosis and late endosomal/lysosomal trafficking, respectively, are reported to be recruited to AMPARs by binding to the AMPAR auxiliary subunit, stargazin (STG), in an AMPAR subunit-independent manner. However, the association of AP-3, but not AP-2, with STG was indirectly inhibited by the phosphomimetic mutation in the MPR of GluA1. Thus, although AMPARs containing the phosphomimetic mutation at the MPR of GluA1 were endocytosed by a LTD-inducing stimulus, they were quickly recycled back to the cell surface in hippocampal neurons. These results could explain how the phosphorylation status of GluA1-MPR plays a dominant role in subunit-independent STG-mediated AMPAR trafficking during LTD.
Genetic and process engineering strategies for enhanced recombinant N-glycoprotein production in bacteria
Authors: Pratama Fenryco , Linton Dennis , Dixon Neil 
Published: November 2020

BackgroundThe production of N-linked glycoproteins in genetically amenable bacterial hosts offers great potential for reduced cost, faster/simpler bioprocesses, greater customisation and utility for distributed manufacturing of glycoconjugate vaccines and glycoprotein therapeutics. Efforts to optimize production hosts have included heterologous expression of glycosylation enzymes, metabolic engineering, use of alternative secretion pathways, and attenuation of gene expression. However, a major bottleneck to enhance glycosylation efficiency, which limits the utility of the other improvements is the impact of target protein sequon accessibility during glycosylation.ResultsHere, we explore a series genetic and process engineering strategies to increase recombinant N-linked glycosylation mediated by the Campylobacter-derived PglB oligosaccharyltransferase inEscherichia coli. Strategies include increasing membrane residency time of the target protein by modifying the cleavage site of its secretion signal, and modulating protein folding in the periplasm by use of oxygen limitation or strains with compromised oxidoreductases or disulphide-bond isomerase activity. These approaches could achieve up to 90% improvement in glycosylation efficiency. Furthermore, we also demonstrated that supplementation with the chemical oxidant cystine enhanced glycoprotein production and improved cell fitness in the oxidoreductase knock out strain.ConclusionsIn this study, we demonstrated that improved glycosylation in the heterologous host could be achieved by mimicking the coordination between protein translocation, folding and glycosylation observed in native such asCampylobacter jejuniand mammalian hosts. Furthermore, it provides insight into strain engineering and bioprocess strategy, to improve glycoprotein yield and to avoid physiological burden of unfolded protein stress to cell growth. The process and genetic strategies identified herein will inform further optimisation and scale-up of heterologous recombinant N-glycoprotein production
Thyroid hormone receptor beta inhibits the PI3K-Akt-mTOR signaling axis in anaplastic thyroid cancer via genomic mechanisms
Authors: Davidson Cole D. , Bolf Eric L. , Gillis Noelle E. , Cozzens Lauren M. , Tomczak Jennifer A. , Carr Frances E. 
Published: November 2020

AbstractThyroid cancer is the most common endocrine malignancy, and the global incidence has increased rapidly over the past few decades. Anaplastic thyroid cancer (ATC) is highly aggressive, dedifferentiated, and patients have a median survival of fewer than six months. Oncogenic alterations in ATC include aberrant PI3K signaling through receptor tyrosine kinase (RTK) amplification, loss of phosphoinositide phosphatase expression and function, and Akt amplification. Furthermore, the loss of expression of the tumor suppressor thyroid hormone receptor beta (TRβ) is strongly associated with ATC. TRβ is known to suppress PI3K in follicular thyroid cancer and breast cancer by binding to the PI3K regulatory subunit p85α. However, the role of TRβ in suppressing PI3K signaling in ATC is not completely delineated. Here we report that TRβ indeed suppresses PI3K signaling in ATC through unreported genomic mechanisms including a decrease in RTK expression and increase in phosphoinositide and Akt phosphatase expression. Furthermore, the reintroduction and activation of TRβ in ATC enables an increase in the efficacy of the competitive PI3K inhibitors LY294002 and buparlisib on cell viability, migration, and suppression of PI3K signaling. These findings not only uncover additional tumor suppressor mechanisms of TRβ but shed light into the implication of TRβ status and activation on inhibitor efficacy in ATC tumors.Abstract FigureGraphical abstract
THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data
Authors: Rowland Bryce , Huh Ruth , Hou Zoe , Wen Jia , Shen Yin , Hu Ming , Giusti-Rodríguez Paola , Sullivan Patrick F , Li Yun 
Published: November 2020

AbstractHi-C data provide population averaged estimates of three-dimensional chromatin contacts across cell types and states in bulk samples. Effective analysis of Hi-C data entails controlling for the potential confounding factor of differential cell type proportions across heterogeneous bulk samples. We propose a novel unsupervised deconvolution method for inferring cell type composition from bulk Hi-C data, the Two-step Hi-c UNsupervised DEconvolution appRoach (THUNDER). We conducted extensive simulations to test THUNDER based on combining two published single-cell Hi-C (scHi-C) datasets. THUNDER more accurately estimates the underlying cell type proportions compared to supervised and unsupervised methods (e.g., MuSiC, TOAST, and NMF). We further demonstrate the practical utility of THUNDER to estimate cell type proportions and identify cell-type-specific interactions in Hi-C data from adult human cortex tissue samples. THUNDER will be a useful tool in adjusting for varying cell type composition in population samples, facilitating valid and more powerful downstream analysis such as differential chromatin organization studies. Additionally, THUNDER estimated contact profiles provide a useful exploratory framework to investigate cell-type-specificity of the chromatin interactome while experimental data is still rare.