bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved RAD51 binders through motif shuffling based on the modularity of BRC repeats
Authors: Lindenburg Laurens H. , Pantelejevs Teodors , Gielen Fabrice , Zuazua-Villar Pedro , Butz Maren , Rees Eric , Kaminski Clemens F. , Downs Jessica A. , Hyvönen Marko , Hollfelder Florian 
Published: May 2020

AbstractExchanges of protein sequence modules support leaps in function unavailable through point mutations during evolution. Here we study the role of the two RAD51-interacting modules within the eight binding BRC repeats of BRCA2. We created 64 chimeric repeats by shuffling these modules and measured their binding to RAD51. We found that certain shuffled repeats were stronger than any of the natural repeats, suggesting balancing of relative properties in BRC repeats. Surprisingly, the contribution from the two modules was poorly correlated with affinities of natural repeats, with weak BRC8 repeat containing the most effective N-terminal module. The binding of the strongest chimera, BRC8-2, to RAD51 was improved by −2.44 kCal/mol compared to the strongest natural repeat, BRC4. Crystal structure of RAD51:BRC8-2 complex shows an improved interface fit and an extended β-hairpin in this repeat. BRC8-2 was shown to function in human cells, preventing the formation of nuclear foci after ionizing radiation.
Similar masking effects of natural backgrounds on detection performances in humans, macaques, and macaque-V1 population responses
Authors: Bai Yoon , Chen Spencer , Chen Yuzhi , Geisler Wilson S. , Seidemann Eyal 
Published: May 2020

AbstractVisual systems evolve to process the stimuli that arise in the organism’s natural environment and hence to fully understand the neural computations in the visual system it is important to measure behavioral and neural responses to natural visual stimuli. Here we measured psychometric and neurometric functions and thresholds in the macaque monkey for detection of a windowed sine-wave target in uniform backgrounds and in natural backgrounds of various contrasts. The neurometric functions and neurometric thresholds were obtained by near-optimal decoding of voltage-sensitive-dye-imaging (VSDI) responses at the retinotopic scale in primary visual cortex (V1). The results were compared with previous human psychophysical measurements made under the same conditions. We found that human and macaque behavioral thresholds followed the generalized Weber’s law as function of contrast, and that both the slopes and the intercepts of the threshold functions match each other up to a single scale factor. We also found that the neurometric thresholds followed the generalized Weber’s law and that the neurometric slopes and intercepts matched the behavioral slopes and intercepts up to a single scale factor. We conclude that human and macaque ability to detect targets in natural backgrounds are affected in the same way by background contrast, that these effects are consistent with population decoding at the retinotopic scale by down-stream circuits, and that the macaque monkey is an appropriate animal model for gaining an understanding of the neural mechanisms in humans for detecting targets in natural backgrounds. Finally, we discuss limitations of the current study and potential next steps.New & NoteworthyWe measured macaque detection performance in natural images and compared their performance to the detection sensitivity of neurophysiological responses recorded in the primary visual cortex (V1), and to the performance of human subjects. We found that (i) human and macaque behavioral performances are in quantitative agreement, (ii) are consistent with near-optimal decoding of V1 population responses.SignificanceNatural selection guarantees that neural computations will be matched to the task-relevant natural stimuli in the organism’s environment, and thus it is crucial to measure behavioral and neural responses to natural stimuli. We measured the ability of macaque monkeys to detect targets in natural images and compared their performance to neurophysiological responses recorded in the macaque’s primary visual cortex (V1), and to the performance of humans under the same conditions. We found that (i) human and macaque behavioral performance are in quantitative agreement, (ii) are consistent with near-optimal population decoding of V1 neural responses, and (iii) that the macaque monkey is an appropriate animal model for gaining understanding of the neural mechanisms in humans for detecting targets in natural backgrounds.
SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts
Authors: Zhang R. , Mirdita M. , Karin E. Levy , Norroy C. , Galiez C. , Söding J. 
Published: May 2020

SummarySpacePHARER (CRISPR Spacer Phage-Host Pair Finder) is a sensitive and fast tool forde novoprediction of phage-host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein level, optimizing its scores for matching very short sequences, and combining evidence from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes.
Electromembrane extraction and mass spectrometry for liver organoid drug metabolism studies
Authors: Skottvoll Frøydis Sved , Hansen Frederik , Harrison Sean , Boger Ida Sneis , Mrsa Ago , Restan Magnus Saed , Stein Matthias , Lundanes Elsa , Pedersen-Bjergaard Stig , Aizenshtadt Aleksandra , Krauss Stefan , Sullivan Gareth , Bogen Inger Lise , Wilson Steven Ray 
Published: May 2020

AbstractLiver organoids are emerging tools for precision drug development and toxicity screening. We demonstrate that electromembrane extraction (EME) based on electrophoresis across an oil membrane is suited for segregating selected organoid-derived drug metabolites prior to mass spectrometry (MS)-based measurements. EME, allowed drugs and drug metabolites to be separated from cell medium components (albumin, etc.) that could interfere with subsequent measurements. Multi-well EME (Parallel-EME) holding 100 μL solutions allowed for simple and repeatable monitoring of heroin phase I metabolism kinetics. Organoid Parallel-EME extracts were compatible with ultrahigh-performance liquid chromatography (UHPLC) used to separate the analytes prior to detection. Taken together, liver organoids are well-matched with EME followed by MS-based measurements.
Structure and function of stator units of the bacterial flagellar motor
Authors: Santiveri Mònica , Roa-Eguiara Aritz , Kühne Caroline , Wadhwa Navish , Berg Howard C. , Erhardt Marc , Taylor Nicholas M. I. 
Published: May 2020

AbstractMany bacteria use the flagellum for locomotion and chemotaxis. Its bi-directional rotation is driven by the membrane-embedded motor, which uses energy from the transmembrane ion gradient to generate torque at the interface between stator units and rotor. The structural organization of the stator unit (MotAB), its conformational changes upon ion transport and how these changes power rotation of the flagellum, remain unknown. Here we present ~3 Å-resolution cryo-electron microscopy reconstructions of the stator unit in different functional states. We show that the stator unit consists of a dimer of MotB surrounded by a pentamer of MotA. Combining structural data with mutagenesis and functional studies, we identify key residues involved in torque generation and present a mechanistic model for motor function and switching of rotational direction.One Sentence SummaryStructural basis of torque generation in the bidirectional bacterial flagellar motor
A vector system for fast-forwardin vivostudies of the ZAR1 resistosome in the model plantNicotiana benthamiana
Authors: Harant Adeline , Sakai Toshiyuki , Kamoun Sophien , Adachi Hiroaki 
Published: May 2020

ABSTRACTNicotiana benthamianahas emerged as a complementary experimental system to Arabidopsis. It enables fast-forwardin vivoanalyses primarily through transient gene expression and is particularly popular in the study of plant immunity. Recently, our understanding of NLR plant immune receptors has greatly advanced following the discovery of Arabidopsis ZAR1 resistosome. Here, we describe a novel vector system of 52 plasmids that enables functional studies of the ZAR1 resistosome inN. benthamiana. We showed that ZAR1 stands out among the coiled coil class of NLRs for being highly conserved across distantly related dicot plant species and confirmed NbZAR1 as theN. benthamianaortholog of Arabidopsis ZAR1. NbZAR1 triggers autoimmune cell death inN. benthamianaand this activity is dependent on a functional N-terminal α1 helix. C-terminally tagged NbZAR1 remains functional inN. benthamianathus enabling cell biology and biochemical studies in this plant system. We conclude that the NbZAR1 open source plasmids form an additional experimental system to Arabidopsis forin plantaresistosome studies.
Alpha-, beta-, and gamma-diversity of bacteria varies across global habitats
Authors: Walters Kendra E. , Martiny Jennifer B.H. 
Published: May 2020

AbstractBacteria are essential parts of ecosystems and are the most abundant organisms on the planet. Yet, we still do not know which habitats support the highest diversity of bacteria across multiple scales. We analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project. We found that soils contained the highest bacterial richness within a single sample (alpha-diversity), but sediment assemblages were the most diverse at a global scale (gamma-diversity). Sediment, biofilms/mats, and inland water exhibited the most variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, and shrublands contained the highest richness, while forests, cold deserts, and tundra biomes consistently harbored fewer bacterial species. Surprisingly, agricultural soils encompassed similar levels of beta-diversity as other soil biomes. These patterns were robust to the alpha- and beta-diversity metrics used and the taxonomic binning approach. Overall, the results support the idea that spatial environmental heterogeneity is an important driver of bacterial diversity.
Supramammillary neurons projecting to the septum regulate dopamine and motivation for environmental interaction
Authors: Kesner Andrew J. , Shin Rick , Calva Coleman B. , Don Reuben F. , Junn Sue , Potter Christian T. , Ramsey Leslie A. , Abou-Elnaga Ahmed F. , Cover Christopher G. , Wang Dong V. , Lu Hanbing , Yang Yihong , Ikemoto Satoshi 
Published: May 2020

AbstractThe supramammillary region (SuM) is a posterior hypothalamic structure, known to regulate hippocampal theta oscillations and arousal. However, recent studies reported that the stimulation of SuM neurons with neuroactive chemicals, including substances of abuse, is reinforcing. We conducted experiments to illuminate how SuM neurons mediate such effects. The excitation of SuM glutamatergic (GLU) neurons was reinforcing in mice; this effect was relayed by the projections to septal GLU neurons. SuM neurons were active during exploration and approach behavior and diminished activity during sucrose consumption. Consistently, inhibition of SuM neurons disrupted approach responses, but not sucrose consumption. Such functions are similar to those of mesolimbic dopamine neurons. Indeed, the stimulation of SuM-to-septum GLU neurons and septum-to-ventral tegmental area (VTA) GLU neurons activated mesolimbic dopamine neurons. We propose that the supramammillo-septo-VTA pathway is important in reinforcement and approach motivation and may play an important role in mood and substance-use disorders.
Cooperation increases robustness to ecological disturbance in microbial cross-feeding networks
Authors: Oña Leonardo , Kost Christian 
Published: May 2020

AbstractMicroorganisms mainly exist within complex networks of ecological interactions. Given that the growth and survival of community members frequently depend on an obligate exchange of essential metabolites, it is generally unclear how such communities can persist despite the destabilizing force of ecological disturbance. Here we address this issue using a population dynamics model. In contrast to previous work that suggests the potential for obligate interaction networks to evolve is limited, we find the opposite pattern: natural selection in the form of ecological disturbance favors both specific network topologies and cooperative cross-feeding among community members. These results establish environmental selection as a key driver shaping the architecture of microbial interaction networks.
Proteasome-mediated regulation of Cdhr1a by Siah1 modulates photoreceptor development and survival in zebrafish
Authors: Piedade Warlen P. , Titialii-Torres Kayla , Morris Ann , Famulski Jakub 
Published: May 2020

AbstractCongenital retinal dystrophies are a major cause of unpreventable and incurable blindness worldwide. Mutations in CDHR1, a retina specific cadherin, are associated with cone-rod dystrophy. The ubiquitin proteasome system (UPS) is responsible for mediating orderly and precise targeting of protein degradation to maintain biological homeostasis and coordinate proper development, including retinal development. Recently, our lab uncovered that the seven in absentia (Siah) family of E3 ubiquitin ligases play a role in optic fissure fusion, and identified Cdhr1a as a potential target of Siah. Using two-color whole mountin situhybridization and immunohistochemistry, we detectedsiah1andcdhr1aco-expression as well as protein co-localization in the retinal outer nuclear layer (ONL), and more precisely in the connecting cilium of rods and cones between 3-5 days post fertilization (dpf). We confirmed that Siah1 targets Cdhr1a for proteasomal degradation by co-transfection and co-immunoprecipitation in cell culture. To analyze the functional importance of this interaction, we created two transgenic zebrafish lines that expresssiah1or an inactivesiah1(siah1ΔRING) under the control of the heat shock promoter to modulate Siah activity during photoreceptor development. Overexpression ofsiah1, but notsiah1ΔRING, resulted in a decrease in the number of rods and cones at 72 hours post fertilization (hpf). The number of retinal ganglion cells, amacrine and bipolar was not affected by Siah1 overexpression, and there was no significant reduction of proliferating cells in the Siah1 overexpressing retina. We did however detect increased cell death, confirmed by an increase in the number of TUNEL+ cells in the ONL, which was proteasome-dependent, as MG132 treatment rescued the cell death phenotype. Lastly, reduction in rods and cones resulting from increased Siah1 expression was rescued by injection ofcdhr1mRNA, and to an even greater extent by injection of a Siah1-insensitivecdhr1avariant mRNA. Taken together, our work provides the first evidence that Cdhr1a plays a role during early photoreceptor development and that Cdhr1a is regulated by Siah1 via the UPS. This work provides new avenues for investigation into the roles of CDHR1, and now also Siah1, in the predisposition and pathogenesis of inherited cone-rod dystrophy.
The impact of genetic background and gender on the increase in mitotic index in response to mating ofDrosophila melanogaster
Authors: Malpe Manashree , Schulz Cordula 
Published: May 2020

SUMMARYThe replenishment of specialized cells depends on the activity of stem cells. Recent advances in stem cell research have shown that the germline stem cells (GSCs) inDrosophila melanogastercan increase their mitotic activity in response to mating. Here, we show that this ability to respond to mating is eliminated if the males are mutant for the ABC transporter, White, the genetic background for a plethora of fly lines. Furthermore, we were not able to reproduce previous findings that female flies increase their GSC numbers and mitotic activity upon mating. Our findings underline the importance of careful experimental design and control specimen.
SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics
Authors: Gupta Ruchir , Charron Jacob , Stenger Cynthia L , Painter Jared , Steward Hunter , Cook Taylor W , Faber William , Frisch Austin , Lind Eric , Bauss Jacob , Li Xiaopeng , Sirpilla Olivia , Soehnlen Xavier , Underwood Adam , Hinds David , Morris Michele , Lamb Neil , Carcillo Joseph A , Bupp Caleb , Uhal Bruce D , Rajasekaran Surender , Prokop Jeremy W 
Published: May 2020

AbstractThe SARS-CoV-2 pandemic, starting in 2019, has challenged the speed at which labs perform science, ranging from discoveries of the viral composition to handling health outcomes in humans. The small ~30kb single-stranded RNA genome of Coronaviruses makes them adept at cross species spread and drift, increasing their probability to cause pandemics. However, this small genome also allows for a robust understanding of all proteins coded by the virus. We employed protein modeling, molecular dynamic simulations, evolutionary mapping, and 3D printing to gain a full proteome and dynamicome understanding of SARS-CoV-2. The Viral Integrated Structural Evolution Dynamic Database (VIStEDD) has been established (prokoplab.com/vistedd), opening future discoveries and educational usage. In this paper, we highlight VIStEDD usage for nsp6, Nucleocapsid (N), and Spike (S) surface glycoprotein. For both nsp6 and N we reveal highly conserved surface amino acids that likely drive protein-protein interactions. In characterizing viral S protein, we have developed a quantitative dynamics cross correlation matrix insight into interaction with the ACE2/SLC6A19 dimer complex. From this quantitative matrix, we elucidated 47 potential functional missense variants from population genomic databases within ACE2/SLC6A19/TMPRSS2, warranting genomic enrichment analyses in SARS-CoV-2 patients. Moreover, these variants have ultralow frequency, but can exist as hemizygous in males for ACE2, which falls on the X-chromosome. Two noncoding variants (rs4646118 and rs143185769) found in ~9% of African descent individuals for ACE2 may regulate expression and be related to increased susceptibility of African Americans to SARS-CoV-2. This powerful database of SARS-CoV-2 can aid in research progress in the ongoing pandemic.
Robust computational design and evaluation of peptide vaccines for cellular immunity with application to SARS-CoV-2
Authors: Liu Ge , Carter Brandon , Bricken Trenton , Jain Siddhartha , Viard Mathias , Carrington Mary , Gifford David K. 
Published: May 2020

ABSTRACTWe present a combinatorial machine learning method to evaluate and optimize peptide vaccine formulations, and we find for SARS-CoV-2 that it provides superior predicted display of viral epitopes by MHC class I and MHC class II molecules over populations when compared to other candidate vaccines. Our method is robust to idiosyncratic errors in the prediction of MHC peptide display and considers target population HLA haplotype frequencies during optimization. To minimize clinical development time our methods validate vaccines with multiple peptide presentation algorithms to increase the probability that a vaccine will be effective. We optimize an objective function that is based on the presentation likelihood of a diverse set of vaccine peptides conditioned on a target population HLA haplotype distribution and expected epitope drift. We produce separate peptide formulations for MHC class I loci (HLA-A, HLA-B, and HLA-C) and class II loci (HLA-DP, HLA-DQ, and HLA-DR) to permit signal sequence based cell compartment targeting using nucleic acid based vaccine platforms. Our SARS-CoV-2 MHC class I vaccine formulations provide 93.21% predicted population coverage with at least five vaccine peptide-HLA hits on average in an individual (≥ 1 peptide 99.91%) with all vaccine peptides perfectly conserved across 4,690 geographically sampled SARS-CoV-2 genomes. Our MHC class II vaccine formulations provide 90.17% predicted coverage with at least five vaccine peptide-HLA hits on average in an individual with all peptides having observed mutation probability ≤ 0.001. We evaluate 29 previously published peptide vaccine designs with our evaluation tool with the requirement of having at least five vaccine peptide-HLA hits per individual, and they have a predicted maximum of 58.51% MHC class I coverage and 71.65% MHC class II coverage given haplotype based analysis. We provide an open source implementation of our design methods (OptiVax), vaccine evaluation tool (EvalVax), as well as the data used in our design efforts.
SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins
Authors: Cortey Martí , Li Yanli , Díaz Ivan , Clilverd Hepzibar , Darwich Laila , Mateu Enric 
Published: May 2020

AbstractTheSevere acute respiratory syndrome coronavirus 2(SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naïve human population. We identified and analysed the amino acid mutations that gained prominence worldwide in the early months of the pandemic. Eight mutations have been identified along the viral genome, mostly located in conserved segments of the structural proteins and showing low variability among coronavirus, which indicated that they might have a functional impact. At the moment of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus population; ranging from a change in the spike protein that becomes absolutely prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, to a mutation in the matrix protein that nearly fades out after reaching a frequency of 20%.
Prophage exotoxins enhance colonization fitness in epidemic scarlet fever-causingStreptococcus pyogenes
Authors: Brouwer Stephan , Barnett Timothy C. , Ly Diane , Kasper Katherine J. , De Oliveira David M.P. , Rivera-Hernandez Tania , Cork Amanda J. , McIntyre Liam , Jespersen Magnus G. , Richter Johanna , Schulz Benjamin L. , Dougan Gordon , Nizet Victor , Yuen Kwok-Yung , You Yuanhai , McCormick John K. , Sanderson-Smith Martina L. , Davies Mark R. , Walker Mark J. 
Published: May 2020

AbstractThe re-emergence of scarlet fever poses a new global public health threat. The capacity of North-East Asian serotype M12 (emm12)Streptococcus pyogenes(group AStreptococcus, GAS) to cause scarlet fever has been linked epidemiologically to the presence of novel prophages, including prophage ΦHKU.vir encoding the secreted superantigens SSA and SpeC and the DNase Spd1. Here we report the comprehensive molecular characterization of ΦHKU.vir-encoded exotoxins. We demonstrate that streptolysin O (SLO)-induced glutathione efflux from host cellular stores is a previously unappreciated GAS virulence mechanism that promotes SSA release and activity, representing the first description of a thiol-activated bacterial superantigen. Spd1 is required for optimal growth in human blood, confers resistance to neutrophil killing, and degrades neutrophil extracellular traps (NETs). Investigating single, double and triple isogenic knockout mutants of the ΦHKU.vir-encoded exotoxins, we find that SpeC and Spd1 act synergistically to facilitate nasopharyngeal colonization in a mouse model. These results offer insight into the etiology and pathogenesis of scarlet fever-causing GAS mediated by phage ΦHKU.vir exotoxins.