bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resource uptake and the evolution of moderately efficient enzymes
Authors: Labourel Florian , Rajon Etienne 
Published: November 2020

AbstractEnzymes speed up reactions that would otherwise be too slow to sustain the metabolism of self-replicators. Yet, most enzymes seem only moderately efficient, exhibiting kinetic parameters orders of magnitude lower than their expected physically achievable maxima and spanning over surprisingly large ranges of values. Here, we question how these parameters evolve using a mechanistic model where enzyme efficiency is a key component of individual competition for resources. We show that kinetic parameters are under strong directional selection only up to a point, above which enzymes appear to evolve under near-neutrality, thereby confirming the qualitative observation of other modeling approaches. While the existence of a large fitness plateau could potentially explain the extensive variation in enzyme features reported, we show using a population genetics model that such a widespread distribution is an unlikely outcome of evolution on a common landscape, as mutation-selection-drift balance occupy a narrow area even when very moderate biases towards lower efficiency are considered. Instead, differences in the evolutionary context encountered by each enzyme should be involved, such that each evolves on an individual, unique landscape. Our results point to drift and effective population size playing an important role, along with the kinetics of nutrient transporters, the tolerance to high concentrations of intermediate metabolites, and the reversibility of reactions. Enzyme concentration also shapes selection on kinetic parameters, but we show that the joint evolution of concentration and efficiency does not yield extensive variance in evolutionary outcomes when documented costs to protein expression are applied.
A motion aftereffect from viewing other people’s gaze
Authors: Randall William , Guterstam Arvid 
Published: November 2020

SummaryRecent work suggests that our brains may generate subtle, false motion signals streaming from other people to the objects of their attention, aiding social cognition. For instance, brief exposure to static images depicting other people gazing at objects made subjects slower at detecting subsequent motion in the direction of gaze, suggesting that looking at someone else’s gaze caused a directional motion adaptation. Here we confirm, using a more stringent method, that viewing static images of another person gazing in a particular direction, at an object, produced motion aftereffects in the opposite direction. The aftereffect was manifested as a change in perceptual decision threshold for detecting left versus right motion. The effect disappeared when the person was looking away from the object. These findings suggest that the attentive gaze of others is encoded as an implied agent-to-object motion that is sufficiently robust to cause genuine motion aftereffects, though subtle enough to remain subthreshold.
Mechanistic analysis of enhancer sequences in the Estrogen Receptor transcriptional program
Authors: Tabe-Bordbar Shayan , Song You Jin , Lunt Bryan J. , Prasanth Kannanganattu V. , Sinha Saurabh 
Published: November 2020

AbstractBackgroundEstrogen Receptor α (ERα) is a major lineage determining transcription factor (TF) in mammary gland development, orchestrating the expression of thousands of genes. Dysregulation of ERα-mediated transcriptional program results in abnormal cell proliferation and cancer. Transcriptomic and epigenomic profiling of breast cancer cell lines has revealed large numbers of enhancers involved in this regulatory program, but how these enhancers encode function in their sequence remains poorly understood.ResultsA subset of ERα-bound enhancers are transcribed into short bidirectional RNA (enhancer RNA or eRNA), and this property is believed to be a reliable marker of active enhancers. We therefore analyze thousands of ERα-bound enhancers and build quantitative, mechanism-aware models to discriminate eRNAs from non-transcribing enhancers based on their sequence. Our thermodynamics-based models provide insights into the roles of specific TFs in ERα-mediated transcriptional program, many of which are supported by the literature. We use in silico perturbations to predict TF-enhancer regulatory relationships and integrate these findings with experimentally determined enhancer-promoter interactions to construct a gene regulatory network. We also demonstrate that the model can prioritize breast cancer-related sequence variants while providing mechanistic explanations for their function. Finally, we experimentally validate the model-proposed mechanisms underlying three such variants.ConclusionsWe modeled the sequence-to-expression relationship in ERα-driven enhancers and gained mechanistic insights into the workings of a major transcriptional program. Our model is consistent with the current body of knowledge and its predictions are confirmed by experimental observations. We believe this to be a promising approach to analysis of regulatory sequences and variants.
Development of Targetable Multi-Drug Nanoparticles for Glioblastoma Treatment and In Vitro Evaluation in Glioblastoma Stem Cells
Authors: Smiley Shelby B. , Yun Yeonhee , Ayyagari Pranav , Shannon Harlan E. , Pollok Karen E. , Vannier Michael W. , Das Sudip K. , Veronesi Michael C. 
Published: November 2020

AbstractGlioblastoma (GBM) is a malignant brain tumor with a poor long-term prognosis. The current median survival is approximately fifteen to twenty months with the standard of care therapy which includes surgery, radiation, and chemotherapy. An important factor contributing to recurrence of GBM is high resistance of GBM cancer stem cells (CSCs) to several anticancer drugs, for which a systemically delivered single drug approach will be unlikely to produce a viable cure. Therefore, multidrug therapies have the potential to improve the survival time. Currently, only temozolomide (TMZ), which is a DNA alkylator, affects overall survival in GBM patients. CSCs regenerate rapidly and over-express a methyl transferase which overrides the DNA-alkylating mechanism of TMZ, leading to drug resistance. Idasanutlin (RG7388, R05503781) is a potent, selective MDM2 antagonist that additively kills GBM CSCs when combined with TMZ. Nanotechnology is an emerging field that shows great promise in drug delivery and diagnostics. The ability to combine both therapy and imaging allows real time assessment of drug delivery in vivo for the field of theranostics.To develop a multi-drug therapy using multi-functional nanoparticles (NPs) that preferentially target the GBM CSC subpopulation and provide in vivo preclinical imaging capability. Polymer-micellar NPs composed of poly(styrene-b-ethylene oxide) (PS-b-PEO) and poly(lactic-co-glycolic) acid (PLGA) were developed investigating both single and double emulsion fabrication techniques as well as combinations of TMZ and RG7388. The NPs were covalently bound to a 15-base-pair CD133 aptamer in order to target the CD133 antigen expressed on the surface of GBM CSC subpopulation. For theranostic functionality, the NPs were also labelled with a radiotracer, Zirconium-89 (89Zr). The NPs maintained a small size of less than 100 nm, a low negative charge and exhibited the ability to effectively target and kill the CSC subpopulation. In addition, the conjugation of the CD133 aptamer was able to promote killing in CSCs leading to the justification of a targeted nanosystem to potentially improve localized therapy in future in vivo models. This work has provided a potentially therapeutic option for GBM specific for CSC targeting and theranostic imaging.
Symptoms suggestive of COVID-19 in households with and without children: a descriptive survey
Authors: Grove Grace , Ziauddeen Nida , Alwan Nisreen A 
Published: November 2020

AbstractBackgroundExploring transmission and symptoms of COVID-19 in children is vital, given that schools have recently fully reopened.ObjectivesThis study aimed to characterise the nature and duration of symptoms suggestive of COVID-19 in UK households, and examine whether the symptoms varied between households with and without children and between adults and children from March to May 2020 in the UK.MethodsAn online questionnaire posted on social media (Mumsnet, Twitter, Facebook) was used to gather demographic and symptom information within UK households.ResultsResults from 508 households (1057 adults and 398 children) were available for analysis. 64.1% of respondent households with children and 59.1% of households without children had adults with symptoms suggestive of COVID-19. The proportion of adults that reported being symptomatic was 46.1% in households with children (and 36.7% in households without children. In 37.8% of households with at least one adult and one child with symptoms, the child’s onset of symptoms started before the adult. Of all children, 35.7% experienced symptoms, with almost a quarter experiencing fluctuating symptoms for more than 2 weeks compared to almost half of symptomatic adults. In general, children had a shorter (median 5 days) and milder illness course than adults (median 10 days). Fatigue was the most common symptom in adults (79.7%) and cough was the most common symptom in children (53.5%). Chest tightness, shortness of breath, fatigue, muscle ache and diarrhoea were more common in adults than children, while cough and fever were equally common.ConclusionChildren had shorter and milder illness than adults, but in almost a quarter of children symptoms lasted more than 2 weeks. In over a third of both adult-child symptomatic households, the child was the first to become ill. Child to adult transmission and clinical presentation in children need to be further characterised.SynopsisStudy question.What is the nature and duration of symptoms suggestive of COVID-19 in UK households with and without children during March and May 2020? Do the symptoms vary between adults and children?What’s already known.There has been uncertainty about the extent to which children get and transmit SARS-CoV-2 within households. Symptoms associated with SARS-CoV-2 infection are well described in adults but symptoms and their duration are less well-characterised in children.What this study addsOn average, children had shorter and milder illness than adults, but still symptoms lasted more than 2 weeks in a significant proportion of children. In over a third of both adult and child symptomatic households, the child was the first to become ill.
Replacing theSpCas9HNH domain by deaminases generates compact base editors with an alternative targeting scope
Authors: Villiger Lukas , Schmidheini Lukas , Mathis Nicolas , Rothgangl Tanja , Marquart Kim , Schwank Gerald 
Published: November 2020

ABSTRACTBase editors are RNA-guided deaminases that enable site-specific nucleotide transitions. The targeting scope of these Cas-deaminase fusion proteins critically depends on the availability of a protospacer adjacent motif (PAM) at the target locus and is limited to a window within the CRISPR-Cas R-loop, where single stranded (ss)DNA is accessible to the deaminase. Here, we reason that the Cas9-HNH nuclease domain sterically constrains ssDNA accessibility, and demonstrate that omission of this domain expands the editing window. By exchanging the HNH nuclease domain with an adenosine deaminase we furthermore engineer adenine base editor variants (HNHx-ABE) with PAM-proximally shifted editing windows. This work expands the targeting scope of base editors, and provides base editor variants that are substantially smaller. It moreover informs of potential future directions in Cas9 protein engineering, where the HNH domain could be replaced by other enzymes that act on ssDNA.
Spatiotemporal model of cellular mechanotransduction via Rho and YAP
Authors: Novev Javor K. , Heltberg Mathias L. , Jensen Mogens H. , Doostmohammadi Amin 
Published: November 2020

AbstractHow cells sense and respond to mechanical stimuli remains an open question. Recent advances have identified the translocation of Yes-associated protein (YAP) between nucleus and cytoplasm as a central mechanism for sensing mechanical forces and regulating mechanotransduction. We formulate a spatiotemporal model of the mechanotransduction signalling pathway that includes coupling of YAP with the cell force-generation machinery through the Rho family of GTPases. Considering the active and inactive forms of a single Rho protein (GTP/GDP-bound) and of YAP (non-phosphorylated/phosphorylated), we study the cross-talk between cell polarization due to active Rho and YAP activation through its nuclear localization.For fixed mechanical stimuli, our model predicts stationary nuclear-to-cytoplasmic YAP ratios consistent with experimental data at varying adhesive cell area. We further predict damped and even sustained oscillations in the YAP nuclear-to-cytoplasmic ratio by accounting for recently reported positive and negative YAP-Rho feedback. Extending the framework to time-varying mechanical stimuli that simulate cyclic stretching and compression, we show that the YAP nuclear-to-cytoplasmic ratio’s time dependence follows that of the cyclic mechanical stimulus. The model presents one of the first frameworks for understanding spatiotemporal YAP mechanotransduction, providing several predictions of possible YAP localization dynamics, and suggesting new directions for experimental and theoretical studies.
Genetic Modification to Design a Stable Yeast-expressed Recombinant SARS-CoV-2 Receptor Binding Domain as a COVID-19 Vaccine Candidate
Authors: Chen Wen-Hsiang , Wei Junfei , Kundu Rakhi Tyagi , Adhikari Rakesh , Liu Zhuyun , Lee Jungsoon , Versteeg Leroy , Poveda Cristina , Keegan Brian , Villar Maria Jose , de Araujo Leao Ana C. , Rivera Joanne Altieri , Gillespie Portia M. , Pollet Jeroen , Strych Ulrich , Zhan Bin , Hotez Peter J. , Bottazzi Maria Elena 
Published: November 2020

ABSTRACTBackgroundCoronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has now spread worldwide to infect over 110 million people, with approximately 2.5 million reported deaths. A safe and effective vaccine remains urgently needed.MethodWe constructed three variants of the recombinant receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein (residues 331-549) in yeast as follows: (1) a “wild type” RBD (RBD219-WT), (2) a deglycosylated form (RBD219-N1) by deleting the first N-glycosylation site, and (3) a combined deglycosylated and cysteine-mutagenized form (C538A-mutated variant (RBD219-N1C1)). We compared the expression yields, biophysical characteristics, and functionality of the proteins produced from these constructs.Results and conclusionsThese three recombinant RBDs showed similar secondary and tertiary structure thermal stability and had the same affinity to their receptor, angiotensin-converting enzyme 2 (ACE-2), suggesting that the selected deletion or mutations did not cause any significant structural changes or alteration of function. However, RBD219-N1C1 had a higher fermentation yield, was easier to purify, was not hyperglycosylated, and had a lower tendency to form oligomers, and thus was selected for further vaccine development and evaluation.General significanceBy genetic modification, we were able to design a better-controlled and more stable vaccine candidate, which is an essential and important criterion for any process and manufacturing of biologics or drugs for human use.
KusakiDB v1.0: a novel approach for validation and completeness of protein orthologous groups
Authors: Ghelfi Andrea , Nakamura Yasukazu , Isobe Sachiko 
Published: November 2020

SummaryPlants have quite a low coverage in the major protein databases despite their roughly 350,000 species. Moreover, the agricultural sector is one of the main categories in bioeconomy. In order to manipulate and/or engineer plant-based products, it is important to understand the essential fabric of an organism, its proteins. Therefore, we created KusakiDB, which is a database of orthologous proteins, in plants, that correlates three major databases, OrthoDB, UniProt and RefSeq. KusakiDB has an orthologs assessment and management tools in order to compare orthologous groups, which can provide insights not only under an evolutionary point of view but also evaluate structural gene prediction quality and completeness among plant species. KusakiDB could be a new approach to reduce error propagation of functional annotation in plant species. Additionally, this method could, potentially, bring to light some orthologs unique to a few species or families that could have evolved at a high evolutionary rate or could have been a result of a horizontal gene transfer.Availability and ImplementationThe software is implemented in R. It is available athttp://pgdbjsnp.kazusa.or.jp/app/kusakidband athttps://hub.docker.com/r/ghelfi/kusakidbunder the MIT license.Contact:andreaghelfi@kazusa.or.jpSupplementary informationSupplementary data are available atBioinformaticsonline.
DR2S: An Integrated Algorithm Providing Reference-Grade Haplotype Sequences from Heterozygous Samples
Authors: Klasberg Steffen , Schmidt Alexander H. , Lange Vinzenz , Schöfl Gerhard 
Published: November 2020

AbstractBackgroundHigh resolutionHLAgenotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic reference sequence databases of allelic variation.ResultsHere, we report onDR2S, an R package that leverages the strengths of two sequencing technologies – the accuracy of next-generation sequencing with the read length of third-generation sequencing technologies like PacBio’s SMRT sequencing or ONT’s nanopore sequencing – to reconstruct fully-phased high-quality full-length haplotype sequences. Although optimised forHLAand KIR genes,DR2Sis applicable to all loci with known reference sequences provided that full-length sequencing data is available for analysis. In addition,DR2Sintegrates supporting tools for easy visualisation and quality control of the reconstructed haplotype to ensure suitability for submission to public allele databases.ConclusionsDR2Sis a largely automated workflow designed to create high-quality fully-phased reference allele sequences for highly polymorphic gene regions such asHLAorKIR. It has been used by biologists to successfully characterise and submit more than 500HLAalleles and more than 500KIRalleles to theIPD-IMGT/HLAandIPD-KIRdatabases.
Correlative 3D microscopy of single cells using super-resolution and scanning ion-conductance microscopy
Authors: Navikas Vytautas , Leitao Samuel M. , Grussmayer Kristin S. , Descloux Adrien , Drake Barney , Yserentant Klaus , Werther Philipp , Herten Dirk-Peter , Wombacher Richard , Radenovic Aleksandra , Fantner Georg E. 
Published: November 2020

AbstractHigh-resolution live-cell imaging is necessary to study complex biological phenomena. Modern fluorescence microscopy methods are increasingly combined with complementary, label-free techniques to put the fluorescence information into the cellular context. The most common high-resolution imaging approaches used in combination with fluorescence imaging are electron microscopy and atomic-force microscopy (AFM), originally developed for solid-state material characterization. AFM routinely resolves atomic steps, however on soft biological samples, the forces between the tip and the sample deform the fragile membrane, thereby distorting the otherwise high axial resolution of the technique. Here we present scanning ion-conductance microscopy (SICM) as an alternative approach for topographical imaging of soft biological samples, preserving high axial resolution on cells. SICM is complemented with live-cell compatible super-resolution optical fluctuation imaging (SOFI). To demonstrate the capabilities of our method we show correlative 3D cellular maps with SOFI implementation in both 2D and 3D with self-blinking dyes for two-color high-order SOFI imaging. Finally, we employ correlative SICM/SOFI microscopy for visualizing actin dynamics in live COS-7 cells with subdiffractional resolution.
Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes
Authors: Yermanos Alexander , Agrafiotis Andreas , Yates Josephine , Papadopoulou Chrysa , Robbiani Damiano , Bieberich Florian , Vazquez-Lombardi Rodrigo , Neumeuer Daniel , Oxenius Annette , Reddy Sai T. 
Published: November 2020

AbstractHigh-throughput single-cell sequencing (scSeq) technologies are revolutionizing the ability to molecularly profile B and T lymphocytes by offering the opportunity to simultaneously obtain information on adaptive immune receptor repertoires (VDJ repertoires) and transcriptomes. An integrated quantification of immune repertoire parameters such as germline gene usage, clonal expansion, somatic hypermutation and transcriptional states opens up new possibilities for the high-resolution analysis of lymphocytes and the inference of antigen-specificity. While multiple tools now exist to investigate gene expression profiles from scSeq of transcriptomes, there is a lack of software dedicated to single-cell immune repertoires. Here, we present Platypus, an open-source software platform providing a user-friendly interface to investigate B cell receptor (BCR) and T cell receptor (TCR) repertoires from single-cell sequencing experiments. Platypus provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression, and gene ontology. To showcase the capabilities of Platypus, we use it to analyze and visualize single-cell immune repertoires and transcriptomes from B and T cells from convalescent COVID-19 patients, revealing unique insight into the repertoire features and transcriptional profiles of clonally expanded lymphocytes. Platypus will expedite progress by increasing accessibility to the broader immunology community by facilitating the analysis of single-cell immune repertoire and transcriptome sequencing.