bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New ‘Comprehensive’ Annotation of Leucine-Rich Repeat-Containing Receptors in Rice
Authors: Gottin Céline , Dievart Anne , Summo Marilyne , Droc Gaëtan , Périn Christophe , Ranwez Vincent , Chantret Nathalie 
Published: January 2021

AbstractRice plays an essential food security role for more than half of the world’s population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large Leucine-Rich Repeat (LRR)-containing receptor (LRR-CR) subfamilies: the LRR-Receptor-Like Kinase (RLK), LRR-Receptor-Like Protein (RLP) and Nucleotide-binding LRR Receptor (NLR) subfamilies. Using LRRprofiler, a pipeline we developed to annotate and classify those proteins, we compared three publicly available annotations of the rice Nipponbare reference genome. The extended discrepancies we observed for LRR-CR gene models led us to perform in-depth manual curation of their annotations while paying special attention to nonsense mutations. We then transferred this manually curated annotation to Kitaake, a Nipponbare closely related cultivar, using an optimised strategy. Here we discuss the breakthrough achieved by manual curation when comparing genomes and, in addition to ‘functional’ and ‘structural’ annotations, we propose the community to adopt this new approach, which we call ‘comprehensive’ annotation. The resulting data are crucial for further studies on the natural variability and evolution of LRR-CR in order to promote their use in breeding future resilient varieties.
Recombinant production of a functional SARS-CoV-2 spike receptor binding domain in the green algaeChlamydomonas reinhardtii
Authors: Berndt A. , Smalley T. , Ren B. , Badary A. , Sproles A. , Fields F. , Torres-Tiji Y. , Heredia V. , Mayfield S. 
Published: January 2021

ABSTRACTRecombinant production of viral proteins can be used to produce vaccine antigens or reagents to identify antibodies in patient serum. Minimally, these proteins must be correctly folded and have appropriate post-translation modifications. Here we report the production of the SARS-CoV-2 spike protein Receptor Binding Domain (RBD) in the green algaeChlamydomonas.RBD fused to a fluorescent reporter protein accumulates as an intact protein when targeted for ER-Golgi retention or secreted from the cell, while a chloroplast localized version is truncated, lacking the amino terminus. The ER-retained RBD fusion protein was able to bind the human ACE2 receptor, the host target of SARS-CoV-2, and was specifically out-competed by mammalian cell-produced recombinant RBD, suggesting that the algae produced proteins are sufficiently post-translationally modified to act as authentic SARS-CoV-2 antigens. Because algae can be grown at large scale very inexpensively, this recombinant protein may be a low cost alternative to other expression platforms.
Distinct classes of lagging chromosome underpin age-related oocyte aneuploidy in mouse
Authors: Mihajlović Aleksandar I. , Haverfield Jenna , FitzHarris Greg 
Published: January 2021

SUMMARYChromosome segregation errors that cause oocyte aneuploidy increase in frequency with maternal age and are considered a major contributing factor of age-related fertility decline in females. A common age-associated chromosome segregation phenomenon in oocytes is the lagging anaphase chromosome, but whether anaphase laggards actually missegregate and cause aneuploidy is unclear. Here we show unexpectedly that lagging chromosomes in mouse oocytes comprise two mechanistically distinct classes of motion that we refer to as ‘Class-I’ and ‘Class-II’. We use imaging approaches and mechanistic interventions to dissociate the two classes, and find that whereas Class-II laggards are benign, Class-I laggards can directly cause aneuploidy. Most notably, a controlled prolongation of meiosis-I specifically lessens Class-I lagging to prevent aneuploidy. Our data thus reveal lagging chromosomes to be a cause of age-related aneuploidy in mouse oocytes and suggest that manipulating the cell cycle could increase the yield of useful oocytes in some contexts.
Impact of Prior Infection on Protection and Transmission of SARS-CoV-2 in Golden Hamsters
Authors: Zhang Cheng , Guo Zhendong , Li Nan , Cui Huan , Meng Keyin , Liu Lina , Zhao Li , Zhang Shanshan , Qin Chengfeng , Liu Juxiang , Gao Yuwei , Zhang Chunmao 
Published: January 2021

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over 100 million confirmed human infections, and 2 million more deaths globally since its emergence in the end of 2019. Several studies have shown that prior infection provided protective immunity against SARS-CoV-2 in non-human primate models. However, the effect of prior infection on blocking SARS-CoV-2 transmission is not clear. Here, we evaluated the impact of prior infection on protection and transmission of the SARS-CoV-2 virus in golden hamsters. Our results showed that prior infection provided protective immunity against SARS-CoV-2 re-challenge, but it was not sterizing immunity. The transmission experiment results showed that SARS-CoV-2 was efficiently transmitted from naive hamsters to prior infected hamsters by direct contact and airborne route, but not by indirect contact. Further, the virus was efficiently transmitted from prior infected hamsters to naive hamsters by direct contact, but not by airborne route and indirect contact. Surprisingly, the virus can be transmitted between prior infected hamsters by direct contact during a short period of early infection. Taken together, our study demonstrated that prior infected hamsters with good immunity can still be naturally re-infected, and the virus can be transmitted between prior infected hamsters and the naive through different transmission routes, implying the potential possibility of human re-infection and the risk of virus transmission between prior infected population and the healthy. Our study will help to calculate the herd immunity threshold more accurately, make more reasonable public health decisions, formulate an optimized population vaccination program, as well as aid the implementation of appropriate public health and social measures to control COVID-19.
Geography, not host identity, shapes bacterial community in reindeer lichens
Authors: Alonso-García Marta , Villarreal A. Juan Carlos 
Published: January 2021

Background and AimsTremendous progress have been recently achieved in host-microbe research, however, there is still a surprising lack of knowledge in many taxa. Despite its dominance and crucial role in boreal forest, reindeer lichens have until now received little attention. We characterize, for the first time, the bacterial community of four species of reindeer lichens from Eastern North America’s boreal forests. We analysed the effect of two factors (host-identity and geography) in the bacterial community composition, we verified the presence of a common core bacteriota and identified the most abundant core taxa.MethodsMorphological and molecular lichen species delimitation was performed based on the ITS region. The bacterial community of around 200 lichen samples was characterised using the 16S rRNA gene.Key ResultsOur results showed that host-lichen identity does not determine bacterial community composition in reindeer lichens, but we confirmed the influence of geography in shaping the diversity and abundance of bacteria associated to the speciesCladonia stellarisfrom lichen woodlands. We also revealed that reindeer lichens share a reduced common core bacteriota composed exclusively by Proteobacteria.ConclusionsThe bacterial community in reindeer lichens is not host-selective. Northern lichen woodlands exhibit a significant higher diversity and abundance of bacteria associated toCladonia stellaris. Nevertheless, the specific role of those bacteria as well as the process of host colonization remains to be determined. Elucidating these two aspects would be key to have a better understanding of the whole boreal ecosystems. The reduced and not diverse core bacteriota of reindeer lichens might be due to the larger size of our study area. The presence of the speciesMethylorosula polarisin the core bacteriota is evident and might have a particular importance for reindeer lichens.
Annelids win again: the first evidence of Hox antisense transcription in Spiralia
Authors: Novikova Elena L. , Bakalenko Nadezhda I. , Kulakova Milana A. 
Published: January 2021

AbstractTo date it is becoming more and more obvious that multiple non-coding RNAs, once considered to be transcriptional noise, play a huge role in gene regulation during animal ontogenesis. Hox genes are key regulators of embryonic development, growth and regeneration of all bilaterian animals. It was shown that mammalian Hox loci are transcribed in both directions and noncoding RNAs maintain and control the normal functioning of Hox clusters. We revealed antisense transcripts of most of Hox genes in two lophotrochozoans, errant annelidsAlitta virensandPlatynereis dumerilii.It is for the first time when non-coding RNAs associated with Hox genes are found in spiralian animals. All these asRNAs can be referred to as natural antisense transcripts (NATs). We analyzed the expression of all detected NATs using sense probes to their Hox mRNAs during larval and postlarval development and regeneration by whole mount in situ hybridization (WMISH). We managed to clone several asRNAs(Avi-antiHox4-1, Avi-antiHox4-2andAvi-antiHox5)of these annelids and analyzed their expression patterns as well. Our data indicate variable and complicated interplay between sense and antisense Hox transcripts during development and growth of two annelids. The presence of Hox antisense transcription in the representatives of different bilaterian clades (mammals, myriapods and annelids) and similar expression relationships in sense-antisense pairs suggest that this can be the ancestral feature of Hox cluster regulation.
Effects of conjugated linoleic acid on proliferation and differentiation of bovine intramuscular preadipocytein vitro
Authors: Wan Rong , Meng Qingxiang , Zhenming Zhou , hao Wu 
Published: January 2021

ABSTRACTConjugated linoleic acid (CLA), a mixture of isomers of linoleic acid, has previously been shown to be able to increase intramuscular fat contentin vivoand stimulate adipogenesis in intramuscular preadipocytes invitroin pig. Unfortunately, there is little data to evaluate the effect of CLA on proliferation and differentiation of bovine intramuscular preadipocytes. This study investigated the regulation by CLA in proliferation and differentiation of bovine intramuscular preadipocytes. The results demonstrated that CLA significantly induced the expression of PPARγ and C/EBPα mRNA of bovine intramuscular preadipocytes as well as the accumulation of lipid in cultured intramuscular preadipocytes. Additionally, CLA significantly decreased the cell proportion of phase G0/G1, and remarkably increased the proportion of phase S+G2/M. Collectively, these results suggest that CLA promotes bovine intramuscular preadipocyte proliferation and differentiation.
A neuronal social trait space for first impressions in the human amygdala and hippocampus
Authors: Cao Runnan , Lin Chujun , Li Xin , Todorov Alexander , Brandmeir Nicholas J , Wang Shuo 
Published: January 2021

AbstractPeople instantaneously evaluate faces with significant agreement on evaluations of social traits. However, the neural basis for such rapid spontaneous face evaluation remains largely unknown. Here, we recorded from 490 neurons in the amygdala and hippocampus in 5 neurosurgical patients and show that amygdala and hippocampal neurons encode a social trait space. We further investigated the temporal evolution and modulation on the social trait representation, and we employed encoding and decoding models to reveal the critical social traits for the trait space. We also recorded from another 259 neurons and replicated our findings using different social traits. Lastly, the neuronal social trait space may have a behavioral consequence likely involved in the abnormal processing of social information in autism. Together, our results suggest that there exists a neuronal population code for a comprehensive social trait space in the human amygdala and hippocampus that underlie spontaneous first impressions.
Sterols lower energetic barriers of membrane bending and fission necessary for efficient clathrin mediated endocytosis
Authors: Anderson Ruthellen H. , Sochacki Kem A. , Vuppula Harika , Scott Brandon L. , Bailey Elizabeth M. , Schultz Maycie M. , Kerkvliet Jason G. , Taraska Justin W. , Hoppe Adam D. , Francis Kevin R. 
Published: January 2021

SUMMARYAs the principal internalization mechanism in mammalian cells, clathrin-mediated endocytosis (CME) is critical for cellular signal transduction, receptor recycling, and membrane homeostasis. Acute depletion of cholesterol disrupts CME, motivating analysis of CME dynamics in the context of disrupted cholesterol synthesis, sterol specificity, mechanisms involved, and relevance to disease pathology. Using genome-edited cell lines, we demonstrate that inhibition of post-squalene cholesterol biosynthesis as observed in inborn errors of cholesterol metabolism, results in striking immobilization of CME and impaired transferrin uptake. Imaging of membrane bending dynamics and CME pit ultrastructure revealed prolonged clathrin pit lifetimes and accumulation of shallow clathrin-coated structures that scaled with diminishing sterol abundance. Moreover, fibroblasts derived from Smith-Lemli-Opitz syndrome subjects displayed reduced CME function. We conclude that sterols lower the energetic costs of membrane bending during pit formation and vesicular scission during CME and suggest reduced CME contributes to cellular phenotypes observed within disorders of cholesterol metabolism.
Matrix-Bound Growth Factors are Released upon Cartilage Compression by an Aggrecan-Dependent Sodium Flux that is Lost in Osteoarthritis
Authors: Keppie Stuart J. , Mansfield Jessica C. , Tang Xiaodi , Philp Christopher J. , Graham Helen K. , Önnerfjord Patrik , Wall Alanna , McLean Celia , Winlove C. Peter , Sherratt Michael J. , Pavlovskaya Galina E. , Vincent Tonia L 
Published: January 2021

AbstractArticular cartilage is a dense extracellular matrix-rich tissue that degrades following chronic mechanical stress, resulting in osteoarthritis (OA). The tissue has low intrinsic repair especially in aged and osteoarthritic joints. Here we describe three pro-regenerative factors; fibroblast growth factor 2 (FGF2), connective tissue growth factor, bound to transforming growth factor-beta (CTGF-TGFβ), and hepatoma-derived growth factor (HDGF), that are rapidly released from the pericellular matrix (PCM) of articular cartilage upon mechanical injury. All three growth factors bound heparan sulfate, and were displaced by exogenous NaCl. We hypothesised that sodium, sequestered within the aggrecan-rich matrix, was freed by injurious compression, thereby enhancing the bioavailability of pericellular growth factors. Indeed, growth factor release was abrogated when cartilage aggrecan was depleted by IL-1 treatment, and in severely damaged human osteoarthritic cartilage. A flux in free matrix sodium upon mechanical compression of cartilage was visualised by23Na magnetic resonance imaging (MRI) just below the articular surface. This corresponded to a region of reduced tissue stiffness, measured by scanning acoustic microscopy and second harmonic generation microscopy, and where Smad2/3 was phosphorylated upon cyclic compression. Our results describe a novel intrinsic repair mechanism, controlled by matrix stiffness and mediated by the free sodium concentration, in which heparan sulfate-bound growth factors are released from cartilage upon injurious load. They identify aggrecan as a depot for sequestered sodium, explaining why osteoarthritic tissue loses its ability to repair. Treatments that restore matrix sodium to allow appropriate release of growth factors upon load are predicted to enable intrinsic cartilage repair in osteoarthritis.Significance StatementOsteoarthritis is the most prevalent musculoskeletal disease, affecting 250 million people worldwide1. We identify a novel intrinsic repair response in cartilage, mediated by aggrecan-dependent sodium flux, and dependent upon matrix stiffness, which results in the release of a cocktail of pro-regenerative growth factors after injury. Loss of aggrecan in late-stage osteoarthritis prevents growth factor release and likely contributes to disease progression. Treatments that restore matrix sodium in osteoarthritis may recover the intrinsic repair response to improve disease outcome.
Trajectory reconstruction identifies dysregulation of perinatal maturation programs in pluripotent stem cell-derived cardiomyocytes
Authors: Kannan Suraj , Miyamoto Matthew , Lin Brian L. , Kwon Chulan 
Published: January 2021

ABSTRACTA primary limitation in the clinical application of pluripotent stem cell derived cardiomyocytes (PSC-CMs) is the failure of these cells to achieve full functional maturity.In vivo, cardiomyocytes undergo numerous adaptive changes during perinatal maturation. By contrast, PSC-CMs fail to fully undergo these developmental processes, instead remaining arrested at an embryonic stage of maturation. To date, however, the precise mechanisms by which directed differentiation differs from endogenous development, leading to consequent PSC-CM maturation arrest, are unknown. The advent of single cell RNA-sequencing (scRNA-seq) has offered great opportunities for studying CM maturation at single cell resolution. However, perinatal cardiac scRNA-seq has been limited owing to technical difficulties in the isolation of single CMs. Here, we used our previously developed large particle fluorescence-activated cell sorting approach to generate an scRNA-seq reference of mousein vivoCM maturation with extensive sampling of perinatal time periods. We subsequently generated isogenic embryonic stem cells and created anin vitroscRNA-seq reference of PSC-CM directed differentiation. Through trajectory reconstruction methods, we identified a perinatal maturation program in endogenous CMs that is poorly recapitulatedin vitro. By comparison of our trajectories with previously published human datasets, we identified a network of nine transcription factors (TFs) whose targets are consistently dysregulated in PSC-CMs across species. Notably, we demonstrated that these TFs are only partially activated in commonex vivoapproaches to engineer PSC-CM maturation. Our study represents the first direct comparison of CM maturationin vivoandin vitroat the single cell level, and can be leveraged towards improving the clinical viability of PSC-CMs.Significance StatementThere is a significant clinical need to generate mature cardiomyocytes from pluripotent stem cells. However, to date, most differentiation protocols yield phenotypically immature cardiomyocytes. The mechanisms underlying this poor maturation state are unknown. Here, we used single cell RNA-sequencing to compare cardiomyocyte maturation pathways in endogenous and pluripotent stem cell-derived cardiomyocytes. We found thatin vitro, cardiomyocytes fail to undergo critical perinatal gene expression changes necessary for complete maturation. We found that key transcription factors regulating these changes are poorly expressedin vitro.Our study provides a better understanding of cardiomyocyte maturation bothin vivoandin vitro, and may lead to improved approaches for engineering mature cardiomyocytes from stem cells.
From heterogeneous datasets to predictive models of embryonic development
Authors: Dutta Sayantan , Patel Aleena L. , Keenan Shannon E. , Shvartsman Stanislav Y. 
Published: January 2021

AbstractModern studies of embryogenesis are increasingly quantitative, powered by rapid advances in imaging, sequencing, and genome manipulation technologies. Deriving mechanistic insights from the complex datasets generated by these new tools requires systematic approaches for data-driven analysis of the underlying developmental processes. Here we use data from our work on signal-dependent gene repression in theDrosophilaembryo to illustrate how computational models can compactly summarize quantitative results of live imaging, chromatin immunoprecipitation, and optogenetic perturbation experiments. The presented computational approach is ideally suited for integrating rapidly accumulating quantitative data and for guiding future studies of embryogenesis.
Experiencing literature on the e‐reader: the effects of reading narrative texts on screen
Authors: Schwabe Annika , Brandl Lukas , Boomgaarden Hajo G. , Stocker Günther 
Published: January 2021

BackgroundThe digitalisation of literature is proliferating, and the increasing spread of digital reading devices and the availability of digital texts is likely to make books on screen a lasting phenomenon, but little attention has been paid to the consequences of digitalisation for the experience of narrative fiction. While on the one hand, reading literature on a digital reading device might trigger a superficial processing of the text, and problems regarding orientation within the narrative, the awareness of reading a literary text might, on the other hand, lead to more in‐depth and complex processing, independent of reading medium. This study examines whether the reading performance and the emotional and cognitive experiences of the reception of a literary text vary between reading a printed book or an e‐reader.MethodsUsing a between‐subjects experimental design, 207 participants read the beginning of a novel either in a printed book or on an e‐reader. They then completed a reading comprehension test and questionnaires about their cognitive and emotional experiences.ResultsOverall, the results do not suggest the clear superiority of either of the two reading media. Neither reading speed nor reading comprehension differed significantly between the two groups. Even though a broad range of reading experiences was measured, neither cognitive nor emotional reading experiences differed significantly between the groups.ConclusionAn e‐reader does not affect either reading performance or cognitive and emotional experience of reading a narrative text, compared with a printed book.
Diffused effort, asset heterogeneity, and real estate brokerage
Authors: Li Zhaohui , Li Qiang , Sun Hua , Sun Li 
Published: January 2021

AbstractWe generalize the classic Williams (1998, Review of Financial Studies, 11, 239–280) brokerage model by introducing diffused effort and asset heterogeneity. The term “diffused effort” refers to the fact that an agent can cross‐utilize effort spending on one listing to another . One counterintuitive finding in Williams' paper is the absence of the agency problem . As a special case in our model, we recover the agency problem. We demonstrate the positive externality due to the diffused effort and show it depends on the agent's inventory size. Hence, there is a trade‐off between agents' effort committed to existing listings and expanding network size by soliciting new listings.