bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genomics of two closely related anhydrobiotic midges reveals differences in adaptation to extreme desiccation
Authors: Shaykhutdinov N.M. , Klink G.V. , Garushyants S.K. , Kozlova O.S. , Cherkasov A.V. , Kikawada T. , Okuda T. , Pemba D. , Deviatiiarov R.M. , Gazizova G.R. , Penin A.A. , Shagimardanova E.I. , Cornette R. , Gusev O.A. , Bazykin G.A. 
Published: August 2020

AbstractThe sleeping chironomidPolypedilum vanderplankiis capable of anhydrobiosis, a striking example of adaptation to extreme desiccation. Tolerance to complete desiccation in this species is associated with the emergence of multiple paralogs of protective genes. One of the gene families highly expressed under anhydrobiosis and involved in this process are protein-L-isoaspartate (D-aspartate) O-methyltransferases (PIMTs). Recently, a closely related anhydrobiotic midge from Malawi,P. pembai, showing the ability to tolerate complete desiccation similar to that ofP. vanderplanki, but experiences more frequent desiccation-rehydration cycles due to differences in ecology, was discovered. Here, we sequenced and assembled the genome ofP. pembaiand performed a population genomics analysis of several populations ofP. vanderplankiand a population ofP. pembai.We observe positive selection and radical changes in the genetic architecture of thePIMTlocus between the two species, including multiple duplication events in theP. pembailineage. In particular,PIMT-4, the most highly expressed of thesePIMTs, is present in six copies in theP. pembai; these copies differ in expression profiles, suggesting possible sub- or neofunctionalization. The nucleotide diversity (π) of the genomic region carrying these new genes is decreased inP. pembai, but not in the orthologous region carrying the ancestral gene inP. vanderplanki, providing evidence for a selective sweep associated with post-duplication adaptation in the former. Overall, our results suggest an extensive recent and likely ongoing, adaptation of the mechanisms of anhydrobiosis.
Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells
Authors: Parker Robert , Partridge Thomas , Wormald Catherine , Kawahara Rebeca , Stalls Victoria , Aggelakopoulou Maria , Parker Jimmy , Doherty Rebecca Powell , Morejon Yoanna Ariosa , Lee Esther , Saunders Kevin , Haynes Barton F. , Acharya Priyamvada , Thaysen-Andersen Morten , Borrow Persephone , Ternette Nicola 
Published: August 2020

ABSTRACTUnderstanding and eliciting protective immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an urgent priority. To facilitate these objectives, we have profiled the repertoire of human leukocyte antigen class II (HLA-II)-bound peptides presented by HLA-DR diverse monocyte-derived dendritic cells pulsed with SARS-CoV-2 spike (S) protein. We identify 209 unique HLA-II-bound peptide sequences, many forming nested sets, which map to sites throughout S including glycosylated regions. Comparison of the glycosylation profile of the S protein to that of the HLA-II-bound S peptides revealed substantial trimming of glycan residues on the latter, likely introduced during antigen processing. Our data also highlight the receptor-binding motif in S1 as a HLA-DR-binding peptide-rich region. Results from this study have application in vaccine design, and will aid analysis of CD4+ T cell responses in infected individuals and vaccine recipients.
Centrosome amplification mediates small extracellular vesicles secretion via lysosome disruption
Authors: Adams Sophie D. , Csere Judit , D’angelo Gisela , Carter Edward P. , Arnandis Teresa , Dodel Martin , Kocher Hemant , Grose Richard , Raposo Graça , Mardakheh Faraz , Godinho Susana A. 
Published: August 2020

SummaryBidirectional communication between cells and their surrounding environment is critical in both normal and pathological settings. Extracellular vesicles (EVs), which facilitate the horizontal transfer of molecules between cells, are recognized as an important constituent of cell-cell communication. In cancer, alterations in EV secretion contribute to the growth and metastasis of tumor cells. However, the mechanisms underlying these changes remain largely unknown. Here, we show that centrosome amplification is associated with and sufficient to promote small extracellular vesicle (SEV) secretion in pancreatic cancer cells. This is a direct result due of lysosomal dysfunction, caused by increased reactive oxygen species (ROS) downstream of extra centrosomes. Defects in lysosome function promotes multivesicular body fusion with the plasma membrane, thereby enhancingSEV secretion. Furthermore, we find thatSEVs secreted in response to amplified centrosomes are functionally distinct and activate pancreatic stellate cells (PSCs). These activated PSCs promote the invasion of pancreatic cancer cells in heterotypic 3-D cultures. We propose thatSEVs secreted by cancer cells with amplified centrosomes influence the bidirectional communication between the tumor cells and the surrounding stroma to promote malignancy.
No evidence for prolactin’s involvement in the post-ejaculatory refractory period
Authors: Valente Susana , Marques Tiago , Lima Susana Q. 
Published: August 2020

AbstractIn many species, ejaculation is followed by a state of decreased sexual motivation, the post-ejaculatory refractory period. Several lines of evidence have suggested prolactin, a pituitary hormone released around the time of ejaculation in humans and other animals, to be a decisive player in the establishment of the refractory period. However, data supporting this hypothesis is controversial. We took advantage of two different strains of house mouse, a wild derived and a classical laboratory strain, that differ substantially in their sexual behavior, to investigate prolactin’s involvement in sexual motivation and the refractory period. First, we show that there is prolactin release during sexual behavior in male mice. Second, using a pharmacological approach, we show that acute manipulations of prolactin levels, either mimicking the natural release during sexual behavior or inhibiting its occurrence, do not affect sexual motivation or shorten the refractory period, respectively. Therefore, we show compelling evidence refuting the idea that prolactin released during copulation is involved in the establishment of the refractory period, a long-standing hypothesis in the field of behavioral endocrinology.
Transcranial Magnetic stimulation (TMS) modulates functional activity of SH-SY5Y cells: An in vitro model provides support for assumed excitability changes
Authors: Thomson Alix C. , de Graaf Tom A. , Schuhmann Teresa , Kenis Gunter , Sack Alexander T. , Rutten Bart P.F. 
Published: August 2020

AbstractRepetitive Transcranial Magnetic Stimulation (rTMS) is an established neuromodulation technique, using electromagnetic pulses that, depending on the precise parameters, are assumedto lead to lasting neural excitability changes. rTMS has widespread applications in both research and therapy, where it has been FDA approved and is considered a first-line treatment for depression, according to recent North American and European guidelines. However, these assumed excitability effects are often difficult to replicate, and highly unreliable on the single subject/patient level. Given the increasing application of rTMS, especially in clinical practice, the absence of a method to unequivocally determine effects of rTMS on human neuronal excitability is problematic. We have taken a first step in addressing this bottleneck, by administering excitatory and inhibitory rTMS protocols, iTBS and cTBS, to a humanin vitroneuron model; differentiated SH-SY5Y cells. We use live calcium imaging to assess changes in neural activity following stimulation, through quantifying fluorescence response to chemical depolarization. We found that iTBS and cTBS have opposite effects on fluorescence response; with iTBS increasing and cTBS decreasing response to chemical depolarization. Our results are promising, as they provide a clear demonstration of rTMS after-effects in a living human neuron model. We here present an in-vitro live calcium imaging setup that can be further applied to more complex human neuron models, for developing and evaluating subject/patient-specific brain stimulation protocols.
Gender (im)balance in citation practices in cognitive neuroscience
Authors: Fulvio Jacqueline M. , Akinnola Ileri , Postle Bradley R. 
Published: August 2020

AbstractIn the field of neuroscience, despite the fact that the proportion of peer-reviewed publications authored by women has increased in recent decades, the proportion of citations of women-led publications has not seen a commensurate increase: In five broad-scope journals, citations of papers first- and/or last-authored by women have been shown to be fewer than would be expected if gender was not a factor in citation decisions (Dworkin et al., 2020). Given the important implications that such underrepresentation may have on the careers of women researchers, it is important to determine whether this same trend is true in subdisciplines of the field, where interventions might be more effective. Here, we report the results of an extension of the analyses carried out by Dworkin et al. (2020) to citation patterns in the Journal of Cognitive Neuroscience (JoCN). The results indicate that the underrepresentation of women-led publications in reference sections is also characteristic of papers published inJoCNover the past decade. Furthermore, this pattern of citation imbalances is present for all gender classes of authors, implicating systemic factors. These results contribute to the growing body of evidence that intentional action is needed to address inequities in the way that we carry out and communicate our science.
Extreme Y chromosome polymorphism corresponds to five male reproductive morphs
Authors: Sandkam Benjamin A , Almeida Pedro , Darolti Iulia , Furman Benjamin , van der Bijl Wouter , Morris Jake , Bourne Godfrey , Breden Felix , Mank Judith E. 
Published: August 2020

AbstractSex chromosomes form once recombination is halted between the X and Y chromosomes. This loss of recombination quickly depletes Y chromosomes of functional content and genetic variation, which is thought to severely limit their potential to generate adaptive diversity. We examined Y diversity inPoecilia parae, where males occur as one of five discrete morphs, all of which shoal together in natural populations where morph frequency has been stable for over 50 years. Each morph utilizes different complex reproductive strategies, and differ dramatically from each other in color, body size, and mating behavior. Remarkably, morph phenotype is passed perfectly from father to son, indicating there are five Y haplotypes segregating in the species, each of which encodes the complex male morph characteristics. Using linked-read sequencing on multipleP. paraefemales and males of all five morphs from natural populations, we found that the genetic architecture of the male morphs evolved on the Y chromosome long after recombination suppression had occurred with the X. Comparing Y chromosomes between each of the morphs revealed that although the Ys of the three minor morphs that differ predominantly in color are highly similar, there are substantial amounts of unique genetic material and divergence between the Ys of the three major morphs that differ in reproductive strategy, body size and mating behavior. Taken together, our results reveal the extraordinary ability of evolution to overcome the constraints of recombination loss to generate extreme diversity resulting in five discrete Y chromosomes that control complex reproductive strategies.Significance StatementThe loss of recombination on the Y chromosome is thought to limit the adaptive potential of this unique genomic region. Despite this, we describe an extraordinary case of Y chromosome adaptation inPoecilia parae. This species contains five co-occurring male morphs, all of which are Y-linked, and which differ in reproductive strategy, body size, coloration, and mating behavior. The five Y-linked male morphs ofP. paraeevolved after recombination was halted on the Y, resulting in five unique Y chromosomes within one species. Our results reveal the surprising magnitude to which non-recombining regions can generate adaptive diversity and have important implications for the evolution of sex chromosomes and the genetic control of sex-linked diversity.
Hemagglutination byB. fragilisis mediated by capsular polysaccharides and is influenced by host ABO blood type
Authors: Arnolds Kathleen L. , Moreno-Huizar Nancy , Stanislawski Maggie A. , Palmer Brent , Lozupone Catherine 
Published: August 2020

Bacterial hemagglutination of red blood cells (RBCs) is mediated by interactions between bacterial cell components and RBC envelope glycans that vary across individuals by ABO blood type. ABO glycans are also expressed on intestinal epithelial cells and in most individuals secreted into the intestinal mucosa, indicating that hemagglutination by bacteria may be informative about bacteria-host interactions in the intestine.Bacteroides fragilis, a prominent member of the human gut microbiota, can hemagglutinate RBCs by an unknown mechanism. Using a novel technology for quantifying bacterial hemagglutination, genetic knockout strains ofB. fragilisand blocking antiserums, we demonstrate that the capsular polysaccharides ofB. fragilis, polysaccharide B (PSB), and PSC are both strong hemagglutinins. Furthermore, the capacity ofB. fragilisto hemagglutinate was much stronger in individuals with Type O blood compared to Types A and B, an adaptation that could impact the capacity ofB. fragilisto colonize and thrive in the host.Importance StatementThis study found that the human pathobiont,B.fragilis, hemagglutinates human red blood cells using specific capsular polysaccharides (PSB and PSC) which are known to be important for interacting with and influencing host immune responses. Because the factors found on red blood cells are also abundantly expressed on other tissues and in the mucous, the ability to hemagglutinate sheds light on interactions between bacteria and host throughout the body. Intriguingly, the strength of hemagglutination varied based on the ABO blood type of the host, a finding which could have implications for understanding if an individual’s blood type may influence interactions withB.fragilisand its potential as a pathogen versus a commensal.
CD300lf conditional knockout mouse reveals strain-specific cellular tropism for murine norovirus
Authors: Graziano Vincent R. , Alfajaro Mia Madel , Schmitz Cameron O. , Filler Renata B. , Strine Madison S. , Wei Jin , Hsieh Leon L. , Baldridge Megan T. , Nice Timothy J. , Lee Sanghyun , Orchard Robert C. , Wilen Craig B. 
Published: August 2020

ABSTRACTNoroviruses are a leading cause of gastrointestinal infection in humans and mice. Understanding human norovirus (HuNoV) cell tropism has important implications for our understanding of viral pathogenesis. Murine norovirus (MNoV) is extensively used as a surrogate model for HuNoV. We previously identified CD300lf as the receptor for MNoV. Here, we generated aCd300lfconditional knockout (CD300lfF/F) mouse to elucidate the cell tropism of persistent and non-persistent strains of murine norovirus. Using this mouse model, we demonstrate that CD300lf expression on intestinal epithelial cells (IECs), and on tuft cells in particular, is essential for transmission of the persistent MNoV strain CR6 (MNoVCR6)in vivo. In contrast, the nonpersistent MNoV strain CW3 (MNoVCW3) does not require CD300lf expression on IECs for infection. However, deletion of CD300lf in myelomonocytic cells (LysM Cre+)partially reduces CW3 viral load in lymphoid and intestinal tissues. Disruption of CD300lf expression on B cells (CD19 Cre), neutrophils (Mrp8 Cre), and dendritic cells (CD11c Cre) did not affect CW3 viral RNA levels. Finally, we show that the transcription factor STAT1, which is critical for the innate immune response, partially restricts the cell tropism of MNoVCW3to LysM+ cells. Taken together, these data demonstrate that CD300lf expression on tuft cells is essential for MNoVCR6, that myelomonocytic cells are a major, but not exclusive, target cell of MNoVCW3, and that STAT1 signaling restricts the cellular tropism of MNoVCW3. This provides the first genetic system to study the cell type-specific role of CD300lf in norovirus pathogenesis.IMPORTANCEHuman noroviruses (HuNoVs) are a leading cause of gastroenteritis resulting in up to 200,000 deaths each year. The receptor and cell tropism of HuNoV in immunocompetent humans are unclear. We use murine norovirus (MNoV) as a model for HuNoV. We recently identified CD300lf as the sole physiologic receptor for MNoV. Here, we leverage this finding to generate aCd300lfconditional knockout mouse to decipher the contributions of specific cell types to MNoV infection. We demonstrate that persistent MNoVCR6requires CD300lf expression on tuft cells. In contrast, multiple CD300lf+ cell types, dominated by myelomonocytic cells, are sufficient for non-persistent MNoVCW3infection. CD300lf expression on epithelial cells, B cells, neutrophils, and dendritic cells is not critical for MNoVCW3infection. Mortality associated with MNoVCW3strain inStat1-/-mice does not require CD300lf expression on LysM+ cells, highlighting that both CD300lf receptor expression and innate immunity regulate MNoV cell tropismin vivo.
Conformational ordering of intrinsically disordered peptides for targeting translation initiation
Authors: Brown Christopher J , Verma Chandra S , Lane David P , Lama Dilraj 
Published: August 2020

AbstractIntrinsically disordered regions (IDRs) in proteins can regulate their activity by facilitating protein-protein interactions (PPIs) as exemplified in the recruitment of the eukaryotic translation initiation factor 4E (eIF4E) protein by the protein eIF4G. Deregulation of this PPI module is central to a broad spectrum of cancer related malignancies and its targeted inhibition through bioactive peptides is a promising strategy for therapeutic intervention. We have employed a structure-guided approach to rationally develop peptide derivatives from the intrinsically disordered eIF4G scaffold by incorporating non-natural amino acids that facilitates disorder-to-order transition. The conformational heterogeneity of these peptides and the degree of structural reorganization required to adopt the optimum mode of interaction with eIF4E underscores their differential binding affinities. The presence of a pre-structured local helical element in the ensemble of structures was instrumental in the efficient docking of the peptides on to the protein surface. These insights were exploited to further design features into the peptide to propagate bound-state conformations in solution which resulted in the generation of a potent eIF4E binder. The study illustrates the molecular basis of eIF4E recognition by a disordered epitope from eIF4G and its modulation to generate peptides that can potentially attenuate translation initiation in oncology.
Development of a high-throughput homogeneous AlphaLISA drug screening assay for the detection of SARS-CoV-2 Nucleocapsid
Authors: Gorshkov Kirill , Chen Catherine Z. , de la Torre Juan Carlos , Martinez-Sobrido Luis , Moran Thomas , Zheng Wei 
Published: August 2020

AbstractThe coronavirus disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is in urgent need of therapeutic options. High-throughput screening (HTS) offers the research field an opportunity to rapidly identify such compounds. In this work, we have developed a homogeneous cell-based HTS system using AlphaLISA detection technology for the SARS-CoV-2 nucleocapsid protein (NP). Our assay measures both recombinant NP and endogenous NP from viral lysates and tissue culture supernatants (TCS) in a sandwich-based format using two monoclonal antibodies against the NP analyte. Viral NP was detected and quantified in both tissue culture supernatants and cell lysates, with large differences observed between 24 hours and 48 hours of infection. We simulated the viral infection by spiking in recombinant NP into 384-well plates with live Vero-E6 cells and were able to detect the NP with high sensitivity and a large dynamic range. Anti-viral agents that inhibit either viral cell entry or replication will decrease the AlphaLISA NP signal. Thus, this assay can be used for high-throughput screening of small molecules and biologics in the fight against the COVID-19 pandemic.
3D mapping reveals a complex and transient interstitial matrix during murine renal development
Authors: Lipp Sarah N. , Jacobson Kathryn R. , Hains David S. , Schwarderer Andrew L. , Calve Sarah 
Published: August 2020

AbstractBackgroundThe extracellular matrix (ECM) is a network of proteins and glycosaminoglycans that provides structural and biochemical cues to cells. In the kidney, the ECM is critical for nephrogenesis; however, the dynamics of ECM composition and how it relates to 3D structure during development is unknown.MethodsUsing embryonic day (E)14.5, E18.5, postnatal day (P)3, and adult kidneys, we fractionated proteins based on differential solubilities, performed liquid chromatography tandem-mass spectrometry, and identified changes in ECM protein content (matrisome). Decellularized kidneys were stained for ECM proteins and imaged in 3D using confocal microscopy.ResultsWe observed an increase in interstitial ECM that connect the stromal mesenchyme to the basement membrane (TNXB, COL6A1, COL6A2, COL6A3) between the embryo and adult, and a transient elevation of interstitial matrix proteins (COL5A2, COL12A1, COL26A1, ELN, EMID1, FBN1, LTBP4, THSD4) at perinatal timepoints. Basement membrane proteins critical for metanephric induction (FRAS1, FREM2) were highest in the embryo, whereas proteins necessary for glomerular basement membrane integrity (COL4A3, COL4A4, COL4A5, LAMB2) were more abundant in the adult. 3D visualization revealed a complex interstitial matrix that dramatically changed over development, including the perinatal formation of fibrillar structures that appear to support the medullary rays.ConclusionBy correlating 3D ECM spatiotemporal organization with global protein abundance, we identified novel changes in the interstitial matrix during kidney development. This new information regarding the ECM in developing kidneys offers the potential to inform the design of regenerative scaffolds that can guide nephrogenesisin vitro.Significance statementEnd-stage renal disease is increasing and there are a limited number of organs available for transplantation. Therefore, researchers have focused on understanding how cellular signaling influences kidney development to expand strategies to rebuild a kidney. However, the extracellular matrix (ECM), another critical component that biomechanically regulates nephrogenesis, has been largely neglected. This paper combines proteomics and 3D imaging of the murine kidney to resolve previously undescribed dynamics of the interstitial matrix in the cortex and corticomedullary junction during development. Combined with cell and growth factors, scaffolds modeled after the composition and organization of the developmental ECM have the potential to improve tissue engineering models of the kidney, like organoids.