bluuebunny/crossref_metadata_2025_split huggingface dataset:
FB5P-seq: FACS-based 5-prime end single-cell RNAseq for integrative analysis of transcriptome and antigen receptor repertoire in B and T cells
Authors: Attaf-Bouabdallah Noudjoud , Cervera-Marzal Iñaki , Dong Chuang , Gil Laurine , Renand Amédée , Spinelli Lionel , Milpied Pierre 
Published: October 2019

AbstractSingle-cell RNA sequencing (scRNA-seq) allows the identification, characterization, and quantification of cell types in a tissue. When focused on B and T cells of the adaptive immune system, scRNA-seq carries the potential to track the clonal lineage of each analyzed cell through the unique rearranged sequence of its antigen receptor (BCR or TCR, respectively), and link it to the functional state inferred from transcriptome analysis. Here we introduce FB5P-seq, a FACS-based 5’-end scRNA-seq method for cost-effective integrative analysis of transcriptome and paired BCR or TCR repertoire in phenotypically defined B and T cell subsets. We describe in details the experimental workflow and provide a robust bioinformatics pipeline for computing gene count matrices and reconstructing repertoire sequences from FB5P-seq data. We further present two applications of FB5P-seq for the analysis of human tonsil B cell subsets and peripheral blood antigen-specific CD4 T cells. We believe our novel integrative scRNA-seq method will be a valuable option to study rare adaptive immune cell subsets in immunology research.
Insights from a survey-based analysis of the academic job market
Authors: Fernandes Jason D. , Sarabipour Sarvenaz , Smith Christopher T. , Niemi Natalie M. , Jadavji Nafisa M. , Kozik Ariangela J. , Holehouse Alex S. , Pejaver Vikas , Symmons Orsolya , Bisson Filho Alexandre W. , Haage Amanda 
Published: October 2019

AbstractApplying for a faculty position is a critical phase of many postdoctoral careers, but most postdoctoral researchers in STEM fields enter the academic job market with little knowledge of the process and expectations. A lack of data has made it difficult for applicants to assess their qualifications relative to the general applicant pool and for institutions to develop effective hiring policies. We analyzed responses to a survey of faculty job applicants between May 2018 and May 2019. We establish various background scholarly metrics for a typical faculty applicant and present an analysis of the interplay between those metrics and hiring outcomes. Traditional benchmarks of a positive research track record above a certain threshold of qualifications were unable to completely differentiate applicants with and without offers. Our findings suggest that there is no single clear path to a faculty job offer and that metrics such as career transition awards and publications in high impact factor journals were neither necessary nor sufficient for landing a faculty position. The applicants perceived the process as unnecessarily stressful, time-consuming, and largely lacking in feedback, irrespective of a successful outcome. Our findings emphasize the need to improve the transparency of the faculty job application process. In addition, we hope these and future data will help empower trainees to enter the academic job market with clearer expectations and improved confidence.
Degradation of the repetitive genomic landscape in a close relative ofC. elegans
Authors: Woodruff Gavin C. , Teterina Anastasia A. 
Published: October 2019

AbstractThe abundance, diversity, and genomic distribution of repetitive elements is highly variable among species. These patterns are thought to be driven in part by reproductive mode and the interaction of selection and recombination, and recombination rates typically vary by chromosomal position. In the nematodeC. elegans,repetitive elements are enriched at chromosome arms and depleted on centers, and this mirrors the chromosomal distributions of other genomic features such as recombination rate. How conserved is this genomic landscape of repeats, and what evolutionary forces maintain it? To address this, we compared the genomic organization of repetitive elements across fiveCaenorhabditisspecies with chromosome-level assemblies. As previously reported, repeat content is enriched on chromosome arms in mostCaenorhabditisspecies, and no obvious patterns of repeat content associated with reproductive mode were observed. However, the fig-associatedCaenorhabditis inopinatahas experienced rampant repetitive element expansion and reveals no association of global repeat content with chromosome position. Patterns of transposable element superfamily-specific distributions reveal this global pattern is driven largely by a few transposable element superfamilies that inC. inopinatahave expanded in number and have weak associations with chromosome position. Additionally, 15% of predicted protein-coding genes inC. inopinataalign to transposon-related proteins. When these are excluded, C. inopinatahas no enrichment of genes in chromosome centers, in contrast to its close relatives who all have such clusters. Forward evolutionary simulations reveal that chromosomal heterogeneity in recombination rate is insufficient for generating structured genomic repetitive landscapes. Instead, heterogeneity in the fitness effects of transposable element insertion is needed to promote heterogeneity in repetitive landscapes. Thus, patterns of gene density along chromosomes are likely drivers of global repetitive landscapes in this group, although other historical or genomic factors are needed to explain the idiosyncrasy of genomic organization of various transposable element taxa withinC. inopinata.Taken together, these results highlight the power of comparative genomics and evolutionary simulations in testing hypotheses regarding the causes of genome organization.
Foreign body responses in central nervous system mimic natural wound responses and alter biomaterial functions
Authors: O’Shea Timothy M. , Wollenberg Alexander L. , Kim Jae H. , Ao Yan , Deming Timothy J. , Sofroniew Michael V. 
Published: October 2019

AbstractBiomaterials hold promise for diverse therapeutic applications in the central nervous system (CNS). Little is known about molecular factors that determine CNS foreign body responses (FBRs)in vivo, or about how such responses influence biomaterial function. Here, we probed these factors using a platform of injectable hydrogels readily modified to present interfaces with different representative physiochemical properties to host cells. We show that biomaterial FBRs mimic specialized multicellular CNS wound responses not present in peripheral tissues, which serve to isolate damaged neural tissue and restore barrier functions. Moreover, we found that the nature and intensity of CNS FBRs are determined by definable properties. For example, cationic, anionic or nonionic interfaces with CNS cells elicit quantifiably different levels of stromal cell infiltration, inflammation, neural damage and amyloid production. The nature and intensity of FBRs significantly influenced hydrogel resorption and molecular delivery functions. These results characterize specific molecular mechanisms that drive FBRs in the CNS and have important implications for developing effective biomaterials for CNS applications.
Small molecule activation of metabolic enzyme pyruvate kinase muscle isozyme 2, PKM2, provides photoreceptor neuroprotection
Authors: Wubben Thomas J. , Pawar Mercy , Weh Eric , Smith Andrew , Sajjakulnukit Peter , Zhang Li , Dai Lipeng , Hager Heather , Pai Manjunath P. , Lyssiotis Costas A. , Besirli Cagri G. 
Published: October 2019

AbstractPhotoreceptor cell death is the ultimate cause of vision loss in many retinal disorders, and there is an unmet need for neuroprotective modalities to improve photoreceptor survival. Similar to cancer cells, photoreceptors maintain pyruvate kinase muscle isoform 2 (PKM2) expression, which is a critical regulator in aerobic glycolysis. Unlike PKM1, which has constitutively high catalytic activity, PKM2 is under complex regulation. Recently, we demonstrated that genetically reprogramming photoreceptor metabolism via PKM2-to-PKM1 substitution is a promising neuroprotective strategy. Here, we explored the neuroprotective effects of pharmacologically activating PKM2 via ML-265, a small molecule activator of PKM2, during acute outer retinal stress. We found that ML-265 increased PKM2 activity in 661W cells and in vivo in rat eyes without affecting the expression of genes involved in glucose metabolism. ML-265 treatment did, however, alter metabolic intermediates of glucose metabolism and those necessary for biosynthesis in cultured cells. Long-term exposure to ML-265 did not result in decreased photoreceptor function or survival under baseline conditions. Notably, though, ML-265-treatment did reduce entrance into the apoptotic cascade in in vitro and in vivo models of outer retinal stress. These data suggest that reprogramming metabolism via activation of PKM2 is a novel, and promising, therapeutic strategy for photoreceptor neuroprotection.
Landscape of Dysregulated Placental RNA Editing Associated with Preeclampsia
Authors: Yang Xiaoxue , Yang Jing , Liang Xiaozhen , Chen Qian , Jiang Sijia , Liu Haihua , Gao Yue , Ren Zhonglu , Yu Yanhong , Zhong Mei , Yang Xinping 
Published: October 2019

AbstractDysregulated RNA editing is well documented in several diseases such as cancer. The extent to which RNA editing might be involved in diseases originated in the placenta remains unknown, because RNA editing has rarely been studied in the placenta. Here, we have systematically profiled RNA editome on the placentae from 9 patients with early-onset severe preeclampsia (EOSPE) and 32 normal subjects, and a widespread RNA editing dysregulation in EOSPE has been identified. The mis-edited gene set is enriched with known preeclampsia-associated genes and differentially expressed genes in EOSPE. The “RNA editing events” at two microRNA binding sites in 3’-UTR of the LEP mRNA were generated, which could lead to increased expression level of LEP in trophoblast cells. Upregulation of LEP were also observed in the placentae of PE patients. These results suggest that widespread placental RNA editing may be involved in placental development and dysregulation of RNA editing in the placenta may contribute to the pathogenesis of preeclampsia.
A Quantitative Proteome Map of the Human Body
Authors: Jiang Lihua , Wang Meng , Lin Shin , Jian Ruiqi , Li Xiao , Chan Joanne , Fang Huaying , Dong Guanlan ,   GTEx Consortium, Tang Hua , Snyder Michael P. 
Published: October 2019

AbstractDetermining protein levels in each tissue and how they compare with RNA levels is important for understanding human biology and disease as well as regulatory processes that control protein levels. We quantified the relative protein levels from 12,627 genes across 32 normal human tissue types prepared by the GTEx project. Known and new tissue specific or enriched proteins (5,499) were identified and compared to transcriptome data. Many ubiquitous transcripts are found to encode highly tissue specific proteins. Discordance in the sites of RNA expression and protein detection also revealed potential sites of synthesis and action of protein signaling molecules. Overall, these results provide an extraordinary resource, and demonstrate that understanding protein levels can provide insights into metabolism, regulation, secretome, and human diseases.SummaryQuantitative proteome study of 32 human tissues and integrated analysis with transcriptome data revealed that understanding protein levels could provide in-depth knowledge to post transcriptional or translational regulations, human metabolism, secretome, and diseases.
Disentangling the Behavioural Variability of Confined Cell Migration
Authors: Brückner David B. , Fink Alexandra , Rädler Joachim O. , Broedersz Chase P. 
Published: October 2019

AbstractCell-to-cell variability is inherent to numerous biological processes, including cell migration. Quantifying and characterizing the variability of migrating cells is challenging, as it requires monitoring many cells for long time windows under identical conditions. Here, we observe the migration of single human breast cancer cells (MDA-MB-231) in confining two-state micropatterns. To describe the stochastic dynamics of this confined migration, we employ a dynamical systems approach. We identify statistics to measure the behavioural variance of the migration, which significantly exceed those predicted by a population-averaged stochastic model. This additional variance can be explained by the combination of an ‘aging’ process and population heterogeneity. To quantify population heterogeneity, we decompose the cells into subpopulations of slow and fast cells, revealing the presence of distinct classes of dynamical systems describing the migration, ranging from bistable to limit cycle behaviour. Our findings highlight the breadth of migration behaviours present in cell populations.
Complex roles for reactive astrocytes in the triple transgenic mouse model of Alzheimer disease
Authors: Guillemaud Océane , Ceyzériat Kelly , Saint-Georges Thomas , Cambon Karine , Petit Fanny , Ben Haim Lucile , Carrillo-de Sauvage Maria-Angeles , Guillermier Martine , Bernier Sueva , Hérard Anne-Sophie , Joséphine Charlène , Pierre Bémelmans Alexis , Brouillet Emmanuel , Hantraye Philippe , Bonvento Gilles , Escartin Carole 
Published: October 2019

ABSTRACTIn Alzheimer disease (AD), astrocytes undergo complex changes and become reactive. The consequences of this reaction are still unclear. To evaluate the net impact of reactive astrocytes in AD, we recently developed viral vectors targeting astrocytes that either activate or inhibit the JAK2-STAT3 pathway, a central cascade controlling astrocyte reaction.We aimed to evaluate whether reactive astrocytes contribute to Tau as well as amyloid pathologies in the hippocampus of 3xTg-AD mice, an AD model that develops Tau hyperphosphorylation and aggregation in addition to amyloid deposition. JAK2-STAT3 pathway-mediated modulation of reactive astrocytes in the hippocampus of 3xTg-AD mice, did not significantly influence Tau phosphorylation or amyloid processing and deposition, at early, advanced and terminal stage of the disease. Interestingly, inhibition of the JAK2-STAT3 pathway in hippocampal astrocytes did not improve short-term spatial memory in the Y maze but it reduced anxiety in the elevated plus maze. Our unique approach to specifically manipulate reactive astrocytes in situ show these cells may impact behavioral outcomes without influencing Tau or amyloid pathology.
Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape
Authors: Nguyen Bryan N. , Shen Elaine W. , Seemann Janina , Correa Adrienne M.S. , O’Donnell James L. , Altieri Andrew H. , Knowlton Nancy , Crandall Keith A. , Egan Scott P. , McMillan W. Owen , Leray Matthieu 
Published: October 2019

AbstractAccurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition, but most studies to date have evaluated its effectiveness in single habitats and for conspicuous taxonomic groups in temperate ecosystems. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07% of the taxa detected by a broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean.
Fatty acid bioconversion in harpacticoid copepods in a changing environment: a transcriptomic approach
Authors: Boyen Jens , Fink Patrick , Mensens Christoph , Hablützel Pascal I. , De Troch Marleen 
Published: October 2019

AbstractBy 2100, global warming is predicted to significantly reduce the capacity of marine primary producers for long-chain polyunsaturated fatty acid (LC-PUFA) synthesis. Primary consumers such as harpacticoid copepods (Crustacea) might mitigate the resulting adverse effects on the food web by increased LC-PUFA bioconversion. Here, we present a high-quality de novo transcriptome assembly of the copepod Platychelipus littoralis, exposed to changes in both temperature (+3°C) and dietary LC-PUFA availability. Using this transcriptome, we detected multiple transcripts putatively encoding for LC-PUFA-bioconverting front-end fatty acid desaturases and elongases, and performed phylogenetic analyses to identify their relationship with sequences of other (crustacean) taxa. While temperature affected the absolute fatty acid concentrations in copepods, LC-PUFA levels remained unaltered even when copepods were fed a LC-PUFA-deficient diet. While this suggests plasticity of LC-PUFA bioconversion within P. littoralis, none of the putative front-end desaturase or elongase transcripts were differentially expressed under the applied treatments. Nevertheless, the transcriptome presented here provides a sound basis for future ecophysiological research on harpacticoid copepods.
A sub-exponential branching process to study early epidemic dynamics with application to Ebola
Authors: Zarebski Alexander E. , Moss Robert , McCaw James M. 
Published: October 2019

AbstractExponential growth is a mathematically convenient model for the early stages of an outbreak of an infectious disease. However, for many pathogens (such as Ebola virus) the initial rate of transmission may be sub-exponential, even before transmission is affected by depletion of susceptible individuals.We present a stochastic multi-scale model capable of representing sub-exponential transmission: an in-homogeneous branching process extending the generalised growth model. To validate the model, we fit it to data from the Ebola epidemic in West Africa (2014–2016). We demonstrate how a branching process can be fit to both time series of confirmed cases and chains of infection derived from contact tracing. Our estimates of the parameters suggest transmission of Ebola virus was sub-exponential during this epidemic. Both the time series data and the chains of infections lead to consistent parameter estimates. Differences in the data sets meant consistent estimates were not a foregone conclusion. Finally, we use a simulation study to investigate the properties of our methodology. In particular, we examine the extent to which the estimates obtained from time series data and those obtained from chains of infection data agree.Our method, based on a simple branching process, is well suited to real-time analysis of data collected during contact tracing. Identifying the characteristic early growth dynamics (exponential or sub-exponential), including an estimate of uncertainty, during the first phase of an epidemic should prove a useful tool for preliminary outbreak investigations.Author SummaryEpidemic forecasts have the potential to support public health decision making in outbreak scenarios for diseases such as Ebola and influenza. In particular, reliable predictions of future incidence data may guide surveillance and intervention responses. Existing methods for producing forecasts, based upon mechanistic transmission models, often make an implicit assumption that growth is exponential, at least while susceptible depletion remains negligible. However, empirical studies suggest that many infectious disease outbreaks display sub-exponential growth early in the epidemic. Here we introduce a mechanistic model of early epidemic growth that allows for sub-exponential growth in incidence. We demonstrate how the model can be applied to the types of data that are typically available in (near) real-time, including time series data on incidence as well as individual-level case series and chains of transmission data. We apply our methods to publically available data from the 2014–2016 West Africa Ebola epidemic and demonstrate that early epidemic growth was sub-exponential. We also investigate the statistical properties of our model through a simulation re-estimation study to identify it performance characteristics and avenues for further methodological research.
Overlapping and distinct roles of CDPK family members in the pre-erythrocytic cycle of the rodent malaria parasite, Plasmodium berghei
Authors: Govindasamy K. , Bhanot P. 
Published: October 2019

AbstractInvasion of, development within, and exit from hepatocytes by Plasmodium is essential for the parasite to establish the malaria-causing erythrocytic cycle. Identification of signaling pathways that operate during the pre-erythrocytic cycle provides insights into a critical stage of infection and potential targets for chemoprevention of disease. Calcium Dependent Protein Kinases (CDPK) represent a kinase family that is present in Plasmodium but absent in mammals. We demonstrate that P. berghei homologs of CDPK1, CDPK4 and CDPK5 play overlapping but distinct roles in sporozoite invasion and parasite egress from hepatocytes. All three kinases are expressed in sporozoites. All three are required for optimal motility of sporozoites and consequently their invasion of hepatocytes. Increased cGMP compensates for the functional loss of CDPK1 and CDPK5 during sporozoite invasion but cannot overcome CDPK4’s loss. CDPK1 and CDPK5 expression is downregulated after sporozoite invasion. CDPK5 reappears in a subset of late stage liver stages and is present in all merosomes. Chemical inhibition of CDPK4 and depletion of CDPK5 in liver stages suggests that these kinases play a role in the formation and/or release of merosomes from mature liver stages. Furthermore, depletion of CDPK5 in merosomes significantly delays a merosome-initiated erythrocytic cycle without affecting the infectivity of hepatic merozoites. These data suggest that CDPK5 is required for the release of hepatic merozoites from merosomes. Our work provides the first evidence that sporozoite invasion requires CDPK1 and CDPK5 and that the release of hepatic merozoites is a regulated process.SignificanceThe malaria-parasite Plasmodium begins its mammalian cycle by infecting hepatocytes in the liver. A single parasite differentiates into tens of thousands of hepatic merozoites which exit the host cell in vesicles called merosomes. Hepatic merozoites initiate the first round of erythrocytic infection that leads to disease symptoms. We show that optimal invasion of liver cells by Plasmodium requires the action of three closely-related parasite kinases, CDPK1, 4 and 5. Loss of any of the three enzymes in the parasite significantly reduces infection of liver cells. CDPK5 is also required for the release of hepatic merozoites from merosomes and therefore for initiating the erythrocytic cycle. A better understanding of how these kinases function could lead to drugs that prevent malaria.