bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ouabain enhances cell-cell adhesion mediated by β1-subunits of the Na+,K+-ATPase in CHO fibroblasts
Authors: Vilchis-Nestor Claudia Andrea , Roldán María Luisa , Padilla-Benavides Teresita , Shoshani Liora 
Published: February 2019

AbstractAdhesion is an important characteristic of epithelial cells to provide a crucial barrier to pathogens and substances. In polarized epithelial cells, cell-adhesion depends on tight junctions, adherent junctions and the Na+,K+-ATPase. All these are located in the basolateral membrane of the cells. The hormone ouabain, a cardiotonic steroid, binds to the α subunit of the Na+,K+-ATPase, and inhibits the pump activity when used at above μM concentrations. At physiological nM concentrations, ouabain affects the adhesive properties of epithelial cells by inducing the expression of cell adhesion molecules through activation of signaling pathways associated to the α subunit. Our group showed that non-adherent CHO cells transfected with the canine β1subunit become adhesive, and that homotypic interactions between β1subunits of the Na+,K+-ATPase occur between neighboring epithelial cells. Therefore, in this study we investigated whether the adhesion between β1subunits was also affected by ouabain. We used CHO fibroblasts stably expressing the β1subunit of the Na+,K+-ATPase (CHO-β1) and studied the effect of ouabain on cell adhesion. Aggregation assays showed that ouabain increased the adhesion between CHO-β1cells. Immunofluorescence and biotinylation assays showed that ouabain (50 nM) increases the expression of the β1 subunit of the Na+,K+-ATPase at the cell membrane. We also screened the effect of ouabain on activation of signaling pathways in CHO-β1cells, and their effect on cell adhesion. We found that c-Src, is activated by ouabain and is therefore likely to regulate the adhesive properties of CHO-β1cells. Collectively, our findings suggest that the β1subunits adhesion is modulated by the levels of expression and activation of the Na+,K+-ATPase at the plasma membrane, which is regulated by ouabain.
An Interscholastic Network to Generate LexA Enhancer Trap Lines inDrosophila
Authors: Kockel Lutz , Griffin Catherine , Ahmed Yaseen , Fidelak Lauren , Rajan Arjun , Gould Ethan P. , Haigney Miles , Ralston Benjamin , Tercek Rex J. , Galligani Lara , Rao Sagar , Huq Lutfi , Bhargava Hersh K. , Dooner Ailis C. , Lemmerman Emily G. , Malusa Ruby F. , Nguyen Tran H. , Chung Julie S. , Gregory Sara M. , Kuwana Kiyomasa M. , Regenold Jonathan T. , Wei Alexander , Ashton Jake , Dickinson Patrick , Kim Steven , Martel Kate , Cai Connie , Chen Carissa , Price Stephen , Qiao Jeffrey , Shepley David , Zhang Joanna , Chalasani Meghana , Nguyen Khanh , Aalto August , Kim ByungJun , Tazawa-Goodchild Erik , Sherwood Amanda , Rahman Ahmad , Wu Sum Ying Celeste , Lotzkar Joel , Michaels Serena , Aristotle Hillary , Clark Antigone , Gasper Grace , Xiang Evan , Schlör Frieda Luna , Lu Melissa , Haering Kate , Friberg Julia , Kuwana Alyssa , Lee Jonathan , Liu Alan , Norton Emma , Hamad Leena , Lee Clara , Okeremi Dara , diTullio Harry , Dumoulin Kat , Chi Sun Yu Gordon , Derossi Grayson S. , Horowitch Rose E. , Issa Elias C. , Le Dan T. , Morales Bryce C. , Noori Ayush , Shao Justin , Cho Sophia , Hoang Mai N. , Johnson Ian M. , Lee Katherine C. , Lee Maria , Madamidola Elizabeth A. , Schmitt Katrina E. , Byan Gabriel , Park Taeyoung , Chen Jonathan , Monovoukas Alexi , Kang Madison J. , McGowan Tanner , Walewski Joseph J. , Simon Brennan , Zu Sophia J. , Miller Gregory P. , Fitzpatrick Kate B. , Lantz Nicole , Fox Elizabeth , Collette Jeanette , Kurtz Richard , Duncan Chris , Palmer Ryan , Rotondo Cheryl , Janicki Eric , Chisholm Townley , Rankin Anne , Park Sangbin , Kim Seung K. 
Published: February 2019

AbstractBinary expression systems like the LexA-LexAop system provide a powerful experimental tool kit to study gene and tissue function in developmental biology, neurobiology and physiology. However, the number of well-defined LexA enhancer trap insertions remains limited. In this study, we present the molecular characterization and initial tissue expression analysis of nearly 100 novel StanEx LexA enhancer traps, derived from theStonEx1index line. This includes 76 insertions into novel, distinct gene loci not previously associated with enhancer traps or targeted LexA constructs. Additionally, our studies revealed evidence for selective transposase-dependent replacement of a previously-undetectedKPelement on chromosome III within the StanEx1genetic background during hybrid dysgenesis, suggesting a molecular basis for the over-representation of LexA insertions at theNK7.1locus in our screen. Production and characterization of novel fly lines were performed by students and teachers in experiment-based genetics classes within a geographically diverse network of public and independent high schools. Thus, unique partnerships between secondary schools and university-based programs have produced and characterized novel genetic and molecular resources inDrosophilafor open-source distribution, and provide paradigms for development of science education through experience-based pedagogy.
Extraction-free direct PCR from dried serum spots permits HBV genotyping and RAS identification by Sanger and minION sequencing
Authors: Astbury Stuart , Costa Nunes Soares Marcia Maria Da , Peprah Emmanuel , King Barnabas , Gomes Jardim Ana Carolina , Shimizu Jacqueline Farinha , Jalal Paywast , Saeed Chiman H , Sabeer Furat T , Irving William L , Tarr Alexander W , McClure C Patrick 
Published: February 2019

AbstractIn order to achieve the commitment made by the World Health Organisation to eliminate viral hepatitis by 2030, it is essential that clinicians can obtain basic sequencing data for hepatitis B virus (HBV) infected patients. While accurate diagnosis of HBV is achievable in most clinical settings, genotyping and identification of resistance-associated substitutions (RAS) present a practical challenge in regions with limited healthcare and biotechnology infrastructure. Here we outline two workflows for generating clinically relevant HBV sequence data directly from dried serum spot (DSS) cards without DNA extraction using either Sanger, or the portable MinION sequencing platforms. Data obtained from the two platforms were highly consistent and allowed determination of HBV genotype and RAS. This is the first demonstration of MinION sequencing from DSS, illustrating the broad utility of this sequencing technology. We demonstrated the clinical application of this technology using sera sampled on DSS cards obtained from both Iraq and Brazil. The sample stability provided by DSS cards, combined with the rapid PCR and sequencing protocols will enable regional/national centres to provide information relevant to patient management. By providing viable workflows for both the Sanger and MinION sequencing platforms, which vary greatly in the infrastructure and expertise required, we demonstrate that MinION sequencing is a viable method for HBV genotyping in resource-limited settings. These workflows could also be applied to sequencing of other blood borne DNA viruses and bacterial pathogens.
Cell type specific transcriptional reprogramming of maize leaves duringUstilago maydisinduced tumor formation
Authors: Villajuana-Bonequi Mitzi , Matei Alexandra , Ernst Corinna , Hallab Asis , Usadel Björn , Doehlemann Gunther 
Published: February 2019

SummaryUstilago maydisis a biotrophic pathogen and well-established genetic model to understand the molecular basis of biotrophic interactions.U. maydissuppresses plant defense and induces tumors on all aerial parts of its host plant maize. In a previous study we found thatU. maydisinduced leaf tumor formation builds on two major processes: the induction of hypertrophy in the mesophyll and the induction of cell division (hyperplasia) in the bundle sheath. In this study we analyzed the cell-type specific transcriptome of maize leaves 4 days post infection. This analysis allowed identification of key features underlying the hypertrophic and hyperplasic cell identities derived from mesophyll and bundle sheath cells, respectively. We examined the differentially expressed (DE) genes with particular focus on maize cell cycle genes and found that three A-type cyclins, one B-, D- and T-type are upregulated in the hyperplasic tumorous cells, in which theU. maydiseffector protein See1 promotes cell division. Additionally, most of the proteins involved in the formation of the pre-replication complex (pre-RC, that assure that each daughter cell receives identic DNA copies), the transcription factors E2Fand DPa as well as several D-type cyclins are deregulated in the hypertrophic cells.
Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing
Authors: Senabouth Anne , Andersen Stacey , Shi Qianyu , Shi Lei , Liu Ping , Jiang Feng , Zhang Wenwei , Wing Kristof , Daniszewski Maciej , Lukowski Samuel W , Hung Sandy SC , Nguyen Quan , Fink Lynn , Beckhouse Ant , Jiang Hui , Pébay Alice , Hewitt Alex W , Powell Joseph E 
Published: February 2019

AbstractThe libraries generated by high-throughput single cell RNA-sequencing platforms such as the Chromium from 10X Genomics require considerable amounts of sequencing, typically due to the large number of cells. The ability to use this data to address biological questions is directly impacted by the quality of the sequence data. Here we have compared the performance of the Illumina NextSeq 500 and NovaSeq 6000 against the BGI MGISEQ-2000 platform using identical Single Cell 3’ libraries consisting of over 70,000 cells. Our results demonstrate a highly comparable performance between the NovaSeq 6000 and MGISEQ-2000 in sequencing quality, and cell, UMI, and gene detection. However, compared with the NextSeq 500, the MGISEQ-2000 platform performs consistently better, identifying more cells, genes, and UMIs at equalised read depth. We were able to call an additional 1,065,659 SNPs from sequence data generated by the BGI platform, enabling an additional 14% of cells to be assigned to the correct donor from a multiplexed library. However, both the NextSeq 500 and MGISEQ-2000 detected similar frequencies of gRNAs from a pooled CRISPR single cell screen. Our study provides a benchmark for high capacity sequencing platforms applied to high-throughput single cell RNA-seq libraries.
In Silico Analysis and Modeling of Novel Pathogenic Single Nucleotide Polymorphisms (SNPs) in HumanCD40LGGene
Authors: Abdelmoneim Abdelrahman H. , Mustafa Mujahed I. , Mahmoud Thwayba A. , Murshed Naseem S. , Hassan Mohamed A. 
Published: February 2019

Abstract:Background:The X-linked hyper-immunoglobulin M syndrome (XHIGM) is a rare, inherited immune deficiency disorder. It is more common in males. Characterized by elevated serum IgM levels and low to undetectable levels of serum IgG, IgA and IgE. Hyper-IgM syndrome is caused by mutations in theCD40LGgene. Located in human Xq26. CD40LG acts as an immune modulator in activated T cells.Method:We used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein.Result:8 novel SNPs out of 233 were found to have most deleterious effect on the protein structure and function.While modeling ofnsSNPs was studied by Project HOPE software.Conclusion:Better understanding of Hyper-IgM syndrome caused by mutations in CD40LG gene was achieved using in silico analysis. This is the first in silico functional analysis of CD40LG gene and 8 novel mutations were found using different bioinformatics tools, and they could be used as diagnostic markers for hyper-IgM syndrome. These 8 novel SNPs may be important candidates for the cause of different types of human diseases byCD40LGgene.
Bdnf promoter IV-expressing cells in the hippocampus modulate fear expression and hippocampal-prefrontal synchrony in mice
Authors: Hallock Henry L. , Quillian Henry M. , Mai Yishan , Maynard Kristen R. , Hill Julia L. , Martinowich Keri 
Published: February 2019

AbstractBrain-derived neurotrophic factor (BDNF) signaling regulates synaptic plasticity in the hippocampus (HC) and prefrontal cortex (PFC), and has been extensively linked with fear memory expression in rodents. Notably, disrupting BDNF production from promoter IV-derived transcripts enhances fear expression in mice, and decreases fear-associated HC-PFC synchrony, suggesting that Bdnf transcription from promoter IV plays a key role in HC-PFC function during fear memory retrieval. To understand how promoter IV-derived BDNF affects fear expression and HC-PFC connectivity, we generated a viral construct that selectively targets cells expressing promoter IV-derived Bdnf transcripts (“p4-cells”) for tamoxifen-inducible Cre-mediated recombination (AAV8-p4Bdnf-ERT2CreERT2-PEST). Using this construct, we found that ventral (vHC) p4-cells are recruited during fear expression, and that activation of these cells causes exaggerated fear expression that co-occurs with disrupted vHC-PFC synchrony in mice. Our data highlight how this novel construct can be used to interrogate genetically-defined cell types that selectively contribute to BDNF-dependent behaviors.
SorCS1-mediated Sorting of Neurexin in Dendrites Maintains Presynaptic Function
Authors: Ribeiro Luís F. , Verpoort Ben , Nys Julie , Vennekens Kristel M. , Wierda Keimpe D. , Wit Joris de 
Published: February 2019

AbstractThe pre- and postsynaptic membranes comprising the synaptic junction differ in protein composition. The mechanisms that maintain the polarized distribution of synaptic membrane proteins are poorly understood. The sorting receptor SorCS1 is a critical trafficking regulator of neuronal receptors, including neurexin (Nrxn), a presynaptic adhesion molecule essential for synaptic transmission. We find that SorCS1 controls a balance between axonal and dendritic Nrxn1α surface levels. Newly synthesized Nrxn1α traffics to the somatodendritic surface, followed by endocytosis. SorCS1 interacts with the Rab11 effector protein Rab11FIP5/Rip11 to facilitate the transition of internalized Nrxn1α from early to recycling endosomes and bias Nrxn1α surface polarization toward the axon. In the absence of SorCS1, Nrxn1α accumulates in early endosomes and mis-polarizes to the dendritic surface, impairing presynaptic function. The axonal/dendritic balance of Nrxn1α surface distribution is activity-dependent, indicating that SorCS1-mediated sorting in somatodendritic endosomes dynamically controls Nrxn1α axonal surface polarization required for proper presynaptic function.
Generalized Rayleigh-Plesset Theory for Cell Size Maintenance in Viruses and Bacteria
Authors: Malmi-Kakkada Abdul N. , Thirumalai D. 
Published: February 2019

ABSTRACTThe envelopes covering bacterial cytoplasm possess remarkable elastic properties. They are rigid enough to resist large pressures while being flexible enough to adapt to growth under environmental constraints. Similarly, the virus shells play an important role in their functions. However, the effects of mechanical properties of the outer shell in controlling and maintaining the sizes of bacteria or viruses are unknown. Here, we present a hydrodynamic “bubbles with shell” model, motivated by the study of bubble stability in fluids, to demonstrate that shell rigidity and turgor pressure control the sizes of bacteria and viruses. A dimensionless compliance parameter, expressed in terms of the Young’s modulus of the shell, its thickness and the turgor pressure, determines membrane response to deformation and the size of the organisms. By analyzing the experiment data, we show that bacterial and viral sizes correlate with shell elasticity, which plays a critical role in regulating size.
A test for Hardy-Weinberg equilibrium on the X chromosome for sex-biased admixed populations
Authors: Backenroth Daniel , Carmi Shai 
Published: February 2019

AbstractGenome-wide scans for deviations from Hardy-Weinberg equilibrium (HWE) are commonly applied to detect genotyping errors. In contrast to the autosomes, genotype frequencies on the X chromosome do not reach HWE within a single generation. Instead, if allele frequencies in males and females initially differ, they oscillate for a few generations towards equilibrium. Several populations world-wide have experienced recent sex-biased admixture, namely, their male and female founders differed in ancestry and thus in allele frequencies. Sex-biased admixture makes testing for HWE difficult on X, because deviations arenaturallyexpected, even under random mating post-admixture and error-free genotyping. In this paper, we develop a likelihood ratio test and aχ2test that detect deviations from HWE on X while allowing for natural deviations due to sex-biased admixture. We demonstrate by simulations that our tests are powerful for detecting deviations due to non-random mating, while at the same time they do not reject the null under historical sex-biased admixture and random mating thereafter. We also demonstrate that when applied to 1000 Genomes project populations (e.g., as a quality control step), our tests reject fewer SNPs (among those showing frequency differences between the sexes) than other tests.
A Molecular Tension Sensor for N-Cadherin Reveals Distinct Forms of Mechanosensitive Adhesion Assembly in Adherens and Synaptic Junctions
Authors: Puranam Ishaan , Urs Aarti , Kirk Brenna , Newell-Litwa Karen A. , Hoffman Brenton 
Published: February 2019

AbstractN-cadherin mediates physical linkages in a variety of force-generating and load-bearing tissues. To enable visualization and quantification of mechanical loads experienced by N-Cadherin, we developed a genetically-encoded FRET-based tension sensor for this protein. We observe that N-Cadherin supports non-muscle myosin II (NMII) activity-dependent loads within the adherens junctions (AJs) of VSMCs and the synaptic junctions (SJs) of neurons. To probe the relationship between mechanical loads and AJ/SJ formation, we evaluated the relationships between N-cadherin tension and the size of these adhesion structures. In VSMCs, no relationship between N-cadherin tension and AJ size was observed, consistent with previously observed homeostatic regulation of mechanical loading. In neurons, a strong correlation between SJ size and N-cadherin load was observed, demonstrating an absence of homeostatic regulation. Treatment with glycine, a known initiator of synapse maturation, lead to increased SJ size and N-cadherin load, suggesting a role for mechanosensitive signaling in this process. Correspondingly, we observe that NMII activity is required for the Src-mediated phosphorylation of NMDAR subunit GluN2B at Tyr 1252, which is a key event in synaptic potentiation. Together these data demonstrate N-cadherin tension is subject to cell type specific regulation and that mechanosensitive signaling occurs within SJs.
Manatee genomics supports a special conservation area in the Guianas coastline under the influence of the Amazon River plume
Authors: Vilaça Sibelle T. , Lima Camilla S. , Mazzoni Camila J. , Santos Fabricio R. , Thoisy Benoit de 
Published: February 2019

AbstractThe West Indian manatee (Trichechus manatus) occurs along the Atlantic coastline and adjacent freshwater systems of South, Central and North America, from Alagoas (Brazil) to Florida (USA) and Greater Antilles. The Amazonian manatee (Trichechus inunguis) is the only Sirenian adapted exclusively to freshwater and endemic to the Amazon River basin. Previous studies have reported hybrids between T. inunguis and T. manatus close to the mouth of the Amazon River, composing a likely extensive hybrid zone along the Guianas coast of South America under the influence of the Amazon River plume. We have used ddRAD SNP data, and sequences of nuclear and mtDNA loci to characterize the genomic composition of manatees along the French Guiana coastline. We found this population to be formed by introgressed or later generation interspecific hybrids, and also describe the first T. inunguis found outside the Amazon River basin. Our results indicate that T. inunguis can survive in the Amazon River plume and have colonized independent water streams of the Guianas coastline where they likely hybridize with T. manatus. This hypothesis offers a plausible explanation for the known extension of the hybrid zone between the two species along the Guianas coastline. It also reinforces the importance of the Amazon plume, which flows westwards to the Guianas coastline and favors the dispersion of the freshwater species. This habitat functions as a large estuary-like system that provides an ecological continuum from Amazon River mouth to the disconnected waterflows of the Guianas, which deserves a status of special conservation area.
F-BAR Cdc15 Promotes Gef1-mediated Cdc42 Activation During Cytokinesis and Cell Polarization inS. pombe
Authors: Hercyk Brian S. , Das Maitreyi E. 
Published: February 2019

ABSTRACTCdc42, a Rho-family GTPase, is a master regulator of cell polarity. Recently it has been shown that Cdc42 also facilitates proper cytokinesis in the fission yeast,Schizosaccharomyces pombe. Cdc42 is activated by two partially redundant GEFs Gef1 and Scd1. Although both the GEFs activate Cdc42, their deletion mutants display distinct phenotypes, indicating that they are differentially regulated, by an unknown mechanism. During cytokinesis, Gef1 localizes to the division site and activates Cdc42 to initiate ring constriction and septum ingression. Here we report that the F-BAR domain containing Cdc15 promotes Gef1 localization to its functional sites. We show thatcdc15promotes Gef1 association with the cytokinetic nodes to activate Cdc42 during ring assembly. Moreover,cdc15phospho-mutants phenocopy polarity phenotypes ofgef1mutants. In a hypermorphiccdc15mutant, Gef1 localizes precociously to the division site, and is readily detected at the cortical patches and the cell cortex. Correspondingly, the hypermorphiccdc15mutant shows increased bipolarity during interphase and precocious Cdc42 activation at the division site during cytokinesis. Finally, loss ofgef1in hypermorphiccdc15mutants abrogates the increased bipolarity and precocious Cdc42 activation phenotype. We did not see any change in the localization of the other GEF Scd1 in a Cdc15-dependent manner. Taken together our data indicates that Cdc15 promotes Cdc42 activation specifically via Gef1 localization to the division site to facilitate proper cytokinesis and to the cell cortex to promote bipolarity.
Active Ageing Index in Korea – Comparison with China and EU countries
Authors: Um Jinpil , Zaidi Asghar , Choi Sung‐Jae 
Published: February 2019

AbstractThe evidence‐based policymaking relies on the use and robustness of the available data. Many conceptual and operational difficulties restrict this process, not least in making use of evidence to identify policy priorities. The Active Ageing Index (AAI), developed originally for the 28 European Union countries, offers a strong motivation in this respect. This paper reports on the development of the AAI for Korea, a country where speed and level of population aging is among the highest in the world. Drawing on the comparative analysis of the AAI results for Korea, China, and European countries, we find that Korea's AAI (35.3) is higher than the average of the AAI for all EU countries (33.9) but lower than China (37.3). Fitting Korea into the overall ranking with the EU countries and China (ranked 7), Korea is ranked 11, just behind Germany (10). The AAI results in Korea show that the employment domain performs extremely well compared with the EU countries, but other domains, especially “Social participation” and “Independent, healthy and secure living,” are achieving less favorable outcomes. High employment among the current cohorts of older workers in Korea can be attributed largely to the constraints of low pension income status.