bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tumor cell-organized fibronectin is required to maintain a dormant breast cancer population
Authors: Barney Lauren E. , Hall Christopher L. , Schwartz Alyssa D. , Parks Akia N. , Sparages Christopher , Galarza Sualyneth , Platt Manu O. , Mercurio Arthur M. , Peyton Shelly R. 
Published: July 2019

AbstractTumors can undergo long periods of dormancy, with cancer cells entering a largely quiescent, non-proliferative state before reactivation and outgrowth. For a patient, these post-remission tumors are often drug resistant and highly aggressive, resulting in poor prognosis. To understand the role of the extracellular matrix (ECM) in regulating tumor dormancy, we created anin vitrocell culture system that combines carefully controlled ECM substrates with nutrient deprivation to observe entranceintoand exitfromdormancy with live imaging. We saw that cell populations capable of surviving entrance into long-term dormancy were heterogeneous, containing quiescent, cell cycle arrested, and actively proliferating cells. Cell populations that endured extended periods of serum-deprivation-induced dormancy formed an organized, fibrillar fibronectin matrix via αvβ3and α5β1integrin adhesion, ROCK-generated tension, and TGFβ2 stimulation. We surmised that the fibronectin matrix was primarily a mediator of cell survival, not proliferation, during the serum-deprivation stress, bacause cancer cell outgrowth after dormancy required MMP-2-mediated fibronectin degradation. Given the difficulty of animal models in observing entrance and exit from dormancy in real-time, we propose this approach as a new,in vitromethod to study factors important in regulating dormancy, and we used it here to elucidate a role for fibronectin deposition and MMP activation.
Chemogenetic silencing of neurons in the mouse anterior cingulate area modulates neuronal activity and functional connectivity
Authors: Peeters Lore M. , Hinz Rukun , Detrez Jan R. , Missault Stephan , De Vos Winnok H. , Verhoye Marleen , Van der Linden Annemie , Keliris Georgios A. 
Published: July 2019

AbstractThe anterior cingulate area (ACA) is an integral part of the prefrontal cortex in mice and has been implicated in several cognitive functions. Previous anatomical and functional imaging studies demonstrated that the ACA is highly interconnected with numerous brain regions acting as a hub region in functional networks. However, the importance of the ACA in regulating functional network activity and connectivity remains to be elucidated. Recently developed neuromodulatory techniques, such as Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) allow for precise control of neuronal activity. In this study, we used an inhibitory kappa-opioid receptor DREADDs (KORD) to temporally inhibit neuronal firing in the right ACA of mice and assessed functional network activity and connectivity using non-invasive functional MRI. We demonstrated that KORD-induced inhibition of the right ACA induced blood oxygenation-level dependent (BOLD) signal decreases and increases in connected brain regions throughout of hemispheres. Furthermore, these modulations in neuronal activity were associated with decreased intra- and interhemispheric functional connectivity. These results demonstrate that the combination of the DREADD technology and non-invasive functional imaging methods is a valuable tool for unraveling the underlying mechanisms of network function and dysfunction.
Systematic phenomics analysis of ASD-associated genes reveals shared functions and parallel networks underlying reversible impairments in habituation learning
Authors: McDiarmid Troy A. , Belmadani Manuel , Liang Joseph , Meili Fabian , Mathews Eleanor A. , Mullen Gregory P. , Rand James B. , Mizumoto Kota , Haas Kurt , Pavlidis Paul , Rankin Catharine H. 
Published: July 2019

SUMMARYA major challenge facing the genetics of Autism Spectrum Disorders (ASD) is the large and growing number of candidate risk genes and gene variants of unknown functional significance. Here, we used Caenorhabditis elegans to systematically functionally characterize ASD-associated genes in vivo. Using our custom machine vision system we quantified 26 phenotypes spanning morphology, locomotion, tactile sensitivity, and habituation learning in 87 strains each carrying a mutation in an ortholog of an ASD-associated gene. We identified hundreds of novel genotype-phenotype relationships ranging from severe developmental delays and uncoordinated movement to subtle deficits in sensory and learning behaviors. We clustered genes by similarity in phenomic profiles and used epistasis analysis to discover parallel networks centered on CHD8•chd-7 and NLGN3•nlg-1 that underlie mechanosensory hyper-responsivity and impaired habituation learning. We then leveraged our data for in vivo functional assays to gauge missense variant effect. Expression of wild-type NLG-1 in nlg-1 mutant C. elegans rescued their sensory and learning impairments. Testing the rescuing ability of all conserved ASD-associated neuroligin variants revealed varied partial loss-of-function despite proper subcellular localization. Finally, we used CRISPR-Cas9 auxin inducible degradation to determine that phenotypic abnormalities caused by developmental loss of NLG-1 can be reversed by adult expression. This work charts the phenotypic landscape of ASD-associated genes, offers novel in vivo variant functional assays, and potential therapeutic targets for ASD.
Wide-field time-gated SPAD imager for phasor-based FLIM applications
Authors: Ulku Arin , Ardelean Andrei , Antolovic Michel , Weiss Shimon , Charbon Edoardo , Bruschini Claudio , Michalet Xavier 
Published: July 2019

AbstractWe describe the performance of a new wide area time-gated single-photon avalanche diode (SPAD) array for phasor-FLIM, exploring the effect of gate length, gate number and signal intensity on the measured lifetime accuracy and precision. We conclude that the detector functions essentially as an ideal shot noise limited sensor and is capable of video rate FLIM measurement. The phasor approach used in this work appears ideally suited to handle the large amount of data generated by this type of very large sensor (512×512 pixels), even in the case of small number of gates and limited photon budget.
Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels
Authors: Nag Abhishek , Kurushima Yuko , Bowyer Ruth C. E. , Wells Philippa M. , Weiss Stefan , Pietzner Maik , Kocher Thomas , Raffler Johannes , Völker Uwe , Mangino Massimo , Spector Timothy D. , Milburn Michael V. , Kastenmüller Gabi , Mohney Robert P. , Suhre Karsten , Menni Cristina , Steves Claire J. 
Published: July 2019

AbstractSaliva, as a biofluid, is inexpensive and non-invasive to obtain, and provides a vital tool to investigate oral health and its interaction with systemic health conditions. There is growing interest in salivary biomarkers for systemic diseases, notably cardiovascular disease. Whereas hundreds of genetic loci have been shown to be involved in the regulation of blood metabolites leading to unprecedented insights into the pathogenesis of complex human diseases, little is known about the impact of host genetics on salivary metabolites. Here we report the first genome-wide association study exploring 476 salivary metabolites in 1,419 subjects of European ancestry from the TwinsUK cohort (discovery phase). A total of 14 salivary metabolites were significantly associated (p<10−10) with genetic variants that mapped to 11 distinct loci, most of which replicated in the Study of Health in Pomerania (SHIP-2) cohort. Interestingly, while only a limited number of the loci that are known to regulate blood metabolites were also associated with salivary metabolites in our study, we identified several novel saliva-specific locus-metabolite associations, including associations for theAGMAT(with the metabolites 4-guanidinobutanoate and beta-guanidinopropanoate),ATP13A5(with the metabolite creatinine) andDPYS(with the metabolites 3-ureidopropionate and 3-ureidoisobutyrate) loci. Our study suggests that there are biological pathways which are specific to the regulation of the salivary metabolome. In addition, some of our findings may have clinical relevance, such as the utility of the pyrimidine (uracil) degradation metabolites in predicting 5-fluorouracil toxicity and the role of the agmatine pathway metabolites as biomarkers of oral health.
Development of a Surface Programmable Activation Receptor system (SPAR): A living cell biosensor for rapid pathogen detection
Authors: Kittle Joseph D. , Lwande Joel S. , Williams M. Russell , Brody Richard , Frenchmeyer Melissa , Hua Jiangzhou , Liang Shengwen , McQuaid Kyle , Mo Min , Neese Allison , Tang Yuanyuan , Vedamoorthy Srikanth , Zeng Lingchun , Zupancic Thomas , McBrairty Charles 
Published: July 2019

AbstractEfficient pathogen detection is essential for the successful treatment and prevention of infectious disease; however, current methods are often too time intensive to be clinically relevant in cases requiring immediate intervention. We have developed a Surface Programmable Activation Receptor (SPAR) diagnostic platform comprised of universal biosensor cells engineered for use in combination with custom or commercial antibodies to achieve rapid and sensitive pathogen detection. SPAR cells are stably transfected Jurkat T cells designed to constitutively express a modified T cell mouse FcγRI receptor on the cell surface and a high level of the luminescent reporter protein aequorin in the cytoplasm. The modified mFcγRI-CD3ζ receptor protein binds with high affinity to the Fc region of any full-length mouse IgG2a and some IgG2 antibodies: this allows customized target detection via the selection of specific antibodies. T-cell receptor aggregation in response to target antigen binding results in signal transduction which, when amplified via the endogenous T cell signal cascade, triggers the rapid intracellular release of calcium. Increased Ca2+ concentrations activate the expressed reporter protein aequorin resulting in the immediate emission of detectable light. Testing demonstrates the accurate and specific detection of numerous targets including P. aeruginosa, E. coli O111, and E. coli O157. We report that the SPAR biosensor cell platform is a reliable pathogen detection method that enables the rapid identification of bacterial causative agents using standard laboratory instrumentation. The technology lends itself to the development of efficient point-of-care testing and may aid in the implementation of effective and pathogen-specific clinical therapies.
Chronic paroxetine blunts stress response and normalizes adverse behavioral effects seen acutely in nulliparous rats
Authors: Tuckute Greta , Overgaard Agnete , Frokjaer Vibe G. 
Published: July 2019

AbstractSelective serotonin reuptake inhibitors (SSRI) are widely used antidepressants and their effect is partly mediated by restoring stress axis dynamics, which may depend on sex and hormonal states. In the present study, we investigate the effect of daily injections of the SSRI paroxetine (5 mg/kg s.c.) on swim stress-induced corticosterone (CORT) response, depressive-like behavior (forced swim test) and anxiety-like behavior (open field test) in nulliparous Sprague Dawley rats. Data were acquired after either 1-3 (acute PXT) or 11-13 (chronic PXT) injections. We found that chronic, but not acute, paroxetine blunted the swim stress-induced CORT response. We observed an increase in depressive-like and anxiety-like behavior following acute PXT, and a normalization after chronic PXT treatment. Intriguingly, our findings of rapid recovery from adverse SSRI effects differ from corresponding studies performed by our group in postpartum rats. Thus, the study emphasizes that mechanisms of action and efficacy of SSRIs differ according to reproductive states, which if translated to humans may inform treatment strategies, beyond SSRIs alone, for hormone transition related depressive states.
Convergent metatarsal fusion in jerboas and chickens is mediated by similarities and differences in the patterns of osteoblast and osteoclast activities
Authors: Gutierrez Haydee L. , Tsutsumi Rio , Moore Talia Y. , Cooper Kimberly L. 
Published: July 2019

AbstractThe extraordinary malleability of the vertebrate limb supports a variety of locomotor functions including running and leaping in cursorial and saltatorial species. In many of these animals, the metatarsals and/or metacarpals are disproportionately elongated to increase stride length and fused into a single larger element, likely to resist fracture due to increased ground reaction forces. Despite the fact that metapodial fusion evolved convergently in modern birds, ungulates, and jerboas, the developmental basis has only been explored in chickens, which diverged from the mammalian lineage approximately 300 million years ago. Here, we use the lesser Egyptian jerboa, Jaculus jaculus, to understand the cellular processes that unite three distinct metatarsal elements into a single cannon bone in a mammal, and we revisit the developing chicken to assess similarities and differences in the localization of osteoblast and osteoclast activities. In both species, adjacent metatarsals align along flat surfaces, osteoblasts cross the periosteal membrane to unite the three elements in a single circumference, and osteoclasts resorb bone at the interfaces leaving a single marrow cavity. However, although spatial and temporal partitioning of osteoblast and osteoclast activities reshape three bones into one in both species, the localization of osteoclasts is distinct. While osteoclasts are uniformly distributed throughout the endosteum of chicken metatarsals, these catabolic cells are highly localized to resorb bone at the interfaces of neighboring jerboa metatarsals. Each species therefore provides an opportunity to better understand the mechanisms that partition osteoblasts and osteoclasts to alter the shape of bone during development and evolution.
The plant pathogenPectobacterium atrosepticumcontains a functional formate hydrogenlyase-2 complex
Authors: Finney Alexander J. , Lowden Rebecca , Fleszar Michal , Albareda Marta , Coulthurst Sarah J. , Sargent Frank 
Published: July 2019

SummaryPectobacterium atrosepticumSCRI1043 is a phytopathogenic gram-negative enterobacterium. Genomic analysis has identified that genes required for both respiration and fermentation are expressed under anaerobic conditions. One set of anaerobically expressed genes is predicted to encode an important but poorly-understood membrane-bound enzyme termed formate hydrogenlyase-2 (FHL-2), which has fascinating evolutionary links to the mitochondrial NADH dehydrogenase (Complex I). In this work, molecular genetic and biochemical approaches were taken to establish that FHL-2 is fully functional inP. atrosepticumand is the major source of molecular hydrogen gas generated by this bacterium. The FHL-2 complex was shown to comprise a rare example of an active [NiFe]-hydrogenase-4 (Hyd-4) isoenzyme, itself linked to an unusual selenium-free formate dehydrogenase in the final complex. In addition, further genetic dissection of the genes encoding the predicted membrane domain of FHL-2 established surprisingly that the majority of genes encoding this domain are not required for physiological hydrogen production activity. Overall, this study presentsP. atrosepticumas a new model bacterial system for understanding anaerobic formate and hydrogen metabolism in general, and FHL-2 function and structure in particular.Significance StatementPectobacterium atrospecticumcontains the genes for the formate hydrogenlyase-2 enzyme, considered the ancient progenitor of mitochondrial respiratory Complex I. In this study, the harnessing ofP. atrosepticumas a new model system for understanding bacterial hydrogen metabolism has accelerated new knowledge in FHL-2 and its component parts. Importantly, those component parts include an unusual selenium-free formate dehydrogenase and a complicated [NiFe]-hydrogenase-4 with a large membrane domain. FHL-2 is established as the major source of molecular hydrogen produced under anaerobic conditions byP. atrospectium, however surprisingly some components of the membrane domain were not essential for this activity.
Classifying disease-associated variants using measures of protein activity and stability
Authors: Jepsen Michael Maglegaard , Fowler Douglas M. , Hartmann-Petersen Rasmus , Stein Amelie , Lindorff-Larsen Kresten 
Published: July 2019

AbstractDecreased cost of human exome and genome sequencing provides new opportunities for diagnosing genetic disorders, but we need better and more robust methods for interpreting sequencing results including determining whether and by which mechanism a specific missense variants may be pathogenic. Using the protein PTEN (phosphatase and tensin homolog) as an example, we show how recent developments in both experiments and computational modelling can be used to determine whether a missense variant is likely to be pathogenic. One approach relies on multiplexed experiments that enable determination of the effect of all possible individual missense variants in a cellular assay. Another approach is to use computational methods to predict variant effects. We compare two different multiplexed experiments and two computational methods to classify variant effects in PTEN. We distinguish between methods that focus on effects on protein stability and protein-specific methods that are more directly related to enzyme activity. Our results on PTEN suggest that ~60% of pathogenic variants cause loss of function because they destabilise the folded protein which is subsequently degraded. Methods that quantify a broader range of effects on PTEN activity perform better at predicting variant effects. Either experimental method performs better than the corresponding computational predictions, so that e.g. experiments that probe cellular abundance perform better at identifying pathogenic variants than predictions of thermodynamic stability. Our results suggest that loss of stability of PTEN is a key driver for disease, and we hypothesize that experiments and prediction methods that probe protein stability can be used to find variants with similar mechanisms in other genes.
Brain Regional Gene Expression Network Analysis Identifies Unique Interactions Between Chronic Ethanol Exposure and Consumption
Authors: Smith M.L. , Lopez M.F. , Wolen A.R. , Becker H.C. , Miles M.F. 
Published: July 2019

AbstractProgressive increases in ethanol consumption is a hallmark of alcohol use disorder (AUD). Persistent changes in brain gene expression are hypothesized to underlie the altered neural signaling producing abusive consumption in AUD. To identify brain regional gene expression networks contributing to progressive ethanol consumption, we performed microarray and scale-free network analysis of expression responses in a C57BL/6J mouse model utilizing chronic intermittent ethanol by vapor chamber (CIE) in combination with limited access oral ethanol consumption. This model has previously been shown to produce long-lasting increased ethanol consumption, particularly when combining oral ethanol access with repeated cycles of intermittent vapor exposure. The interaction of CIE and oral consumption was studied by expression profiling and network analysis in medial prefrontal cortex, nucleus accumbens, hippocampus, bed nucleus of the stria terminalis, and central nucleus of the amygdala. Brain region expression networks were analyzed for ethanol-responsive gene expression, correlation with ethanol consumption and functional content using extensive bioinformatics studies. In all brain-regions studied the largest number of changes in gene expression were seen when comparing ethanol naïve mice to those exposed to CIE and drinking. In the prefrontal cortex, however, unique patterns of gene expression were seen compared to other brain-regions. Network analysis identified modules of co-expressed genes in all brain regions. The prefrontal cortex and nucleus accumbens showed the greatest number of modules with significant correlation to drinking behavior. Across brain-regions, however, many modules with strong correlations to drinking, both baseline intake and amount consumed after CIE, showed functional enrichment for synaptic transmission and synaptic plasticity.
Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development
Authors: Wineberg Yishay , Bar-Lev Tali Hana , Futorian Anna , Ben-Haim Nissim , Armon Leah , Ickowicz Debby , Oriel Sarit , Bucris Efrat , Yehuda Yishai , Pode-Shakked Naomi , Gilad Shlomit , Benjamin Sima , Hohenstein Peter , Dekel Benjamin , Urbach Achia , Kalisky Tomer 
Published: July 2019

ABSTRACTDuring mammalian kidney development, nephron progenitors undergo a mesenchymal to epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, the different cell types in the developing kidney were characterized using the Dropseq single cell RNA sequencing technology for measuring gene expression from thousands of individual cells. However, many genes can also be alternatively spliced and this creates an additional layer of heterogeneity. We therefore used full transcript length single-cell RNA sequencing to obtain the transcriptomes of 544 individual cells from mouse embryonic kidneys. We first used gene expression levels to identify each cell type. Then, we comprehensively characterized the splice isoform switching that occurs during the transition between mesenchymal and epithelial cellular states and identified several putative splicing regulators, including the genes Esrp1/2 and Rbfox1/2. We anticipate that these results will improve our understanding of the molecular mechanisms involved in kidney development.