bluuebunny/crossref_metadata_2025_split huggingface dataset:
A limbic circuit selectively linking active escape to food suppression
Authors: Azevedo Estefania P. , Tan Bowen , Pomeranz Lisa E. , Ivan Violet , Fetcho Robert N. , Schneeberger Marc , Doerig Katherine R. , Liston Conor , Friedman Jeffrey M. , Stern Sarah A. 
Published: June 2019

AbstractStress and anxiety are precipitating factors for eating disorders, but the neural basis linking stress to alterations in feeding is not well understood. Here we describe a novel population of stress-responsive neurons in the lateral septum (LS) of mice that express neurotensin (LSNTS) in a sexually dimorphic, estrous cycle-dependent manner. We used in vivo imaging to show that LSNTS neurons are activated by stressful experiences when flight is a viable option, but not by a stressful experience associated with freezing or immobility. LSNTS activation leads to a decrease of food intake and body weight in mice, without altering locomotion or other behaviors associated with anxiety. Molecular profiling of LSNTS neurons showed that these neurons co-express Glp1r (glucagon-like peptide 1 receptor), and both pharmacologic and genetic manipulations of Glp1r signaling in the LS recapitulates the behavioral effects of LSNTS activation. Finally, we mapped the outputs of LSNTS neurons and show that activation of LSNTS nerve terminals in the lateral hypothalamus (LH), a well-established feeding center, also decrease food intake. Taken together, these results show that LSNTS neurons link stress and anorexia via effects on hypothalamic pathways regulating food intake.
The emergence of successfulStreptococcus pyogeneslineages through convergent pathways of capsule loss and recombination directing high toxin expression
Authors: Turner Claire E. , Holden Matthew T. G. , Blane Beth , Horner Carolyne , Peacock Sharon J. , Sriskandan Shiranee 
Published: June 2019

AbstractGene transfer and homologous recombination inStreptococcus pyogeneshas the potential to trigger the emergence of pandemic lineages, as exemplified by lineages ofemm1 andemm89 that emerged in the 1980s and 2000s respectively. Although near-identical replacement gene transfer events in thenga(NADase) andslo(Streptolysin O) locus conferring high expression of these toxins underpinned the success of these lineages, extension to otheremm-genotype lineages is unreported. The emergentemm89 lineage was characterised by five regions of homologous recombination additional tonga/slo, including complete loss of the hyaluronic acid capsule synthesis locushasABC,a genetic trait replicated in two other leadingemmtypes and recapitulated by otheremmtypes by inactivating mutations. We hypothesised that other leading genotypes may have undergone a similar recombination events. We analysed a longitudinal dataset of genomes from 344 clinical invasive disease isolates representative of locations across England, dating from 2001 to 2011, and an international collection ofS. pyogenesgenomes representing 54 different genotypes, and found frequent evidence of recombination events at thenga-slolocus predicted to confer higher toxin expression. We identified multiple associations between recombination at this locus and inactivating mutations withinhasA/B,suggesting convergent evolutionary pathways in successful genotypes. This included common genotypesemm28 andemm87. The combination of no or low capsule, and high expression ofngaandslo,may underpin the success for many emergentS. pyogeneslineages of different genotypes, triggering new pandemics and could change the wayS. pyogenescauses disease.ImportanceStreptococcus pyogenesis a genetically diverse pathogen, with over 200 different genotypes defined byemmtyping, but only a minority of these genotypes are responsible for majority of human infection in high income countries. Two prevalent genotypes associated with disease rose to international dominance following recombination of a toxin locus that conferred increased expression. Here, we found that recombination of this locus and promoter has occurred in other diverse genotypes, events that may allow these genotypes to expand in the population. We identified an association between the loss of hyaluronic acid capsule synthesis and high toxin expression, which we propose may be associated with an adaptive advantage. AsS. pyogenespathogenesis depends both on capsule and toxin production, new variants with altered expression may result in abrupt changes in the molecular epidemiology of this pathogen in the human population over time.
Validation and characterisation of a wheat GENIE3 network using an independent RNA-Seq dataset
Authors: Harrington Sophie A. , Backhaus Anna E. , Singh Ajit , Hassani-Pak Keywan , Uauy Cristobal 
Published: June 2019

AbstractGene regulatory networks are powerful tools which facilitate hypothesis generation and candidate gene discovery. However, the extent to which the network predictions are biologically relevant is often unclear. Recently, as part of an analysis of the RefSeqv1.0 wheat transcriptome, a GENIE3 network which predicted targets of wheat transcription factors was produced. Here we have used an independent and publicly-available RNA-Seq dataset to validate the predictions of the wheat GENIE3 network for the senescence-regulating transcription factor NAM-A1 (TraesCS6A02G108300). We re-analysed the RNA-Seq data against the RefSeqv1.0 genome and identified a de novo set of differentially expressed genes (DEGs) between the wild-type and nam-a1 mutant which recapitulated the known role of NAM-A1 in senescence and nutrient remobilisation. We found that the GENIE3-predicted target genes of NAM-A1 overlap significantly with the de novo DEGs, more than would be expected for a random transcription factor. Based on high levels of overlap between GENIE3-predicted target genes and the de novo DEGs, we also identified a set of candidate senescence regulators. We then explored genome-wide trends in the network related to polyploidy and homoeolog expression levels and found that only homoeologous transcription factors are likely to share predicted targets in common. However, homoeologs in dynamic triads, i.e. with higher variation in homoeolog expression levels across tissues, are less likely to share predicted targets than stable triads. This suggests that homoeologs in dynamic triads are more likely to act on distinct pathways. This work demonstrates that the wheat GENIE3 network can provide biologically-relevant predictions of transcription factor targets, which can be used for candidate gene prediction and for global analyses of transcription factor function. The GENIE3 network has now been integrated into the KnetMiner web application, facilitating its use in future studies.
The anti-apoptotic proteins Bcl-2 and Bcl-xL suppress Beclin1/Atg6-mediated lethal autophagy in polyploid cells
Authors: Zhang Jing , Zhang Shenqiu , Wu Fachi , Shi Qiong , Allen Thaddeus , You Fengming , Yang Dun 
Published: June 2019

AbstractInhibition of Aurora-B kinase is a synthetic lethal therapy for tumors that overexpress the MYC oncoprotein. It is currently unclear whether co-occurring oncogenic alterations might influence this synthetic lethality by confering more or less potency in the killing of tumor cells. To identify such modifers, we utilized isogenic cell lines to test a variety of cancer genes that have been previously demonstrated to promote survival under conditions of cellular stress, contribute to chemoresistance and/or suppress MYC-primed apoposis. We found that Bcl-2 and Bcl-xL, two antiapoptotic members of the Bcl-2 family, can partially suppress the synthetic lethality, but not multinucleation, elicited by a panaurora kinase inhibitor, VX-680. We demonstrate that this suppression stems from the rescue of autophagic cell death, specifically of multinucleated cells, rather than a general inhibition of apoptosis. Bcl-2 inhibits VX-680-induced death of polyploid cells by interacting with the autophagy protein Beclin1/Atg6 and rescue requires localization of Bcl-2 to the endoplasmic reticulum. These findings expand on previous conclusions that autophagic death of polyploid cells is mediated by Atg6. Bcl-2 and Bcl-xL negatively modulate MYC-VX-680 synthetic lethality and it is the anti-autophagic activity of these two Bcl-2 family proteins, specifically in multinucleate cells, that contributes to resistance to Aurora kinase-targeting drugs.
GraphDTA: Predicting drug–target binding affinity with graph neural networks
Authors: Nguyen Thin , Le Hang , Quinn Thomas P. , Nguyen Tri , Le Thuc Duy , Venkatesh Svetha 
Published: June 2019

AbstractThe development of new drugs is costly, time consuming, and often accompanied with safety issues. Drug repurposing can avoid the expensive and lengthy process of drug development by finding new uses for already approved drugs. In order to repurpose drugs effectively, it is useful to know which proteins are targeted by which drugs. Computational models that estimate the interaction strength of new drug--target pairs have the potential to expedite drug repurposing. Several models have been proposed for this task. However, these models represent the drugs as strings, which is not a natural way to represent molecules. We propose a new model called GraphDTA that represents drugs as graphs and uses graph neural networks to predict drug--target affinity. We show that graph neural networks not only predict drug--target affinity better than non-deep learning models, but also outperform competing deep learning methods. Our results confirm that deep learning models are appropriate for drug--target binding affinity prediction, and that representing drugs as graphs can lead to further improvements.Availability of data and materialsThe proposed models are implemented in Python. Related data, pre-trained models, and source code are publicly available at https://github.com/thinng/GraphDTA. All scripts and data needed to reproduce the post-hoc statistical analysis are available from https://doi.org/10.5281/zenodo.3603523.ContactThin.Nguyen@deakin.edu.au
SmartRNASeqCaller: improving germline variant calling from RNAseq
Authors: Bosio Mattia , Valencia Alfonso , Capella-Gutierrez Salvador 
Published: June 2019

AbstractBackgroundTranscriptomics data, often referred as RNA-Seq, are increasingly being adopted in clinical practice due to the opportunity to answer several questions with the same data - e.g. gene expression, splicing, allele-specific expression even without matching DNA. Indeed, recent studies showed how RNA-Seq can contribute to decipher the impact of germline variants. These efforts allowed to dramatically improved the diagnostic yield in specific rare disease patient cohorts. Nevertheless, RNA-Seq is not routinely adopted for germline variant calling in the clinic. This is mostly due to a combination of technical noise and biological processes that affect the reliability of results, and are difficult to reduce using standard filtering strategies.ResultsTo provide reliable germline variant calling from RNA-Seq for clinical use, such as for mendelian diseases diagnosis, we developed SmartRNASeqCaller: a Machine Learning system focused to reduce the burden of false positive calls from RNA-Seq. Thanks to the availability of large amount of high quality data, we could comprehensively train SmartRNASeqCaller using a suitable features set to characterize each potential variant.The model integrates information from multiple sources, capturing variant-specific characteristics, contextual information, and external sources of annotation. We tested our tool against state-of-the-art workflows on a set of 376 independent validation samples from GIAB, Neuromics, and GTEx consortia. SmartRNASeqCaller remarkably increases precision of RNA-Seq germline variant calls, reducing the false positive burden by 50% without strong impact on sensitivity. This translates to an average precision increase of 20.9%, showing a consistent effect on samples from different origins and characteristics.ConclusionsSmartRNASeqCaller shows that a general strategy adopted in different areas of applied machine learning can be exploited to improve variant calling. Switching from a naïve hard-filtering schema to a more powerful, data-driven solution enabled a qualitative and quantitative improvement in terms of precision/recall performances. This is key for the intended use of SmartRNASeqCaller within clinical settings to identify disease-causing variants.
Widespread positive selection for mRNA secondary structure at synonymous sites in domesticated yeast
Authors: Yu Minghao , Guo Wenna , Wang Qiang , Chen Jian-Qun 
Published: June 2019

AbstractmRNA secondary structure assumes a critical role in gene regulation, especially for translational efficiency. Previous studies have a growing appreciation of purifying selection for the conserved mRNA structure across lineages of different species. However, the effect of mRNA structure on positive evolution remains unclear. Here, we construct a large-scale dataset of single nucleotide polymorphisms (SNPs) at synonymous sites in the population ofSaccharomyces cerevisiae, combined with the experimental assessment of mRNA structure, and perform empirical population genetics data analysis through unfolded site-frequency spectra. Our results suggest that functional mRNA stem drives faster evolution of increasing GC contents itself with the purpose of regulating translational speed, which is greatly influenced by length. At the synonymous site without codon usage bias, this kind of positive selection still exists. Furthermore, mRNA secondary structure is subject to positive selection widespread among the yeast genome, particularly related to mitochondria activities, which is possibly aimed to achieve a balance between cellular respiration and alcoholic fermentation precisely at a non-protein level. It is conducive to the adaption of the dramatic environment alterations from wild to man-made environments during the domestication.
In silicoidentification of putativeTrypanosoma cruzienolase inhibitors
Authors: Valera-Vera Edward A. , Sayé Melisa , Reigada Chantal , Miranda Mariana R. , Pereira Claudio A. 
Published: June 2019

AbstractEnolase is a glycolytic enzyme that catalyzes the interconversion between 2-phosphoglycerate and phosphoenolpyruvate. In trypanosomatids enolase was proposed as a key enzyme afterin silicoandin vivoanalysis and it was validated as a protein essential for the survival of the parasite. Therefore, enolase constitutes an interesting enzyme target for the identification of drugs against Chagas disease. In this work, a combined virtual screening strategy was implemented, employing similarity virtual screening, molecular docking and molecular dynamics. First, two known enolase inhibitors and the enzyme substrates were used as queries for the similarity screening on the Sweetlead database using five different algorithms. Compounds retrieved in the top 10 of at least three search algorithms were selected for further analysis, resulting in six compounds of medical use (etidronate, pamidronate, fosfomycin, acetohydroximate, triclofos, and aminohydroxybutyrate). Molecular docking simulations predicted acetohydroxamate and triclofos would not bind to the active site of the enzyme, and a re-scoring of the obtained poses signaled fosfomycin and aminohydroxybutyrate as bad enzyme binders. Docking poses obtained for etidronate, pamidronate, and PEP, were used for molecular dynamics calculations to describe their mode of binding. From the obtained results, we propose etidronate as a possibleTcENO inhibitor, and describe desirable and undesirable molecular motifs to be taken into account in the repurposing or design of drugs aiming this enzyme active site.
Defective base excision repair in the response to DNA damaging agents in triple negative breast cancer
Authors: Lee Kevin J. , Piett Cortt G. , Andrews Joel F , Mann Elise , Nagel Zachary D. , Gassman Natalie R. 
Published: June 2019

AbstractDNA repair defects have been increasingly focused on as therapeutic targets. In hormone positive breast cancer, XRCC1-deficient tumors have been identified and proposed as targets for combination therapies that damage DNA and inhibit DNA repair pathways. XRCC1 is a scaffold protein that functions in base excision repair (BER) by mediating essential interactions between DNA glycosylases, AP endonuclease, poly(ADP-ribose) polymerase 1, DNA polymerase β (POL β), and DNA ligases. Loss of XRCC1 confers BER defects and hypersensitivity to DNA damaging agents. BER defects have not been evaluated in triple negative breast cancer (TNBC), for which new therapeutic targets and therapies are needed. To evaluate the potential of XRCC1 as an indicator of BER defects in TNBC, we examined XRCC1 expression and localization in the TCGA database and in TNBC cell lines. High XRCC1 expression was observed for TNBC tumors in the TCGA database and expression of XRCC1 varied between TNBC cell lines. We also observed changes in XRCC1 subcellular localization in TNBCs that alter the ability to repair base lesions and single-strand breaks. Subcellular localization changes were also observed for POL β that did not correlate with XRCC1 localization. Basal levels of DNA damage were also measured in the TNBC cell lines, and damage levels correlated with observed changes in XRCC1 expression, localization, and repair functions. The results confirmed that XRCC1 expression changes may indicate DNA repair capacity changes but emphasize that basal DNA damage levels along with expression and localization are better indicators of DNA repair defects. Given the observed over-expression of XRCC1 in TNBC preclinical models and the TCGA database, XRCC1 expression levels should be considered when evaluating treatment responses of TNBC preclinical model cells.
The effect of meal temperature on heart rate inRhodnius prolixus
Authors: Lahondère Chloé , Buradino Maurane , Lazzari Claudio R. 
Published: June 2019

AbstractRhodnius prolixusis able to cool down the ingested blood during feeding on a warm-blooded host. This is possible because of a counter-current heat exchanger located in its head, which transfers heat from the warm blood to the insect haemolymph and can dissipate through the head cuticle. Given the key role haemolymph circulation in thermoregulation, we investigated the modulation of the activity of the heart during the warmed meal intake. We evaluated the impact of meal temperature on the heart rate and found that feeding led to an increase in the frequency of heart contractions, which increases with increasing food temperature. We also found that females have a higher heart rate during feeding compare to males.HIGHLIGHTSFeeding increases the heart rate ofRhodnius prolixusThe higher the meal temperature, the higher the heart rate becomesFemales have a higher heart rate than males
Brain functional connectivity dynamics in the aftermaths of affective and cognitive events
Authors: Gaviria Julian , Rey Gwladys , Bolton Thomas , Delgado Jaime , Van de Ville Dimitri , Vuilleumier Patrik 
Published: June 2019

AbstractNeuroimaging studies have shown carry-over effects on brain activity and connectivity following both emotional and cognitive events, persisting even during subsequent rest. Here, we investigate the functional dynamics of such effects by identifying recurring co-activation patterns (CAPs). Using the precuneus as seed region, we compare carrying-over effects on brain-wide CAPs and their modulation after both affective and cognitive challenges. Female volunteers (n=19) underwent fMRI scanning during emotional induction with sad movie clips, and executive control tasks, each followed by resting periods. Several CAPs, overlapping the default mode, salience, attention, and social cognition networks were impacted by both the preceding events (movie or task) and their valence (neutral or negative), with differential fluctuations over time. Specifically, a modulation of CAPs in posterior cingulate and ventromedial prefrontal cortex was observed after exposure to negatively valenced emotional content and predicted changes in subjective affect. Additionally, CAPs in anterior cingulate cortex and dorsal fronto-parietal areas were induced by cognitive control in a negative, but not neutral context, and amplified by the task difficulty. These findings provide new insights on the anatomical organization and temporal inertia of intrinsic functional brain networks, engaged by transient emotions and presumably involved in subsequent adaptive homeostatic processes.
Dynamic reconfiguration of functional brain networks during working memory training
Authors: Finc Karolina , Bonna Kamil , He Xiaosong , Lydon-Staley David M. , Kühn Simone , Duch Włodzisław , Bassett Danielle S. 
Published: June 2019

AbstractThe functional network of the brain continually adapts to changing environmental demands. The consequence of behavioral automation for task-related functional network architecture remains far from understood. We investigated the neural reflections of behavioral automation as participants mastered a dual n-back task. In four fMRI scans equally spanning a 6-week training period, we assessed brain network modularity, a substrate for adaptation in biological systems. We found that whole-brain modularity steadily increased during training for both conditions of the dual n-back task. In a dynamic analysis, we found that the autonomy of the default mode system and integration among task-positive systems were modulated by training. The automation of the n-back task through training resulted in non-linear changes in integration between the fronto-parietal and default mode systems, and integration with the subcortical system. Our findings suggest that the automation of a cognitively demanding task may result in more segregated network organization.
Loss of β-arrestin2 in D2 cells alters neuronal excitability in the nucleus accumbens and behavioral responses to psychostimulants and opioids
Authors: Porter-Stransky Kirsten A. , Petko Alyssa K. , Karne Saumya L. , Liles L. Cameron , Urs Nikhil M. , Caron Marc G. , Paladini Carlos A. , Weinshenker David 
Published: June 2019

AbstractPsychostimulants and opioids increase dopamine (DA) neurotransmission, activating D1 and D2 G protein-coupled receptors. β-arrestin2 (βarr2) desensitizes and internalizes these receptors and initiates G protein-independent signaling. Previous work revealed that mice with a global or cell-specific knockout of βarr2 have altered responses to certain drugs; however, the effects of βarr2 on the excitability of medium spiny neurons (MSNs) and its role in mediating the rewarding effects of drugs of abuse are unknown. D1-Cre and D2-Cre transgenic mice were crossed with floxed βarr2 mice to eliminate βarr2 specifically in cells containing either D1 (D1βarr2-KO) or D2 (D2βarr2-KO) receptors. We used slice electrophysiology to characterize the role of βarr2 in modulating D1 and D2 nucleus accumbens MSN intrinsic excitability in response to DA and tested the locomotor-activating and rewarding effects of cocaine and morphine in these mice. We found that eliminating βarr2 attenuated the ability of DA to inhibit D2-MSNs but had little effect on the DA response of D1-MSNs. While D1βarr2-KO mice had mostly normal drug responses, D2βarr2-KO mice showed dose-dependent reductions in acute locomotor responses to cocaine and morphine, attenuated locomotor sensitization to cocaine, and blunted cocaine reward measured with conditioned place preference. Both D2βarr2-KO and D1βarr2-KO mice displayed an enhanced conditioned place preference for the highest dose of morphine. These results indicate that D2-derived βarr2 functionally contributes to the ability of DA to inhibit D2-MSNs and multiple behavioral responses to psychostimulants and opioids, while loss of βarr2 in D1 neurons has little impact on D1-MSN excitability or drug-induced behaviors.