bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellular compartment analysis of temporal activity by fluorescent in situ hybridization (catFISH) in the transcardially perfused rat brain
Authors: Gheidi Ali , Kumar Vivek , Fitzpatrick Christopher J , Atkinson Rachel L , Morrow Jonathan D 
Published: September 2019

AbstractCellular compartment analysis of temporal activity by fluorescent in situ hybridization (catFISH) allows high spatiotemporal resolution mapping of immediate early genes in the brain in response to internal/external stimuli. One caveat of this technique and indeed other methods of in situ hybridization is the necessity of flash-freezing the brain prior to staining. Often however, the mammalian brain is transcardially perfused to use the brain tissue for immunohistochemistry, the most widely-used technique to study gene expression. The present study illustrates how the original catFISH protocol can be modified for use in adult rats that have been transcardially perfused with 4% paraformaldehyde. c-Fos activity induced by either an auditory tone or status epilepticus was visualized using the catFISH procedure. Analysis of the rat prefrontal cortex, hippocampus and amygdala shows that a clear distinction can be made between the compartmental distribution of c-Fos mRNA in the nuclei and cytoplasmic regions. Furthermore, the qualitative proportion of c-Fos compartmentalization is similar to previous reports of c-Fos expression pattern in rodents navigating novel environments. c-Fos catFISH on perfused rodent brains is an valuable addition to the traditional histological methods using fluorescently labeled riboprobes, and opens several avenues for future investigations.
Improving the coverage of credible sets in Bayesian genetic fine-mapping
Authors: Hutchinson Anna , Watson Hope , Wallace Chris 
Published: September 2019

AbstractGenome Wide Association Studies (GWAS) have successfully identified thousands of loci associated with human diseases. Bayesian genetic fine-mapping studies aim to identify the specific causal variants within GWAS loci responsible for each association, reporting credible sets of plausible causal variants, which are interpreted as containing the causal variant with some “coverage probability”.Here, we use simulations to demonstrate that the coverage probabilities are over-conservative in most fine-mapping situations. We show that this is because fine-mapping data sets are not randomly selected from amongst all causal variants, but from amongst causal variants with larger effect sizes. We present a method to re-estimate the coverage of credible sets using rapid simulations based on the observed, or estimated, SNP correlation structure, we call this the “corrected coverage estimate”. This is extended to find “corrected credible sets”, which are the smallest set of variants such that their corrected coverage estimate meets the target coverage.We use our method to improve the resolution of a fine-mapping study of type 1 diabetes. We found that in 27 out of 39 associated genomic regions our method could reduce the number of potentially causal variants to consider for follow-up, and found that none of the 95% or 99% credible sets required the inclusion of more variants – a pattern matched in simulations of well powered GWAS.Crucially, our correction method requires only GWAS summary statistics and remains accurate when SNP correlations are estimated from a large reference panel. Using our method to improve the resolution of fine-mapping studies will enable more efficient expenditure of resources in the follow-up process of annotating the variants in the credible set to determine the implicated genes and pathways in human diseases.Author summaryPinpointing specific genetic variants within the genome that are causal for human diseases is difficult due to complex correlation patterns existing between variants. Consequently, researchers typically prioritise a set of plausible causal variants for functional validation - these sets of putative causal variants are called “credible sets”. We find that the probabilistic interpretation that these credible sets do indeed contain the true causal variant is variable, in that the reported probabilities often underestimate the true coverage of the causal variant in the credible set. We have developed a method to provide researchers with a “corrected coverage estimate” that the true causal variant appears in the credible set, and this has been extended to find “corrected credible sets”, allowing for more efficient allocation of resources in the expensive follow-up laboratory experiments. We used our method to reduce the number of genetic variants to consider as causal candidates for follow-up in 27 genomic regions that are associated with type 1 diabetes.
The mitochondrial Ca2+uniporter MCU is required for normal glucose-stimulated insulin secretionin vitroandin vivo
Authors: Haythorne Elizabeth , Georgiadou Eleni , Dickerson Matthew T. , Lopez-Noriega Livia , Pullen Timothy J. , da Silva Xavier Gabriela , Davis Samuel P.X. , Martinez-Sanchez Aida , Semplici Francesca , Rizzuto Rosario , McGinty James A. , French Paul M. , Cane Matthew C. , Jacobson David A. , Leclerc Isabelle , Rutter Guy A. 
Published: September 2019

AbstractMitochondrial oxidative metabolism is central to glucose-stimulated insulin secretion (GSIS). Whether Ca2+uptake into pancreatic β-cell mitochondria potentiates or antagonises this process is still a matter of debate. Although the mitochondrial importer (MCU) complex is thought to represent the main route for Ca2+transport across the inner mitochondrial membrane, its role in β-cells has not previously been examinedin vivo. Here, we inactivated the pore-forming subunit MCUa (MCU) selectively in the β-cell in mice usingIns1Cre-mediated recombination. Glucose-stimulated mitochondrial Ca2+accumulation, ATP production and insulin secretion were strongly (p<0.05 and p<0.01) inhibited inMCUnull animals (βMCU-KO)in vitro. Interestingly, cytosolic Ca2+concentrations increased (p<0.001) whereas mitochondrial membrane depolarisation improved in βMCU-KO animals. Male βMCU-KO mice displayed impairedin vivoinsulin secretion at 5 (p<0.001) but not 15 min. post intraperitoneal (IP) injection of glucose while the opposite phenomenon was observed following an oral gavage at 5 min. Unexpectedly, glucose tolerance was improved (p<0.05) in young βMCU-KO (<12 weeks), but not older animals. We conclude that MCU is crucial for mitochondrial Ca2+uptake in pancreatic β-cells and is required for normal GSIS. The apparent compensatory mechanisms which maintain glucose tolerance in βMCU-KO mice remain to be established.
EAGLE: an algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions
Authors: Gao Tianshun , Qian Jiang 
Published: September 2019

AbstractLong-range regulation by distal enhancers is crucial for many biological processes. The existing methods for enhancer-target gene prediction often require many genomic features. This makes them difficult to be applied to many cell types, in which the relevant datasets are not always available. Here, we design a tool EAGLE, an enhancer and gene learning ensemble method for identification of Enhancer-Gene (EG) interactions. Unlike existing tools, EAGLE used only six features derived from the genomic features of enhancers and gene expression datasets. Cross-validation revealed that EAGLE outperformed other existing methods. Enrichment analyses on special transcriptional factors, epigenetic modifications, and eQTLs demonstrated that EAGLE could distinguish the interacting pairs from non- interacting ones. Finally, EAGLE was applied to mouse and human genomes and identified 7,680,203 and 7,437,255 EG interactions involving 31,375 and 43,724 genes, 138,547 and 177,062 enhancers across 89 and 110 tissue/cell types in mouse and human, respectively. The obtained interactions are accessible through an interactive database enhanceratlas.org. The EAGLE method is available at https://github.com/EvansGao/EAGLE and the predicted datasets are available in http://www.enhanceratlas.org/.Author summaryEnhancers are DNA sequences that interact with promoters and activate target genes. Since enhancers often located far from the target genes and the nearest genes are not always the targets of the enhancers, the prediction of enhancer-target gene relationships is a big challenge. Although a few computational tools are designed for the prediction of enhancer-target genes, it’s difficult to apply them in most tissue/cell types due to a lack of enough genomic datasets. Here we proposed a new method, EAGLE, which utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions. Comparing with other existing tools, EAGLE displayed a better performance in the 10-fold cross-validation and cross-sample test. Moreover, the predictions by EAGLE were validated by other independent evidence such as the enrichment of relevant transcriptional factors, epigenetic modifications, and eQTLs.Finally, we integrated the enhancer-target relationships obtained from human and mouse genomes into an interactive database EnhancerAtlas, http://www.enhanceratlas.org/.
The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization
Authors: Mezencev Roman , Auerbach Scott 
Published: September 2019

AbstractWhole-genome expression data generated by microarray studies have shown promise for quantitative human health risk assessment. While numerous approaches have been developed to determine benchmark doses (BMDs) from probeset-level dose responses, sensitivity of the results to methods used for normalization of the data has not yet been systematically investigated. Normalization of microarray data converts raw hybridization signals to expression estimates that are expected to be proportional to the amounts of transcripts in the profiled specimens. Different approaches to normalization have been shown to greatly influence the results of some downstream analyses, including biological interpretation. In this study we evaluate the influence of microarray normalization methods on the transcriptomic BMDs. We demonstrate using in vivo data that the use of alternative pipelines for normalization of Affymetrix microarray data can have a considerable impact on the number of detected differentially expressed genes and pathways (processes) determined to be treatment responsive, which may lead to alternative interpretations of the data. In addition, we found that normalization can have a considerable effect (as much as ∼30-fold in this study) on estimation of the minimum biological potency (transcriptomic point of departure). We argue for consideration of alternative normalization methods and their data-informed selection to most effectively interpret microarray data for use in human health risk assessment.
DNAJB1-PRKACA fusion induces liver inflammation in zebrafish model of Fibrolamellar Hepatocellular Carcinoma
Authors: de Oliveira Sofia , Houseright Ruth A. , Korte Benjamin G. , Huttenlocher Anna 
Published: September 2019

AbstractFibrolamellar Hepatocellular Carcinoma (FLC) is a rare liver cancer that primarily affects adolescents and young adults. Up to now there is only one identified molecular target responsible for driving the disease, the chimeric protein encoded by DNAJB1-PRKACA (J-PKAca). Immune cells have been identified as key players in liver cancer biology, however the effect of J-PKAca on inflammation in the liver microenvironment is not known. Here we report a new zebrafish model of FLC with non-invasive live imaging capabilities that allows the study of the interactions between immune cells and transformed hepatocytes. We found that overexpression of the dnajb1a-prkcaaa fusion gene specifically in hepatocytes induces early malignancy features in FLC transgenic larvae, such as increased liver and hepatocyte size. In addition, this aberrant form of PKA promotes a pro-inflammatory liver microenvironment by increasing the number of neutrophils and macrophages in the liver area and inducing macrophage polarization to a pro-inflammatory phenotype. Increased caspase-a activity was also found in the liver of FLC transgenic larvae. Importantly, pharmacological inhibition of TNFα secretion and caspase-a activity decreased liver size and inflammation. Overall, these findings suggest that inflammation may be an early feature of FLC involved in progression, and that targeting TNFαand caspase-1 may be beneficial in treating FLC.
Identification of a parasitic symbiosis between respiratory metabolisms in the biogeochemical chlorine cycle
Authors: Barnum Tyler P. , Cheng Yiwei , Hill Kaisle A. , Lucas Lauren N. , Carlson Hans K. , Coates John D. 
Published: September 2019

AbstractA key step in the chlorine cycle is the reduction of perchlorate (ClO4-) and chlorate (ClO3-) to chloride by microbial respiratory pathways. Perchlorate-reducing bacteria and chlorate-reducing bacteria differ in that the latter cannot use perchlorate, the most oxidized chlorine compound. However, a recent study identified a bacterium with the chlorate reduction pathway dominating a community provided only perchlorate. Here we confirm a metabolic interaction between perchlorate- and chlorate-reducing bacteria and define its mechanism. Perchlorate-reducing bacteria supported the growth of chlorate-reducing bacteria to up to 90% of total cells in communities and co-cultures. Chlorate-reducing bacteria required the gene for chlorate reductase to grow in co-culture with perchlorate-reducing bacteria, demonstrating that chlorate is responsible for the interaction, not the subsequent intermediates chlorite and oxygen. Modeling of the interaction suggested that cells specialized for chlorate reduction have a competitive advantage for consuming chlorate produced from perchlorate, especially at high concentrations of perchlorate, because perchlorate and chlorate compete for a single enzyme in perchlorate-reducing cells. We conclude that perchlorate-reducing bacteria inadvertently support large populations of chlorate-reducing bacteria in a parasitic relationship through the release of the intermediate chlorate. An implication of these findings is that undetected chlorate-reducing bacteria have likely negatively impacted efforts to bioremediate perchlorate pollution for decades.
High-resolution MEMRI characterizes laminar specific ascending and descending spinal cord pathways in rats
Authors: Krishnan Vijai , Xu Jiadi , Mendoza German Alberto , Koretsky Alan , Anderson Stasia A , Pelled Galit 
Published: September 2019

AbstractManganese Enhanced MRI (MEMRI) utilizing different manganese chloride (MnCl2) delivery methods, has yielded valuable architectural, functional and connection information about the brain. MEMRI also has the potential in characterizing neural pathways in the spinal cord. The spinal cord grey matter is anatomically composed of nine distinct cellular laminae, where each of the laminae receives input from a specific type of neuronal population and process or serves as a relay region in a specific sensory or motor pathway. This type of laminar arrangement in the spinal cord is currently only visualized by histological methods. It is of significant interest to determine whether laminar specific enhancement by Mn2+ can be achieved in the spinal cord, as has been reported in the brain and olfactory pathway. Here we focus on using MEMRI to determine the specific laminae of the thoracic region of the spinal cord. We focus on MnCl2 changes in the ascending and descending tracts of the spinal cord. Major factors in applying this technique in the spinal cord are the ability to acquire high-resolution spinal cord images and to determine a noninvasive route of administration which will result in uptake by the central nervous system.We have applied the MEMRI approach by intraperitoneal (i.p). delivery of MnCl2 and imaged lumbar and thoracic spinal cord levels in rats to determine whether T1 weighted MRI can detect spinal cord laminae 48 hours following MnCl2 administration. T1 weighted images of the lower lumbar level were obtained from MnCl2 injected and control rats. Here we demonstrate laminar specific signal enhancement in the spinal cord of rats administered with MnCl2 vs. controls in MRI of the cord with ultra-high, 69 μm in-plane resolution. We also report reduced T1 values over time in MnCl2 groups across laminae I-IX. The regions with the largest T1 enhancements were observed to correspond to laminae that contain either high cell density or large motor neurons, making MEMRI an excellent tool for studying spinal cord architecture, physiology and function in different animal models.
Components of the endocytic and recycling trafficking pathways interfere with the integrity of theLegionella-containing vacuole
Authors: Anand Ila S. , Choi Won Young , Isberg Ralph R. 
Published: September 2019

SummaryLegionella pneumophilarequires the Dot/Icm translocation system to replicate in a vacuolar compartment within host cells. Strains lacking the translocated substrate SdhA form a permeable vacuole during residence in the host cell, exposing bacteria to the host cytoplasm. In primary macrophages, mutants are defective for intracellular growth, with a pyroptotic cell death response mounted due to bacterial exposure to the cytosol. To understand how SdhA maintains vacuole integrity during intracellular growth, we performed high-throughput RNAi screens against host membrane trafficking genes to identify factors that antagonize vacuole integrity in the absence of SdhA. Depletion of host proteins involved in endocytic uptake and recycling resulted in enhanced intracellular growth and lower levels of permeable vacuoles surrounding the ΔsdhAmutant. Of interest were three different Rab GTPases involved in these processes: Rab11b, Rab8b and Rab5 isoforms, that when depleted resulted in enhanced vacuole integrity surrounding thesdhAmutant. Proteins regulated by these Rabs are responsible for interfering with proper vacuole membrane maintenance, as depletion of the downstream effectors EEA1, Rab11FIP1, or VAMP3 rescued vacuole integrity and intracellular growth of thesdhAmutant. To test the model that specific vesicular components associated with these effectors could act to destabilize the replication vacuole, EEA1 and Rab11FIP1 showed enhanced colocalization with the vacuole surrounding thesdhAmutant compared with the WT vacuole. Depletion of Rab5 isoforms or Rab11b reduced this aberrant colocalization. These findings are consistent with SdhA interfering with both endocytic and recycling membrane trafficking events that act to destabilize vacuole integrity during infection.
A synthetic likelihood solution to the silent synapse estimation problem
Authors: Lynn Michael , Lee Kevin F.H. , Soares Cary , Naud Richard , Béïque Jean-Claude 
Published: September 2019

SummaryFunctional features of populations of synapses are typically inferred from random electrophysiological sampling of small subsets of synapses. Are these samples unbiased? Here, we developed a biophysically constrained statistical framework for addressing this question and applied it to assess the performance of a widely used method based on a failure-rate analysis to quantify the occurrence of silent (AMPAR-lacking) synapses in neural networks. We simulated this method in silico and found that it is characterized by strong and systematic biases, poor reliability and weak statistical power. Key conclusions were validated by whole-cell recordings from hippocampal neurons. To address these shortcomings, we developed a simulator of the experimental protocol and used it to compute a synthetic likelihood. By maximizing the likelihood, we inferred silent synapse fraction with no bias, low variance and superior statistical power over alternatives. Together, this generalizable approach highlights how a simulator of experimental methodologies can substantially improve the estimation of physiological properties.
White matter in infancy is prospectively associated with language outcome in kindergarten
Authors: Zuk Jennifer , Yu Xi , Sanfilippo Joseph , Figuccio Michael Joseph , Dunstan Jade , Carruthers Clarisa , Sideridis Georgios , Gagoski Borjan , Grant Patricia Ellen , Gaab Nadine 
Published: September 2019

AbstractLanguage acquisition is of central importance to a child’s development. Although the trajectory of acquisition is shaped by input and experience postnatally, the neural basis for language emerges prenatally. Thus a fundamental question remains unexamined: to what extent may the structural foundations for language established in infancy predict long-term language abilities? In this longitudinal neuroimaging investigation of children from infancy to kindergarten, we find that white matter organization in infancy is prospectively associated with subsequent language abilities, specifically between: (i) the left arcuate fasciculus in infancy and subsequent phonological awareness and vocabulary knowledge, and (ii) the left corticospinal tract in infancy and phonological awareness and phonological memory in kindergarten. Results are independent of age and home literacy environment. These findings directly link white matter organization in infancy with language abilities after school entry, and suggest that structural organization in infancy sets an important foundation for subsequent language development.
Standing genetic variation and chromosomal rearrangements facilitate local adaptation in a marine fish
Authors: Cayuela Hugo , Rougemont Quentin , Laporte Martin , Mérot Claire , Normandeau Eric , Dorant Yann , Tørresen Ole K. , Hoff Siv Nam Khang , Jentoft Sissel , Sirois Pascal , Castonguay Martin , Jansen Teunis , Praebel Kim , Clément Marie , Bernatchez Louis 
Published: September 2019

AbstractPopulation genetic theory states that adaptation most frequently occurs from standing genetic variation, which results from the interplay between different evolutionary processes including mutation, chromosomal rearrangements, drift, gene flow and selection. To date, empirical work focusing on the contribution of standing genetic variation to local adaptation in the presence of high gene flow has been limited to a restricted number of study systems. Marine organisms are excellent biological models to address this issue since many species have to cope with variable environmental conditions acting as selective agents despite high dispersal abilities. In this study, we examined how, demographic history, standing genetic variation linked to chromosomal rearrangements and shared polymorphism among glacial lineages contribute to local adaptation to environmental conditions in the marine fish, the capelin (Mallotus villosus). We used a comprehensive dataset of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,359 individuals collected from 31 spawning sites in the northwest Atlantic (North America and Greenland waters). First, we reconstructed the history of divergence among three glacial lineages and showed that they diverged from 3.8 to 1.8 MyA. Depending on the pair of lineages considered, historical demographic modelling provided evidence for divergence with gene flow and secondary contacts, shaped by barriers to gene flow and linked selection. We next identified candidate loci associated with reproductive isolation of these lineages. Given the absence of physical or geographic barriers, we thus propose that these lineages may represent three cryptic species of capelin. Within each of these, our analyses provided evidence for largeNeand high gene flow at both historical and contemporary time scales among spawning sites. Furthermore, we detected a polymorphic chromosomal rearrangement leading to the coexistence of three haplogroups within the Northwest Atlantic lineage, but absent in the other two clades. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Altogether, our study shows that standing genetic variation associated with both chromosomal rearrangements and ancestral polymorphism contribute to local adaptation in the presence of high gene flow.