bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of an imaging probe to monitor real-time redistribution of L-type voltage gated calcium channels in astrocytic glutamate signalling
Authors: Sadat Tabatabaee Mitra , Kerkovius Jeff , Menard Frederic 
Published: November 2020

ABSTRACTPurposeIn the brain, astrocytes are non-excitable cells that undergo rapid morphological changes when stimulated by the excitatory neurotransmitter glutamate. We developed a chemical probe to monitor how glutamate affects the density and distribution of astrocytic L-type voltage-gated calcium channels (LTCC).ProceduresThe imaging probe FluoBar1 was created from a barbiturate ligand modified with a fluorescent coumarin moiety. The probe selectivity was examined with colocalization analyses of confocal fluorescence imaging in U118-MG and transfected COS-7 cells. Living cells treated with 50 nM FluoBar1 were imaged in real time to reveal changes in density and distribution of astrocytic LTCCs upon exposure to glutamate.ResultsFluoBar1 was synthesized in ten steps. The selectivity of the probe was demonstrated with immunoblotting and confocal imaging of immunostained cells expressing the CaV1.2 isoform of LTCCs proteins. Applying FluoBar1 to astrocyte model cells U118-MG allowed us to measure a 5-fold increase in fluorescence density of LTCCs upon glutamate exposure.ConclusionsImaging probe FluoBar1 allows the real-time monitoring of LTCCs in living cells, revealing for first time that glutamate causes a rapid increase of LTCC membranar density in astrocyte model cells. FluoBar1 may help tackle previously intractable questions about LTCC dynamics in cellular events.
Passive visual stimulation induces fatigue or improvement depending on cognitive load
Authors: Ioannucci Stefano , Borragán Guillermo , Zénon Alexandre 
Published: November 2020

AbstractTheories of mental fatigue disagree on whether performance decrement is caused by motivational or functional alterations. We tested the assumption that keeping neural networks active for an extensive period of time entrains consequences at the subjective and objective level – the defining characteristics of fatigue – when confounds such as motivation, boredom and level of skill are controlled. We reveal that passive visual stimulation affects the performance of a subsequent task that is carried out in the same portion of visual space. This outcome, consisting either in an enhancement or deterioration of performance, was determined by the participants’ level of cognitive load and arousal, which were manipulated through variations in the difficulty of concurrent auditory tasks. Thus, repeated stimulation of neural networks leads to their altered functional performance, a mechanism which may play a role in the development of global mental fatigue.
Migraine Attacks as a Result of Hypothalamic Loss of Control
Authors: Stankewitz Anne , Keidel Leonie , Rehm Mathias , Irving Stephanie , Kaczmarz Stephan , Preibisch Christine , Witkovsky Viktor , Zimmer Claus , Schulz Enrico , Toelle Thomas R 
Published: November 2020

AbstractTo assess the natural trajectory of brain activity over the migraine cycle, we assessed (1) the cerebral perfusion and (2) the hypothalamic connectivity during spontaneous headache attacks with follow-up recordings towards the next migraine attack. Using pseudo-continuous arterial spin labelling and resting-state functional magnetic resonance imaging, 12 migraine patients were examined in 82 sessions. We detected cyclic changes of brain perfusion in the limbic circuit (insula, hippocampus, and nucleus accumbens), with the highest perfusion during headache attacks. In addition, we found an increase of hypothalamic connectivity to the limbic system over the interictal interval, then collapsing during the headache. Our data provide strong evidence for the predominant role of the hypothalamus as a zeitgeber for generating migraine attacks. Our findings suggest that migraine attacks are the result of the hypothalamus losing control over the limbic system.
Copper Containing Glass-Based Bone Adhesives for Orthopaedic Applications: Glass Characterization and Advanced Mechanical Evaluation
Authors: Mokhtari Sahar. , Wren Anthony.W. 
Published: November 2020

AbstractThis study addresses issues with currently used bone adhesives, by producing novel glass based skeletal adhesives through modification of the base glass composition to include copper (Cu) and by characterizing each glass with respect to structural changes. Bioactive glasses have found applications in fields such as orthopedics and dentistry, where they have been utilized for the restoration of bone and teeth. The present work outlines the formation of flexible organic-inorganic polyacrylic acid (PAA) – glass hybrids, commercial forms are known as glass ionomer cements (GICs). Initial stages of this research will involve characterization of the Cu-glasses, significant to evaluate the properties of the resulting adhesives. Scanning electron microscopy (SEM) of annealed Cu glasses indicates the presence of partial crystallization in the glass. The structural analysis of the glass using Raman suggests the formation of CuO nanocrystals on the surface. X-ray diffraction (XRD) pattern and X-ray photoelectron spectroscopy (XPS) further confirmed the formation of crystalline CuO phases on the surface of the annealed Cu-glass. The setting reaction was studied using Fourier transform infrared spectroscopy (ATR-FTIR). The mechanical properties of the Cu containing adhesives exhibited gel viscoelastic behavior and enhanced mechanical properties when compared to the control composition. Compression data indicated the Cu glass adhesives were efficient at energy dissipation due to the reversible interactions between CuO nano particles and PAA polymer chains.
BETA- AND GAMMA-SYNUCLEINS MODULATE SYNAPTIC VESICLE-BINDING OF ALPHA-SYNUCLEIN
Authors: Carnazza Kathryn E. , Komer Lauren , Pineda André , Na Yoonmi , Ramlall Trudy , Buchman Vladimir L. , Eliezer David , Sharma Manu , Burré Jacqueline 
Published: November 2020

SUMMARYα-Synuclein (αSyn), β-synuclein (βSyn), and γ-synuclein (γSyn) are abundantly expressed in the vertebrate nervous system. αSyn functions in neurotransmitter release via binding to and clustering synaptic vesicles and chaperoning of SNARE-complex assembly. The functions of βSyn and γSyn are unknown. Functional redundancy of the three synucleins and mutual compensation when one synuclein is deleted have been proposed, but with conflicting evidence. Here, we demonstrate that βSyn and γSyn have a reduced affinity towards membranes compared to αSyn, and that direct interaction of βSyn or γSyn with αSyn results in reduced membrane binding of αSyn. Our data suggest that all three synucleins affect synapse function, but only αSyn mediates the downstream function of vesicle clustering and SNARE-complex assembly, while βSyn and γSyn modulate the activity of αSyn through regulating its binding to synaptic vesicles.
Cancer cells are sensitive to wild-type IDH1 inhibition under nutrient limitation
Authors: Vaziri-Gohar Ali , Hue Jonathan J. , Graor Hallie J. , Prendergast Erin , Chen Vanessa , Cassel Joel , Mohammed Farheen S. , Abbas Ata , Dukleska Katerina , Khokhar Imran , Hajhassani Omid , Zarei Mahsa , Wang Rui , Rothermel Luke D. , Bederman Ilya , Browers Jessica , Getts Robert , Brunengraber Henri , Salvino Joseph M. , Brody Jonathan R. , Winter Jordan M. 
Published: November 2020

AbstractPancreatic cancer cells alter their metabolism to survive cancer-associated stress (1-4). For example, cancer cells must adapt to steep nutrient gradients that characterize the natural tumor microenvironment (TME) (5-7). In the absence of adaptive strategies, harsh metabolic conditions promote the generation of free radicals (8) and impair energy production in tumor cells. Towards this end, wild-type isocitrate dehydrogenase 1 (IDH1) activity is a metabolic requirement for cancer cells living in a harsh metabolic milieu. The cytosolic enzyme interconverts isocitrate and alpha-ketoglutarate, and uses NADP(H) as a cofactor. We show that under low nutrient conditions, the enzymatic reaction favors oxidative decarboxylation to yield NADPH and alpha-ketoglutarate. Metabolic studies showed that the IDH1 products directly support antioxidant defense and mitochondrial function in stressed cancer cells. Genetic IDH1 suppression reduced growth of pancreatic cancer cells in vitro under low nutrient conditions and in mouse models of pancreatic cancer. Surprisingly, allosteric inhibitors of mutant IDH1 proved to be potent wild-type IDH1 inhibitors under conditions specific to the TME, highlighting a natural therapeutic window. The presence of low magnesium enhanced allosteric inhibition by the drug, and ambient low glucose levels enhanced cancer cells’ dependence on wild-type IDH1. Thus, intrinsic TME conditions sensitized wild-type IDH1 to FDA-approved AG-120 (ivosidenib), and revealed the drug to be a potent single-agent therapeutic in cell culture and diverse in vivo cancer models. This work identified a potentially new repertoire of safe cancer therapies, including a clinically available compound, for the treatment of multiple wild-type IDH1 cancers (e.g., pancreatic).
Are fleas highly modified Mecoptera? Phylogenomic resolution of Antliophora (Insecta: Holometabola)
Authors: Meusemann Karen , Trautwein Michelle , Friedrich Frank , Beutel Rolf G. , Wiegmann Brian M. , Donath Alexander , Podsiadlowski Lars , Petersen Malte , Niehuis Oliver , Mayer Christoph , Bayless Keith M. , Shin Seunggwan , Liu Shanlin , Hlinka Ondrej , Minh Bui Quang , Kozlov Alexey , Morel Benoit , Peters Ralph S. , Bartel Daniela , Grove Simon , Zhou Xin , Misof Bernhard , Yeates David K. 
Published: November 2020

AbstractInsect orders have been defined and stable for decades, with few notable exceptions (e.g., Blattodea and Psocoptera). One of the few remaining questions of order-level monophyly is that of Mecoptera in respect to the phylogenetic placement of Siphonaptera (fleas). We used a large set of transcriptomic nucleotide sequence data representing 56 species and more than 3,000 single-copy genes to resolve the evolutionary history of Antliophora, including fleas (Siphonaptera), scorpionflies and relatives (Mecoptera), and true flies (Diptera). We find that fleas and mecopterans together are the sister group of flies. However, our data and/or analyses are unable to distinguish whether fleas are sister to a monophyletic Mecoptera, or whether they arose from within extant mecopteran families, rendering Mecoptera paraphyletic. We did not detect parameter bias in our dataset after applying a broad range of detection methods. Counter to a previous hypothesis that placed fleas within Mecoptera as the sister group to wingless boreids (snow fleas), we found a potential sister group relationship between fleas and the enigmatic family Nannochoristidae. Although we lack conclusive evidence, it seems possible that fleas represent the most-species rich group of modern mecopterans and that their parasitic lifestyle and morphological adaptations have simply made them unrecognizable in respect to their order-level classification.
Encoding of odor information and reward anticipation in anterior cortical amygdaloid nucleus
Authors: Shiotani Kazuki , Tanisumi Yuta , Hirokawa Junya , Sakurai Yoshio , Manabe Hiroyuki 
Published: November 2020

AbstractOlfactory information directly reaches the amygdala through the olfactory cortex, without the involvement of thalamic areas, unlike other sensory systems. The anterior cortical amygdaloid nucleus (ACo) is one of the olfactory cortices that receives olfactory sensory input, and is part of the olfactory cortical amygdala, which relays olfactory information to the amygdala. To examine its electrophysiological features, we recorded individual ACo neurons during the odor-guided go/no-go task to obtain a water reward. Many ACo neurons exhibited odor-evoked go cue-preferred during the late phase of odor-sampling supporting the population dynamics that differentiate go/no-go responses before executing the odor-evoked behaviors. We observed two types of neurons with different anticipation signals: one neuron type exhibited gradual increases of activity toward reward delivery, while another type exhibited a phasic go cue-preferred activity during odor sampling as well as another phasic anticipatory activity for rewards. These results suggest that the ACo may be involved in reward-related behavioral learning by associating the olfactory information with reward anticipation.
Assessing and Maximizing Cultivated Diversity with Plate-Wash PCR and High Throughput Sequencing
Authors: Junkins Emily N. , Stevenson Bradley S. 
Published: November 2020

AbstractMolecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Molecular methods indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments werenotdetected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete, albeit more complex, understanding of which organisms were present compared to what was eventually cultivated. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against a multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.ImportanceCultivation is the definitive tool to understand a microorganism’s physiology, metabolism, and ecological role(s). Despite continuous efforts to hone this skill, researchers are still observing yet-to-be cultivated organisms through high-throughput sequencing studies. Here, we use the very same tool that highlights biodiversity to assess cultivation efficiency. When applied to drug discovery, where screening a vast number of isolates for bioactive metabolites is common, cultivating redundant organisms is a hindrance. However, we observed that cultivating in combination with molecular tools can expand the observed diversity of an environment and its community, potentially increasing the number of microorganisms to be screened for natural products.
Sex of donor cell and reprogramming conditions predict the extent and nature of imprinting defects in mouse iPSCs
Authors: Arez Maria , Eckersley-Maslin Melanie , Klobučar Tajda , von Gilsa Lopes João , Krueger Felix , Raposo Ana Cláudia , Gendrel Anne-Valerie , de Jesus Bruno Bernardes , da Rocha Simão Teixeira 
Published: November 2020

ABSTRACTReprogramming of somatic cells into induced Pluripotent Stem Cells (iPSCs) is a major leap towards personalized approaches to disease modelling and cell-replacement therapies. However, we still lack the ability to fully control the epigenetic status of iPSCs, which is a major hurdle for their downstream applications. A sensible indicator for epigenetic fidelity is genomic imprinting, a phenomenon dependent on DNA methylation, which is frequently perturbed in iPSCs by yet unidentified reasons. By using a secondary reprogramming system with murine hybrid donor cells, we conducted a thorough imprinting analysis using IMPLICON in multiple female and male iPSCs generated under different culture conditions. Our results show that imprinting defects are remarkably common in mouse iPSCs causing dysregulation of the typical monoallelic expression of imprinted genes. Interestingly, the nature of imprinting defects depends on the sex of the donor cell and their respective response to culture conditions. Under serum-free conditions, male iPSCs show global hypomethylation at imprinted regions, whereas in serum conditions show focal hypermethylation at specific loci. In contrast, female iPSCs always exhibit hypomethylation defects regardless of culture conditions. These imprinting defects are more severe than the global changes in DNA methylation, highlighting the sensitivity of imprinting loci to current iPSC generation protocols. Our results reveal clear predictors underlying different types of imprinting defects in mouse iPSCs. This knowledge is essential to devise novel reprogramming strategies aiming at generating epigenetically faithful iPSCs.
Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon
Authors: Verta Jukka-Pekka , Barton Henry , Pritchard Victoria , Primmer Craig 
Published: November 2020

AbstractWhole genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Mya. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained asymmetric regulatory evolution. Patterns of genetic diversity across natural populations inferred from re-sequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift.Significance statementRegulatory evolution following whole genome duplications (WGD) has been investigated at the gene expression level, but studies of the regulatory elements that control expression have been lacking. By investigating regulatory elements in the Atlantic salmon genome, which has undergone a whole genome duplication 100-80 million years ago, we discovered patterns suggesting that neutral divergence is the prevalent mode of regulatory element evolution post-WGD. Our results suggest mechanisms for explaining the prevalence of asymmetric gene expression evolution following whole genome duplication, as well as the mismatch between evolutionary rates in enhancers versus that of promoters.
Exploring the limits of ComBat method for multi-site diffusion MRI harmonization
Authors: Cetin-Karayumak Suheyla , Stegmayer Katharina , Walther Sebastian , Szeszko Philip R. , Crow Tim , James Anthony , Keshavan Matcheri , Kubicki Marek , Rathi Yogesh 
Published: November 2020

AbstractThe findings from diffusion-weighted magnetic resonance imaging (dMRI) studies often show inconsistent and sometimes contradictory results due to small sample sizes as well as differences in acquisition parameters and pre-/post-processing methods. To address these challenges, collaborative multi-site initiatives have provided an opportunity to collect larger and more diverse groups of subjects, including those with neuropsychiatric disorders, leading to increased power and findings that may be more representative at the group and individual level. With the availability of these datasets openly, the ability of joint analysis of multi-site dMRI data has become more important than ever. However, intrinsic- or acquisition-related variability in scanner models, acquisition protocols, and reconstruction settings hinder pooling multi-site dMRI directly. One powerful and fast statistical harmonization method called ComBat (https://github.com/Jfortin1/ComBatHarmonization) was developed to mitigate the “batch effect” in gene expression microarray data and was adapted for multi-site dMRI harmonization to reduce scanner/site effect. Our goal is to evaluate this commonly used harmonization approach using a large diffusion MRI dataset involving 542 individuals from 5 sites. We investigated two important aspects of using ComBat for harmonization of fractional anisotropy (FA) across sites: First, we assessed how well ComBat preserves the inter-subject biological variability (measured by the effect sizes of between-group FA differences) after harmonization. Second, we evaluated the effect of minor differences in pre-processing on ComBat’s performance. While the majority of effect sizes are mostly preserved in some sites after harmonization, they are not well-preserved at other sites where non-linear scanner contributions exist. Further, even minor differences in pre-processing can yield unwanted effects during ComBat harmonization. Thus, our findings suggest paying careful attention to the data being harmonized as well as using the same processing pipeline while using ComBat for data harmonization.
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation
Authors: Bonora Giancarlo , Ramani Vijay , Singh Ritambhara , Fang He , Jackson Dana , Srivatsan Sanjay , Qiu Ruolan , Lee Choli , Trapnell Cole , Shendure Jay , Duan Zhijun , Deng Xinxian , Noble William S. , Disteche Christine M. 
Published: November 2020

AbstractMammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a ‘bookkeeping’ mechanism. In differentiating embryonic stem cells, changes in contact decay profiles are detected in parallel on both the X chromosomes and autosomes, suggesting profound simultaneous reorganization. The onset of the inactive X-specific structure in single cells is notably delayed relative to that of gene silencing, consistent with the idea that chromatin compaction is a late event of X inactivation. Novel computational approaches to effectively align single-cell gene expression, chromatin accessibility, and 3D chromosome structure reveal that long-range structural changes to chromosomes appear as discrete events, unlike progressive changes in gene expression and chromatin accessibility.