bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanophenotyping of 3D Multicellular Clusters using Displacement Arrays of Rendered Tractions
Authors: Leggett Susan E. , Patel Mohak , Valentin Thomas M. , Gamboa Lena , Khoo Amanda S. , Williams Evelyn Kendall , Franck Christian , Wong Ian Y. 
Published: October 2019

ABSTRACTEpithelial tissues mechanically deform the surrounding extracellular matrix during embryonic development, wound repair, and tumor invasion. Ex vivo measurements of such multicellular tractions within three-dimensional (3D) biomaterials could elucidate collective dissemination during disease progression, and enable preclinical testing of targeted anti-migration therapies. However, past 3D traction measurements have been low throughput due to the challenges of imaging and analyzing information-rich 3D material deformations. Here, we demonstrate a method to profile multicellular clusters in a 96-well plate format based on spatially heterogeneous contractile, protrusive, and circumferential tractions. As a case study, we profile multicellular clusters across varying states of the epithelial-mesenchymal transition, revealing a successive loss of protrusive and circumferential tractions, as well as the formation of localized contractile tractions with elongated cluster morphologies. These cluster phenotypes were biochemically perturbed using drugs, biasing towards traction signatures of different epithelial or mesenchymal states. This higher-throughput analysis is promising to systematically interrogate and perturb aberrant mechanobiology, which could be utilized with human patient samples to guide personalized therapies.
Sex classification using long-range temporal dependence of resting-state functional MRI time series
Authors: Dhamala Elvisha , Jamison Keith W. , Sabuncu Mert R. , Kuceyeski Amy 
Published: October 2019

AbstractA thorough understanding of sex differences, if any, that exist in the brains of healthy individuals is crucial for the study of neurological illnesses that exhibit differences in clinical and behavioural phenotypes between males and females. In this work, we evaluate sex differences in regional temporal dependence of resting-state brain activity using 195 male-female pairs (aged 22-37) from the Human Connectome Project. Male-female pairs are strictly matched for total grey matter volume. We find that males have more persistent long-range temporal dependence than females in regions within temporal, parietal, and occipital cortices. Machine learning algorithms trained on regional temporal dependence measures achieve sex classification accuracies of up to 81%. Regions with the strongest feature importance in the sex classification task included cerebellum, amygdala, frontal cortex, and occipital cortex. Additionally, we find that even after males and females are strictly matched on total grey matter volume, significant regional volumetric sex differences persist in many cortical and subcortical regions. Our results indicate males have larger cerebella, hippocampi, parahippocampi, thalami, caudates, and amygdalae while females have larger cingulates, precunei, frontal cortices, and parietal cortices. Sex classification based on regional volume achieves accuracies of up to 85%; cerebellum, cingulate cortex, and temporal cortex are the most important features. These findings highlight the important role of strict volume matching when studying brain-based sex differences. Differential patterns in regional temporal dependence between males and females identifies a potential neurobiological substrate underlying sex differences in functional brain activation patterns and the behaviours with which they correlate.
γH2AX in the S Phase After UV Irradiation Corresponds to DNA Replication and Not to the Extent of DNA Damage
Authors: Dhuppar Shivnarayan , Roy Sitara , Mazumder Aprotim 
Published: October 2019

AbstractUltraviolet (UV) radiation is a major environmental mutagen. Exposure to UV leads to a sharp peak of γH2AX – the phosphorylated form of a histone variant H2AX – in the S phase within an asynchronous population of cells. γH2AX is often considered as a definitive marker of DNA damage inside a cell. In this report we show that γH2AX in the S phase cells after UV irradiation does not report on the extent of primary DNA damage in the form of cyclobutane pyrimidine dimers or on the extent of its secondary manifestations as DNA double strand breaks or in the inhibition of global transcription. Instead γH2AX in the S phase corresponds to the sites of active replication at the time of UV irradiation – despite which, the cells complete the replication of their genomes and arrest within the G2 phase. Moreover, cells in all the phases of the cell cycle develop similar levels of DNA damage. Our study suggests that it is not DNA damage but the response elicited, which peaks in the S phase upon UV damage.
The spatial heterogeneity of the gut limits bacteriophage predation leading to the coexistence of antagonist populations of bacteria and their viruses
Authors: Lourenço Marta , Chaffringeon Lorenzo , Lamy-Besnier Quentin , Campagne Pascal , Eberl Claudia , Bérard Marion , Stecher Bärbel , Debarbieux Laurent , De Sordi Luisa 
Published: October 2019

AbstractBacteria and their viruses, bacteriophages (phages), are the most abundant components of the mammalian gut microbiota where these two entities coexist over time. The ecological dynamics underlying the coexistence between these two antagonistic populations in the gut are unknown. We challenged a murine synthetic bacterial community with a set of virulent phages, to study the factors allowing phages-bacteria coexistence in the gut. We found that coexistence was neither dependent on an arms race between bacteria and phages, nor on the ability of phages to extend host range. Instead, our data suggest that some phage-inaccessible sites in the mucosa of the ileum serve as a spatial refuge for bacteria, which from there disseminate in the gut lumen. Luminal phages amplify by infecting luminal bacteria maintaining phage throughout the gut. We conclude that the heterogeneous distribution of microbes in the gut contributes to the long-term coexistence of phages with phage-susceptible bacteria. This observation could explain the persistence in the human gut of intestinal phages, such as the crAssphage, as well as the low efficiency of oral phage therapy against enteric pathogens in animal models and clinical trials.
GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment
Authors: Rautiainen Mikko , Marschall Tobias 
Published: October 2019

AbstractGenome graphscan represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pan-genome graph. Yet, so far this step is often prohibitively slow. We present GraphAligner, a tool for aligning long reads to genome graphs. Compared to state-of-the-art tools, GraphAligner is 12x faster and uses 5x less memory, making it as efficient as aligning reads to linear reference genomes. When employing GraphAligner for error correction, we find it to be almost 3x more accurate and over 15x faster than extant tools.Availability Package managerhttps://anaconda.org/bioconda/graphalignerand source code:https://github.com/maickrau/GraphAligner
Changes in cross-frequency coupling following closed-loop auditory stimulation in non-rapid eye movement sleep
Authors: Elena Krugliakova , Carina Volk , Valeria Jaramillo , Georgia Sousouri , Reto Huber 
Published: October 2019

AbstractThe activity of different brain networks in non-rapid eye movement (NREM) sleep is regulated locally in an experience-dependent manner, reflecting the extent of the network load during wakefulness. In particular, improved task performance after sleep correlates with the local post-learning power increase of neocortical slow waves and faster oscillations such as sleep spindles and their temporal coupling. Recently, it was demonstrated that by targeting slow waves in a particular region at a particular phase with closed-loop auditory stimulation it is possible to locally manipulate slow-wave activity and interact with training-induced neuroplastic changes. Based on this finding, we tested whether closed-loop auditory stimulation targeting the up-phase of slow-waves over the right sensorimotor area might affect power in delta, theta and sigma bands and coupling between these oscillations within the circumscribed region. We demonstrate that while closed-loop auditory stimulation globally enhances power in delta, theta and sigma bands, changes in cross-frequency coupling of these oscillations were more spatially restricted. In particular, stimulation induced a significant decrease of delta-theta coupling in frontal channels, within the area of the strongest baseline coupling between these frequency bands. In contrast, a significant increase in delta-sigma coupling was observed over the right parietal area, located directly posterior to the target electrode. These findings suggest that closed-loop auditory stimulation locally modulates coupling between delta phase and sigma power in a targeted region, which could be used to manipulate sleep-dependent memory formation within the brain network of interest.
Statistical Analysis of Spatial Expression Pattern for Spatially Resolved Transcriptomic Studies
Authors: Sun Shiquan , Zhu Jiaqiang , Zhou Xiang 
Published: October 2019

ABSTRACTRecent development of various spatially resolved transcriptomic techniques has enabled gene expression profiling on complex tissues with spatial localization information. Identifying genes that display spatial expression pattern in these studies is an important first step towards characterizing the spatial transcriptomic landscape. Detecting spatially expressed genes requires the development of statistical methods that can properly model spatial count data, provide effective type I error control, have sufficient statistical power, and are computationally efficient. Here, we developed such a method, SPARK. SPARK directly models count data generated from various spatial resolved transcriptomic techniques through generalized linear spatial models. With a new efficient penalized quasi-likelihood based algorithm, SPARK is scalable to data sets with tens of thousands of genes measured on tens of thousands of samples. Importantly, SPARK relies on newly developed statistical formulas for hypothesis testing, producing well-calibratedp-values and yielding high statistical power. We illustrate the benefits of SPARK through extensive simulations and in-depth analysis of four published spatially resolved transcriptomic data sets. In the real data applications, SPARK is up to ten times more powerful than existing approaches. The high power of SPARK allows us to identify new genes and pathways that reveal new biology in the data that otherwise cannot be revealed by existing approaches.
From behavior to circuit modeling of light-seeking navigation in zebrafish larvae
Authors: Karpenko Sophia , Wolf Sébastien , Lafaye Julie , Goc Guillaume Le , Panier Thomas , Bormuth Volker , Candelier Raphaël , Debrégeas Georges 
Published: October 2019

AbstractBridging brain-scale circuit dynamics and organism-scale behavior is a central challenge in neuroscience. It requires the concurrent development of minimal behavioral and neural circuit models that can quantitatively capture basic sensorimotor operations. Here we focus on light-seeking navigation in zebrafish larvae. Using a virtual reality assay, we first characterize how motor and visual stimulation sequences govern the selection of discrete swim-bout events that subserve the fish navigation in the presence of a distant light source. These mechanisms are combined into a comprehensive Markov-chain model of navigation that quantitatively predict the stationary distribution of the fish’s body orientation under any given illumination profile. We then map this behavioral description onto a neuronal model of the ARTR, a small neural circuit involved in the orientation-selection of swim bouts. We demonstrate that this visually-biased decision-making circuit can similarly capture the statistics of both spontaneous and contrast-driven navigation.
Ketamine anesthesia induces gain enhancement via recurrent excitation in granular input layers of the auditory cortex
Authors: Deane Katrina E. , Brunk Michael G. K. , Curran Andrew W. , Zempeltzi Marina M. , Ma Jing , Lin Xiao , Abela Francesca , Aksit Sümeyra , Deliano Matthias , Ohl Frank W. , Happel Max F. K. 
Published: October 2019

The N-methyl-D-aspartate (NMDA) receptor antagonist, ketamine, is commonly used as an anesthetic agent and has more recently gained attention as an antidepressant. Ketamine has been linked to increased stimulus-locked excitability, inhibition of interneurons, and modulation of intrinsic neuronal oscillations. However, the functional network mechanisms are still elusive. A better understanding of these anesthetic network effects may improve upon previous interpretations of seminal studies conducted under anesthesia and have widespread relevance for neuroscience with awake and anesthetized subjects as well as in medicine. Here, we investigated the effects of anesthetic doses of ketamine (15mg kg−1/h i.p.) on the network activity after pure tone stimulation within the auditory cortex of male Mongolian gerbils (Meriones unguiculatus). We used laminar current source density (CSD) analysis and subsequent layer-specific continuous wavelet analysis to investigate spatiotemporal response dynamics on cortical columnar processing in awake and ketamine-anesthetized animals. We found thalamocortical input processing within granular layers III/IV to be significantly increased under ketamine. This effect on early thalamocortical input processing was not due to changes in cross-trial phase coherence. Rather, the layer-dependent gain enhancement under ketamine was attributed to a broadband increase in amplitude reflecting an increase in recurrent excitation. The time-frequency analysis is further indicative of a prolonged period of stimulus-induced excitation possibly due to a reduced coupling of excitation and inhibition in granular input circuits—in line with the common hypothesis of cortical disinhibition via NMDA-mediated suppression of GABAergic interneurons.Statement of significanceKetamine is a common anesthetic agent and is known to alter excitability and neuronal synchronicity in the cortex. We reveal here that anesthetic doses of ketamine increase recurrent excitation of thalamic input in the granular layers of the auditory cortex of Mongolian gerbils. This leads to a layer-specific gain enhancement of the time-locked response to external stimuli. Analysis of tone-evoked amplitudes and cross-trial variability of cortical current sources and sinks indicate a mechanism of cortical disinhibition via NMDA-mediated suppression of GABAergic interneurons. Our findings might help to understand the functional mechanisms of the clinical effects of ketamine promoting the development of new therapeutic agents with lower side effects.
What is in a lichen? A metagenomic approach to reconstruct the holo-genome of Umbilicaria pustulata
Authors: Tzovaras Bastian Greshake , Segers Francisca H.I.D. , Bicker Anne , Grande Francesco Dal , Otte Jürgen , Anvar Seyed Yahya , Hankeln Thomas , Schmitt Imke , Ebersberger Ingo 
Published: October 2019

AbstractLichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are generally poor candidates for experimentation. Obtaining contiguous, high quality genomes for such symbiotic communities is technically challenging. Here we present the first assembly of a lichen holo-genome from metagenomic whole genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis – the fungus Umbilicaria pustulata (33 Mbp) and the green alga Trebouxia sp. (53 Mbp) – were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative cellular abundance of approximately 20:1 (fungus:alga). Gap-free, circular sequences for all organellar genomes were obtained. The community of lichen-associated bacteria is dominated by Acidobacteriaceae, and the two largest bacterial contigs belong to the genus Acidobacterium. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that G/C-rich inverted repeats paired with non-random sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.
Evidence for a role for BK channels in the regulation of ADAM17 activity
Authors: Yoshida Minae , Willis Dean 
Published: October 2019

AbstractLarge-conductance voltage and calcium activated channels, KCa1.1, have a large single conductance (~p250) and are highly selective for potassium ions. As a result they have been termed big potassium channels (BK channels). Because of the channel’s ability to integrate multiple physical and chemical signals they have received much attention in excitable cells. In comparison they have received relatively little attention in non-excitable cells in those of the immune system. Here we report evidence that the BK channel regulates ADAM17 activity. Upon macrophage activation, BK channels translocate to the cell membrane. Genetic or pharmacological inhibition of the cell membrane BK channels resulted in elevated TNF-α release and increased metalloproteinase a disintegrin and metalloproteinase domain 17 (ADAM17) activity. Inhibitors of BK channels also increased IL-6Rα release, a second ADAM17 substrate. In comparison, a BK channel opener decreases TNF-α release. Taken together, our results demonstrate a novel mechanism by which ion channel regulates ADAM17 activity. Given the broad range of ADAM17 substrates, this finding has implications in many fields of cell biology including immunology, neurology and cancer biology.
CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex
Authors: Gerbracht Jennifer V. , Boehm Volker , Britto-Borges Thiago , Kallabis Sebastian , Wiederstein Janica L. , Ciriello Simona , Aschemeier Dominik U. , Krüger Marcus , Frese Christian K. , Altmüller Janine , Dieterich Christoph , Gehring Niels H. 
Published: October 2019

AbstractThe exon junction complex (EJC) is an essential constituent and regulator of spliced messenger ribonucleoprotein particles (mRNPs) in metazoans. As a core component of the EJC, CASC3 was described to be pivotal for EJC-dependent nuclear and cytoplasmic processes. However, recent evidence suggests that CASC3 functions differently from other EJC core proteins. Here, we have established human CASC3 knockout cell lines to elucidate the cellular role of CASC3. In the knockout cells, overall EJC composition and EJC-dependent splicing are unchanged. A transcriptome-wide analysis reveals that hundreds of mRNA isoforms targeted by nonsense-mediated decay (NMD) are upregulated. Mechanistically, recruiting CASC3 to reporter mRNAs by direct tethering or via binding to the EJC stimulates mRNA decay and endonucleolytic cleavage at the termination codon. Building on existing EJC-NMD models, we propose that CASC3 equips the EJC with the ability to communicate with the NMD machinery in the cytoplasm. Collectively, our results characterize CASC3 as a peripheral EJC protein that tailors the transcriptome by promoting the degradation of EJC-dependent NMD substrates.
Selective disruption of synaptic BMP signaling by a Smad mutation adjacent to the highly conserved H2 helix
Authors: Nguyen Tho Huu , Han Tae Hee , Newfeld Stuart , Serpe Mihaela 
Published: October 2019

ABSTRACTBone morphogenetic proteins (BMPs) shape normal development and function via canonical and non-canonical signaling pathways. When activating the canonical pathway, BMPs initiate signaling by binding to transmembrane receptors that phosphorylate pathway effectors, the Smad proteins, inducing their translocation into the nucleus and thus regulation of target genes. Phosphorylated Smads also accumulate at cellular junctions, but this non-canonical signaling modality remains less defined. We have recently reported that phosphorylated Smad (pMad inDrosophila) accumulates at synaptic junctions in complexes with genetically distinct composition and regulation. Here we examined a wide collection ofDrosophila Madalleles and searched for molecular features relevant to pMad accumulation at synaptic junctions. We found that strongMadalleles generally disrupt both synaptic and nuclear pMad accumulation, whereas moderateMadalleles have a wider range of phenotypes and could selectively impact different BMP signaling modalities. Interestingly, synaptic pMad appeared more sensitive to net reduction in Mad levels than nuclear pMad. Importantly, a previously uncharacterized allele,Mad8, showed markedly reduced synaptic pMad levels but only moderately diminished nuclear pMad signals. The postsynaptic composition and electrophysiological properties ofMad8NMJs were similarly altered. Using biochemical approaches, we examined how single point mutations such as S359L, present inMad8, could influence the Mad-receptor interface and we identified a key molecular determinant, the H2 helix. Our study highlights the biological relevance of the Smad-dependent, non-canonical BMP signaling and uncovers a highly conserved structural feature of Smads, critical for normal development and function.
IL-15 re-programming compensates for NK cell mitochondrial dysfunction in HIV-1 infection
Authors: Cubero Elia Moreno , Balint Stefan , Alrubayyi Aljawharah , Ogbe Ane , Matthews Rebecca , Burns Fiona , Rowland-Jones Sarah , Borrow Persephone , Schurich Anna , Dustin Michael , Peppa Dimitra 
Published: October 2019

AbstractDynamic regulation of cellular metabolism is important for maintaining homeostasis and can directly influence immune cell function and differentiation including Natural Killer (NK) cell responses. Persistent HIV-1 infection leads to a state of chronic activation, subset redistribution and progressive NK cell dysregulation. In this study we examined the metabolic processes that characterise NK cell subsets in HIV-1 infection, including adaptive NK cell subpopulations expressing the activating receptor NKG2C, which expand during chronic infection. These adaptive NK cells exhibit an enhanced metabolic profile in human cytomegalovirus (HCMV) infected HIV-1 seronegative individuals. However, the bioenergetic advantage of adaptive CD57+NKG2C+ NK cells is diminished during chronic HIV-1 infection, where NK cells uniformly display reduced oxidative phosphorylation (OXPHOS) and limited fuel flexibility upon CD16 stimulation. Defective OXPHOS was accompanied by increased mitochondrial depolarisation and structural alterations indicative of mitochondrial dysfunction, suggesting that mitochondrial defects are restricting the metabolic plasticity of NK cell subsets in HIV-1 infection. The metabolic requirement for receptor stimulation was alleviated upon IL-15 pre-treatment enhancing mammalian target of rapamycin complex1 (mTORC1) activity and NK cell functionality in HIV-1 infection, representing an effective strategy for pharmacologically boosting NK cell responses.