bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionarily Conserved Transcription Factors Drive the Oxidative Stress Response in Drosophila
Authors: Ryan Sarah M. , Wildman Kaitie , Oceguera-Perez Briseida , Barbee Scott , Mortimer Nathan T. , Vrailas-Mortimer Alysia D. 
Published: August 2019

AbstractAs organisms are constantly exposed to the damaging effects of oxidative stress through both environmental exposure as well as internal metabolic processes, they have evolved a variety of mechanisms to cope with this stress. One such mechanism is the highly conserved p38 MAPK (p38K) pathway, which is known to be to post-translationally activated in response to oxidative stress resulting in the activation of downstream antioxidant targets. However, little is known about the role of p38K transcriptional regulation in response to oxidative stress. Therefore, we analyzed the p38K gene family across the genus Drosophila to identify conserved regulatory elements. We find that oxidative stress exposure results in increased p38K protein levels in multiple Drosophila species and is associated with increased oxidative stress resistance. We also find that the p38Kb genomic locus includes conserved binding sites for the AP-1 and lola-PT transcription factors. Accordingly, over-expression of these transcription factors in D. melanogaster is sufficient to induce transcription of p38Kb and enhances resistance to oxidative stress. We further find that the presence of a lola-PT binding site in the p38Kb locus of a given species is predictive of the species’ survival in response to oxidative stress. Through our comparative genomics approach, we have identified biologically relevant transcription factor binding sites that regulate the expression of p38Kb and are associated with resistance to oxidative stress. These findings reveal a novel mode of regulation for p38K genes and suggests that transcription may play as important a role in p38K mediated stress responses as post-translational modifications.Significance StatementOrganisms encounter a variety of environmental stresses such as oxidative stress throughout their lifetime. Therefore, organisms have evolved a number of mechanisms to combat these stresses. In order to understand how these mechanisms evolved, we have compared the genomes of a diverse set of species across the genus Drosophila to examine the p38 MAPK stress response gene family. Our analysis was able to successfully predict transcription factors that not only regulate our target gene, p38Kb, but do so under different conditions to ensure an appropriate stress response. Therefore, we find that in addition to post-translational regulation, transcriptional regulation of signaling pathways may also play an important role in how organisms are able to adapt to stressful environments or respond to stress conditions as they arise. Furthermore, our comparative genomics approach may be utilized to identify transcriptional regulators of other highly conserved signaling pathways.
The chromosomal-level genome assembly and comprehensive transcriptomes of Chinese razor clam (Sinonovacula constricta) with deep-burrowing life style and broad-range salinity adaptation
Authors: Dong Yinghui , Zeng Qifan , Ren Jianfeng , Yao Hanhan , Ruan Wenbin , Lv Liyuan , He Lin , Xue Qinggang , Bao Zhenmin , Wang Shi , Lin Zhihua 
Published: August 2019

AbstractBackgroundThe Chinese razor clam, Sinonovacula constricta, is one of the commercially important marine bivalves with deep-burrowing lifestyle and remarkable adaptability of broad-range salinity. Despite its economic impact and representative of the less-understood deep-burrowing bivalve lifestyle, there are few genomic resources for exploring its unique biology and adaptive evolution. Herein, we reported a high-quality chromosomal-level reference genome of S. constricta, the first genome of the family Solenidae, along with a large amount of short-read/full-length transcriptomic data of whole-ontogeny developmental stages, all major adult tissues, and gill tissues under salinity challenge.FindingsA total of 101.79 Gb and 129.73 Gb sequencing data were obtained with the PacBio and Illumina platforms, which represented approximately 186.63X genome coverage. In addition, a total of 160.90 Gb and 24.55 Gb clean data were also obtained with the Illumina and PacBio platforms for transcriptomic investigation. A de novo genome assembly of 1,340.13 Mb was generated, with a contig N50 of 689.18 kb. Hi-C scaffolding resulted in 19 chromosomes with a scaffold N50 of 57.99 Mb. The repeat sequences account for 50.71% of the assembled genome. A total of 26,273 protein-coding genes were predicted and 99.5% of them were annotated. Phylogenetic analysis revealed that S. constricta diverged from the lineage of Pteriomorphia at approximately 494 million years ago. Notably, cytoskeletal protein tubulin and motor protein dynein gene families are rapidly expanded in the S. constricta genome and are highly expressed in the mantle and gill, implicating potential genomic bases for the well-developed ciliary system in the S. constricta.ConclusionsThe high-quality genome assembly and comprehensive transcriptomes generated in this work not only provides highly valuable genomic resources for future studies of S. constricta, but also lays a solid foundation for further investigation into the adaptive mechanisms of benthic burrowing mollusks.
Characterizing upper extremity motor behavior in the first week after stroke
Authors: Barth Jessica , Geed Shashwati , Mitchell Abigail , Lum Peter S. , Edwards Dorothy F. , Dromerick Alexander W. 
Published: August 2019

AbstractBackgroundAnimal models of brain recovery identify the first days after lesioning as a time of great flux in sensorimotor function and physiology; these findings have implications for human stroke recovery. After rodent motor system lesioning, daily skill training in the less affected forelimb reduces skill acquisition in the more affected forelimb. We asked whether spontaneous human motor behaviors of the less affected upper extremity (UE) early after stroke resemble the animal training model, with the potential to suppress clinical recovery.MethodsThis prospective observational study used a convenience sample of patients <7 days after stroke (n=25) with a wide severity range; Controls were hospitalized for non-neurological conditions (n=12). Outcome measures were Accelerometry, Upper-Extremity Fugl-Meyer (UEFM), Action Research Arm Test (ARAT), Shoulder Abduction/ Finger Extension Test (SAFE), NIH Stroke Scale (NIHSS).ResultsAccelerometry indicated total paretic UE movement was reduced compared to controls, primarily due to a 44% reduction of bilateral UE use. Unilateral paretic movement was unchanged. Movement shifted to unilateral use of the nonparetic UE, which increased by 77%. Low correlations between movement time and motor performance prompted an exploratory factor analysis (EFA) revealing a 2-component solution; motor performance tests load on one component (motor performance) whereas accelerometry-derived variables load on a second non-orthogonal component (quantity of movement).ConclusionsEarly after stroke, spontaneous overall UE movement is reduced, and movement shifts to unilateral use of the nonparetic UE. Thus, spontaneously-arising UE motor behaviors early after stroke are potential substrates for two mechanisms associated with poorer motor outcomes in animal models: learned non-use and inhibition of motor recovery through training of the nonparetic side. Accurate UE motor assessment requires two independent constructs: motor performance and quantity of movement. These findings provide opportunities and measurement methods for studies to develop new behaviorally-based stroke recovery treatments that begin early after onset.
Cholinergic-like neurons carrying PSEN1 E280A mutation from familial Alzheimer’s disease reveal intraneuronal Aβ42 peptide accumulation, hyperphosphorylation of TAU, oxidative stress, apoptosis and Ca2+ flux dysregulation: Therapeutic Implications
Authors: Soto-Mercado Viviana , Mendivil-Perez Miguel , Velez-Pardo Carlos , Lopera Francisco , Jimenez-Del-Rio Marlene 
Published: August 2019

AbstractAlzheimer’s disease (AD) is a neurodegenerative disorder characterized by progressive memory loss and cognitive disturbance as a consequence of the loss of cholinergic neurons in the brain, neuritic plaques and hyperphosphorylation of TAU protein. Although the underlying mechanisms leading to these events are unclear, mutations in presenilin 1 (PSEN1), e.g., E280A (PSEN1 E280A), are causative factors for autosomal dominant early-onset familial AD (FAD). Despite advances in the understanding of the physiopathology of AD, there are no efficient therapies to date. Limitations in culturing brain-derived live neurons might explain the limited effectiveness of AD research. Here, we show that mesenchymal stromal (stem) cells (MSCs) can be used to model FAD, providing novel opportunities to study cellular mechanisms and to establish therapeutic strategies. Indeed, we cultured MSCs with the FAD mutation PSEN1 E280A and wild-type (WT) PSEN1 from umbilical cords and characterized the transdifferentiation of these cells into cholinergic-like neurons (ChLNs). PSEN1 E280A ChLNs but not WT PSEN1 ChLNs exhibited increased intra- and extracellular Aβ42 peptide and TAU phosphorylation (at residues Ser202/Thr205), recapitulating the molecular pathogenesis of FAD caused by mutant PSEN1. Furthermore, PSEN1 E280A ChLNs presented oxidative stress (OS) as evidenced by the oxidation of DJ-1Cys106-SH into DJ-1Cys106-SO3 and the detection of DCF-positive cells and apoptosis markers such as activated pro-apoptosis proteins p53, c-JUN, PUMA and CASPASE-3 and the concomitant loss of the mitochondrial membrane potential and DNA fragmentation. Additionally, mutant ChLNs displayed Ca2+ flux dysregulation and deficient acetylcholinesterase (AChE) activity compared to control ChLNs. Interestingly, the inhibitor JNK SP600125 almost completely blocked TAU phosphorylation. Our findings demonstrate that FAD MSC-derived cholinergic neurons with the PSEN1 E280A mutation are a valid model of AD and provide important clues for the identification of targetable pathological molecules.
Level of completion along continuum of care for maternal and child health services and factors associated with it among women in Arba Minch Zuria Woreda, Gamo Zone, Southern Ethiopia: a community based cross-sectional study
Authors: Haile Dereje , Kondale Mekdes , Andarge Eshetu , Tunje Abayneh , Fikadu Teshale , Boti Nigussie 
Published: August 2019

ABSTRACTBackgroundCompletion along continuum of care for maternal and newborn health(MNH) service like antenatal care, skilled birth attendance and postnatal care services is one of the currently recommended strategies to reduce both maternal and neonatal mortality to achieve the global target of ending preventable maternal and under five children’s mortality. Although studies on factors affecting each segment of MNH services were well documented in Ethiopia, there is a dearth of evidence on the level of continuum of care and factors associated with it. Thus, this study tries to fill this gap in the country in general and in the study area in particular.MethodsA community-based cross sectional study was conducted among 438 postnatal women who gave births in the last one year in Arba Minch Health and Demographic Surveillance Site. The sample women were selected by using computer generated random numbers from the list of women who gone at least six-weeks after birth. A pre-tested structured interviewer-administered questionnaire was used for data collection. Data was entered and coded in Epi-data and analysed using SPSS software version 23. Binary logistic regression model was fitted to identify factors associated with the outcome variable.ResultsThe overall completion along the continuum of care was 42(9.7%). The factors significantly associated with continuum of care completion were early antenatal booking (before 16 weeks) [AOR: 10.751, CI (5.095, 22.688], birth preparedness and complication readiness [AOR: 2.934, CI (1.414, 6.087), pre-pregnancy contraception utilization [AOR: 3.963, CI: 1.429,10.990], employed women [AOR: 2.586, CI: ((1.245, 5.371))], and planned pregnancy [AOR: 3.494 CI :(1.068, 11.425)].ConclusionCompletion along continuum of care was low in the study area. Thus, efforts in improving completion of the cares should focus on early booking during antenatal period, reducing unplanned pregnancy, and improvement on birth preparedness and complication readiness interventions.
Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms
Authors: Morgan Daniel , Studham Matthew , Tjärnberg Andreas , Weishaupt Holger , Swartling Fredrik J. , Nordling Torbjörn E. M. , Sonnhammer Erik L.L. 
Published: August 2019

AbstractThe gene regulatory network (GRN) of human cells encodes mechanisms to ensure proper functioning. However, if this GRN is dysregulated, the cell may enter into a disease state such as cancer. Understanding the GRN as a system can therefore help identify novel mechanisms underlying disease, which can lead to new therapies. Reliable inference of GRNs is however still a major challenge in systems biology.To deduce regulatory interactions relevant to cancer, we applied a recent computational inference framework to data from perturbation experiments in squamous carcinoma cell line A431. GRNs were inferred using several methods, and the false discovery rate was controlled by the NestBoot framework. We developed a novel approach to assess the predictiveness of inferred GRNs against validation data, despite the lack of a gold standard. The best GRN was significantly more predictive than the null model, both in crossvalidated benchmarks and for an independent dataset of the same genes under a different perturbation design. It agrees with many known links, in addition to predicting a large number of novel interactions from which a subset was experimentally validated. The inferred GRN captures regulatory interactions central to cancer-relevant processes and thus provides mechanistic insights that are useful for future cancer research.Data available at GSE125958Inferred GRNs and inference statistics available at https://dcolin.shinyapps.io/CancerGRN/ Software available at https://bitbucket.org/sonnhammergrni/genespider/src/BFECV/Author SummaryCancer is the second most common cause of death globally, and although cancer treatments have improved in recent years, we need to understand how regulatory mechanisms are altered in cancer to combat the disease efficiently. By applying gene perturbations and inference of gene regulatory networks to 40 genes known or suspected to have a role in cancer due to interactions with the oncogene MYC, we deduce their underlying regulatory interactions. Using a recent computational framework for inference together with a novel method for cross validation, we infer a reliable regulatory model of this system in a completely data driven manner, not reliant on literature or priors. The novel interactions add to the understanding of the progressive oncogenic regulatory process and may provide new targets for therapy.
Placebo-induced pain reduction is associated with inverse network coupling at rest
Authors: Wagner Isabella C. , Rütgen Markus , Hummer Allan , Windischberger Christian , Lamm Claus 
Published: August 2019

AbstractPlacebos can reduce pain by inducing beliefs in the effectiveness of an actually inert treatment. Such top-down effects on pain typically engage lateral and medial prefrontal regions, the insula, somatosensory cortex, as well as the thalamus and brainstem during pain anticipation or perception. Considering the level of large-scale brain networks, these regions spatially align with fronto-parietal/executive control, salience, and sensory-motor networks, but it is unclear if and how placebos alter interactions between them during rest. Here, we investigated how placebo analgesia affected intrinsic network coupling. Ninety-nine human participants were randomly assigned to a placebo or control group and underwent resting-state fMRI after pain processing. Results revealed inverse coupling between sensory-motor and salience-like networks in placebo but not control participants. Specifically, networks were centered on the bilateral somatosensory cortex, as well as on the brainstem, thalamus, striatal regions, dorsal and rostral anterior cingulate cortex, and the insula, respectively. Across participants, more negative between-network coupling was associated with lower individual pain intensity as assessed during a preceding pain task, but was unrelated to expectations of medication effectiveness in the placebo group. Altogether, these findings provide initial evidence that placebo analgesia affects the intrinsic communication between large-scale brain networks, even in the absence of pain. We suggest a model where placebo analgesia increases activation within a descending pain-modulatory network, segregating it from somatosensory regions that might code for painful experiences.HighlightsPlacebo analgesia affects resting-state connectivity between networks.Salience-related and somatosensory regions are negatively coupled at rest.This coupling is negative following placebo, but not in control participants.More negative between-network coupling is related to lower pain intensity.
Volumetric Lissajous Confocal Microscopy
Authors: Deguchi Takahiro , Bianchini Paolo , Palazzolo Gemma , Oneto Michele , Diaspro Alberto , Duocastella Martí 
Published: August 2019

AbstractDynamic biological systems present challenges to existing three-dimensional (3D) optical microscopes because of their continuous temporal and spatial changes. Most techniques are based on rigid architectures, as in confocal microscopy, where a laser beam is sequentially scanned at a predefined spatial sampling rate and pixel dwell time. Here, we developed volumetric Lissajous confocal microscopy to achieve unsurpassed 3D scanning speed with a tunable sampling rate. The system combines an acoustic liquid lens for continuous axial focus translation with a resonant scanning mirror. Accordingly, the excitation beam follows a dynamic Lissajous trajectory enabling sub-millisecond acquisitions of image series containing 3D information at a sub-Nyquist sampling rate. By temporal accumulation and/or advanced interpolation algorithms, volumetric imaging rate is selectable using a post-processing step at the desired spatiotemporal resolution for events of interest. We demonstrate multicolor and calcium imaging over volumes of tens of cubic microns with acquisition speeds up to 5 kHz.
Selectivity filter instability dominates the low intrinsic activity of the TWIK-1 K2P K+ Channel
Authors: Nematian-Ardestani Ehsan , Abd-Wahab M. Firdaus , Chatelain Franck C. , Sun Han , Schewe Marcus , Baukrowitz Thomas , Tucker Stephen J 
Published: August 2019

ABSTRACTTwo-pore domain (K2P) K+ channels have many important physiological functions. However, the functional properties of the TWIK-1 (K2P1.1/KCNK1) K2P channel remain poorly characterized because heterologous expression of this ion channel yields only very low levels of functional activity. Several underlying reasons have been proposed, including TWIK-1 retention in intracellular organelles, inhibition by post-translational sumoylation, a hydrophobic barrier within the pore, and a low open probability of the selectivity filter (SF) gate. By evaluating these various potential mechanisms, we found that the latter dominates the low intrinsic functional activity of TWIK-1. Investigating the underlying mechanism, we observed that the low activity of the SF gate appears to arise from the inefficiency of K+ in stabilizing an active (i.e. conductive) SF conformation. In contrast, other permeant ion species, such as Rb+, NH4+, and Cs+, strongly promoted a pH-dependent activated conformation. Furthermore, many K2P channels are activated by membrane depolarization via a SF-mediated gating mechanism, but we found here that only very strong, non-physiological depolarization produces voltage-dependent activation of heterologously expressed TWIK-1. Remarkably, we also observed that TWIK-1 Rb+ currents are potently inhibited by intracellular K+ (IC50 = 2.8 mM). We conclude that TWIK-1 displays unique SF gating properties among the family of K2P channels. In particular, the apparent instability of the conductive conformation of the TWIK-1 SF in the presence of K+ appears to dominate the low levels of intrinsic functional activity observed when the channel is expressed at the cell surface.
Single Cell RNAseq Reveals A Critical Role of Chloride Channels in Airway Development
Authors: He Mu , Wu Bing , Le Daniel D. , Ye Wenlei , Sinclair Adriane W. , Padovano Valeria , Chen Yuzhang , Li Kexin , Sit Rene , Tan Michelle , Caplan Michael J. , Neff Norma , Jan Yuh Nung , Darmanis Spyros , Jan Lily Y. 
Published: August 2019

SUMMARYThe conducting airway forms a protective mucosal barrier and is the primary target of airway disorders. To better understand how airway developmental programs are established to support air breathing and barrier functions, we constructed a single-cell atlas of the human and mouse developing trachea. In this study, we uncover hitherto unrecognized heterogeneity of cell states with distinct differentiation programs and immune features of the developing airway. In addition, we find ubiquitous expression ofCFTRandANO1/TMEM16Achloride channels in the embryonic airway epithelium. We show that genetic inactivation of TMEM16A leads to airway defects commonly seen in cystic fibrosis patients with deficient CFTR, alters the differentiation trajectory of airway basal progenitors, and results in mucus cell hyperplasia and aberrant epithelial antimicrobial expression. Together, our study illuminates conserved developmental features of the mammalian airway and implicates chloride homeostasis as a key player in regulating mucosal barrier formation and function relevant to early onset airway diseases.
Collective interactions augment influenza A virus replication in a host-dependent manner
Authors: Phipps Kara L. , Ganti Ketaki , Jacobs Nathan T. , Lee Chung-Young , Carnaccini Silvia , White Maria C. , Manandhar Miglena , Pickett Brett E. , Tan Gene S. , Ferreri Lucas M. , Perez Daniel R. , Lowen Anice C. 
Published: August 2019

AbstractInfection with a single influenza A virus (IAV) is only rarely sufficient to initiate productive infection. Here, we exploit both single-cell approaches and whole-animal systems to show that IAV reliance on multiple infection can form an important species barrier to infection. Namely, we find that H9N2 subtype viruses representative of those circulating widely at the poultry-human interface exhibit acute dependence on collective interactions in mammalian systems. This need for multiple infection is greatly reduced in the natural host. Quantification of incomplete viral genomes showed that their complementation accounts for the more moderate reliance on coinfection seen in avian cells, but not the added reliance seen in mammalian cells. This finding suggests an additional form of virus-virus interaction is needed to support infection in mammalian cells. Genetic mapping implicated the PA gene segment as a major driver of this phenotype and quantification of viral RNA synthesis indicated that both replication and transcription were affected. These findings indicate that multiple distinct mechanisms underlie IAV reliance on multiple infection and underscore the importance of virus-virus interactions in IAV infection, evolution and emergence.