bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting dormant ovarian cancer cellsin vitroand in anin vivomodel of platinum resistance
Authors: Huang Zhiqing , Kondoh Eiji , Visco Zachary , Baba Tsukasa , Matsumura Noriomi , Dolan Emma , Whitaker Regina S. , Konishi Ikuo , Fujii Shingo , Berchuck Andrew , Murphy Susan K. 
Published: July 2019

ABSTRACTObjectiveOvarian cancer cells often existin vivoas multicellular spheroids. Spheroid formationin vitrohas been used to enrich for cancer stem cell populations from primary tumors. Such spheroids exhibit drug resistance and slow proliferation, suggesting involvement in disease recurrence. Our objectives were to characterize cancer spheroid phenotypes, determine gene expression profiles associated with spheroid forming capacity and to evaluate the responsiveness of spheroids to commonly used and novel therapeutic agents.MethodsTumorigenic potential was assessed using anchorage independent growth assays in 24 cell lines. Spheroids from cell lines (N=12) and from primary cancers (N=8) were grown on non-adherent tissue culture plates in serum-free media. Cell proliferation was measured using MTT assays and Ki67 immunostaining. Affymetrix HT U133A gene expression data was used to identify differentially expressed genes based on spheroid forming capacity. Matched monolayers and spheroids (N=7 pairs) were tested for response to cisplatin, paclitaxel and 7-hydroxystaurosporine (UCN-01) while mitochondrial inhibition was performed using oligomycin. Xenograft tumors from intraperitoneal injection of CAOV2-GFP/LUC ovarian cancer cells into nude mice were treated with carboplatin to reduce tumor burden followed by secondary treatment with carboplatin, UCN-01, or Oltipraz. Tumor formation and response was monitored using live imaging.ResultsOf 12 cell lines with increased anchorage-independent growth, 8 also formed spheroids under serum-free spheroid culture conditions. Spheroids showed reduced proliferation (p<0.0001) and Ki67 immunostaining (8% versus 87%) relative to monolayer cells. Spheroid forming capacity was associated with increased mitochondrial pathway activity (p ≤ 0.001). The mitochondrial inhibitors, UCN-01 and Oligomycin, demonstrated effectiveness against spheroids, while spheroids were refractory to cisplatin and paclitaxel. By livein vivoimaging, ovarian cancer xenograft tumors were reduced after primary treatment with carboplatin. Continued treatment with carboplatin was accompanied by an increase in tumor signal while there was little or no increase in tumor signal observed with subsequent treatment with UCN-01 or Oltipraz.ConclusionsOur findings suggest that the mitochondrial pathway in spheroids may be an important therapeutic target in preventing disease recurrence.
Functional innovation in the evolution of the calcium-dependent system of the eukaryotic endoplasmic reticulum
Authors: Schäffer Daniel E. , Iyer Lakshminarayan M. , Burroughs A. Maxwell , Aravind L. 
Published: July 2019

AbstractThe origin of eukaryotes was marked by the emergence of several novel subcellular systems. One such is the calcium (Ca2+)-stores system of the endoplasmic reticulum, which profoundly influences diverse aspects of cellular function including signal transduction, motility, division, and biomineralization. We use comparative genomics and sensitive sequence and structure analyses to investigate the evolution of this system. Our findings reconstruct the core form of the Ca2+- stores system in the last eukaryotic common ancestor as having at least 15 proteins that constituted a basic system for facilitating both Ca2+flux across endomembranes and Ca2+-dependent signaling. We present evidence that the key EF-hand Ca2+-binding components had their origins in a likely bacterial symbiont other than the mitochondrial progenitor, whereas the protein phosphatase subunit of the ancestral calcineurin complex was likely inherited from the asgardarchaeal progenitor of the stem eukaryote. This further points to the potential origin of the eukaryotes in a Ca2+-rich biomineralized environment such as stromatolites. We further show that throughout eukaryotic evolution there were several acquisitions from bacteria of key components of the Ca2+-stores system, even though no prokaryotic lineage possesses a comparable system. Further, using quantitative measures derived from comparative genomics we show that there were several rounds of lineage-specific gene expansions, innovations of novel gene families, and gene losses correlated with biological innovation such as the biomineralized molluscan shells, coccolithophores, and animal motility. The burst of innovation of new genes in animals included the wolframin protein associated with Wolfram syndrome in humans. We show for the first time that it contains previously unidentified Sel1, EF-hand, and OB-fold domains, which might have key roles in its biochemistry.
Dopamine in the basal amygdala signals salient somatosensory events during fear learning
Authors: Tang Wei , Kochubey Olexiy , Kintscher Michael , Schneggenburger Ralf 
Published: July 2019

SummaryThe amygdala is a brain area critical for the formation of threat memories. However, the nature of the teaching signal(s) that drive plasticity in the amygdala are still under debate. Here, we use optogenetic methods to investigate whether dopamine release in the amygdala contributes to fear learning. Antero- and retrograde labeling showed that a sparse, and relatively evenly distributed population of ventral tegmental area (VTA) neurons projects to the basal amygdala (BA). In-vivo optrode recordings in behaving mice showed that many VTA neurons, amongst them putative dopamine neurons, are excited by footshocks. Correspondingly, in-vivo fiber photometry of dopamine in the BA revealed robust dopamine concentration transients upon footshock presentation. Finally, silencing VTA dopamine neurons, or their axon terminals in the BA during the footshock, reduced the extent of threat memory retrieval one day later. Thus, VTA dopamine neurons projecting to the BA code for the saliency of the footshock event, and the resulting dopamine release in the BA facilitates threat memory formation.
Withdraw of prophylactic antimicrobials does not change the pigs’ resistome
Authors: Fernanda Loayza-Villa , Alejandro Torres , Lixin Zhang , Gabriel Trueba 
Published: July 2019

AbstractThe use of antimicrobials in the animal industry has increased the prevalence of antimicrobial resistant commensal bacteria in food products derived from animals, which could be associated with antimicrobial resistance in human pathogens. To reduce the influx of antibiotic resistant bacteria (and genes) to the human microbiota, restrictions on antimicrobials (in food animals) have been implemented in different countries. We investigated the impact of antimicrobial restriction in the frequency of antimicrobial resistant bacteria in pigs. No differences in antimicrobial resistance or antimicrobial resistance genes (richness or abundance) was found when we compared animals fed with and without antibiotics. Fitness costs of antimicrobial resistance in bacteria (in the field) seems to be overestimated.
Use of multivariable Mendelian randomization to address biases due to competing risk before recruitment
Authors: Schooling C Mary , Lopez Priscilla M , Yang Zhao , Zhao J V , Au Yeung SL , Huang Jian V 
Published: July 2019

AbstractBackgroundMendelian randomization (MR) provides unconfounded estimates. MR is open to selection bias particularly when the underlying sample is selected on surviving the genetically instrumented exposure and other conditions that share etiology with the outcome (competing risk before recruitment). Few methods to address this bias exist.MethodsWe use directed acyclic graphs to show this selection bias can be addressed by adjusting for common causes of survival and outcome. We use multivariable MR to obtain a corrected MR estimate, specifically, the effect of statin use on ischemic stroke, because statins affect survival and stroke typically occurs later in life than ischemic heart disease so is open to competing risk.ResultsIn univariable MR the genetically instrumented effect of statin use on ischemic stroke was in a harmful direction in MEGASTROKE and the UK Biobank (odds ratio (OR) 1.33, 95% confidence interval (CI) 0.80 to 2.20). In multivariable MR adjusted for major causes of survival and ischemic stroke, (blood pressure, body mass index and smoking initiation) the effect of statin use on stroke in the UK Biobank was as expected (OR 0.81, 95% CI 0.68 to 0.98) with a Q-statistic indicating absence of genetic pleiotropy or selection bias, but not in MEGASTROKE.ConclusionMR studies concerning late onset chronic conditions with shared etiology based on samples recruited in later life need to be conceptualized within a mechanistic understanding, so as to any identify potential bias due to competing risk before recruitment, and to inform the analysis and interpretation.
The single-progenitor model as the unifying paradigm of squamous epithelial maintenance
Authors: Piedrafita Gabriel , Kostiou Vasiliki , Wabik Agnieszka , Colom Bartomeu , Fernandez-Antoran David , Herms Albert , Murai Kasumi , Hall Benjamin A , Jones Philip H 
Published: July 2019

AbstractAdult tissues such as the epidermis of the skin and the epithelium lining the esophagus are continuously turned over throughout life. Cells are shed from the tissue surface and replaced by cell division. Yet, the cellular mechanisms that underpin these tissues homeostasis remain poorly established, having important implications for wound healing and carcinogenesis. Lineage tracing, in which of a cohort of proliferating cells and their descendants are genetically labelled in transgenic mice, has been used to study the fate behavior of the proliferating cells that maintain these tissues. However, based on this technique, distinct mutually irreconcilable models, differing in the implored number and hierarchy of proliferating cell types, have been proposed to explain homeostasis. To elucidate which of these conflicting scenarios should prevail, here we performed cell proliferation assays across multiple body sites in transgenic H2BGFP mouse epidermis and esophagus. Cell-cycle properties were then extracted from the H2BGFP dilution kinetics and adopted in a common analytic approach for a refined analysis of a new lineage-tracing experiment and eight published clonal data sets from esophagus and different skin territories. Our results show H2BGFP dilution profiles remained unimodal over time, indicating the absence of slow-cycling stem cells across all tissues analyzed. We find that despite using diverse genetic labelling approaches, all lineage-tracing data sets are consistent with tissues maintenance by a single population of proliferating cells. The outcome of a given division is unpredictable but, on average the likelihood of producing proliferating and differentiating cells is balanced, ensuring tissue homeostasis. The fate outcomes of sister cells are anticorrelated. We conclude a single cell population maintains squamous epithelial homeostasis.
Uncoupling sodium channel dimers rescues phenotype of pain-linked Nav1.7 mutation
Authors: Rühlmann Annika H. , Körner Jannis , Bebrivenski Nikolay , Detro-Dassen Silvia , Hautvast Petra , Benasolo Carène A. , Meents Jannis , Machtens Jan-Philipp , Schmalzing Günther , Lampert Angelika 
Published: July 2019

AbstractThe voltage-gated sodium channel Nav1.7 is essential for an adequate perception of painful stimuli. Its mutations cause various pain syndromes in human patients. The hNav1.7/A1632E mutation induces symptoms of erythromelalgia and paroxysmal extreme pain disorder (PEPD), and its main gating change is a strongly enhanced persistent current.Using molecular simulations, we demonstrate that the disease causing persistent current of hNav1.7/A1632E is due to impaired binding of the IFM motif, thus affecting proper function of the recently proposed allosteric fast inactivation mechanism. By using native polyacrylamide gel electrophoresis (PAGE) gels, we show that hNav1.7 dimerizes. The disease-linked persistent current depends on the channel’s functional dimerization status: Using difopein, a 14-3-3 inhibitor known to uncouple dimerization of hNav1.5, we detect a significant decrease in hNav1.7/A1632E induced persistent currents.Our work identifies that functional uncoupling of hNav1.7/A1632E dimers rescues the pain-causing molecular phenotype by interferes with an allosteric fast inactivation mechanism, which we link for the first time to channel dimerization. Our work supports the concept of sodium channel dimerization and reveals its relevance to human pain syndromes.
Quantitative, super-resolution localization of small RNAs with sRNA-PAINT
Authors: Huang Kun , Demirci Feray , Batish Mona , Meyers Blake C. , Caplan Jeffrey L. 
Published: July 2019

AbstractSmall RNAs are non-coding RNAs that play important roles in the lives of both animals and plants. They are 21- to 24-nt in length and around 10 nanometers (nm) in size. Their small size and high diversity have made it challenging to develop detection methods that have sufficient resolution and specificity to multiplex and quantify. We created a method, sRNA-PAINT, for the detection of small RNAs with 20 nm resolution by combining the super-resolution method, DNA-based points accumulation in nanoscale topography (DNA-PAINT), and the specificity of locked nucleic acid (LNA) probes for thein situdetection of multiple small RNAs. The method relies on designing probes to target small RNAs that combine DNA oligonucleotides (oligos) for PAINT with LNA-containing oligos for hybridization; therefore, we developed an online tool called “Vetting & Analysis of RNA forin situHybridization probes” (VARNISH) for probe design. Our method utilizes advances in DNA-PAINT methodologies, including qPAINT for quantification, and Exchange-PAINT for multiplexing. We demonstrated these capabilities of sRNA-PAINT by detecting and quantifying small RNAs in different cell layers of early developmental stage maize anthers that are important for male sexual reproduction.
State and trait characteristics of anterior insula time-varying functional connectivity
Authors: Pasquini Lorenzo , Toller Gianina , Staffaroni Adam , Brown Jesse A. , Deng Jersey , Lee Alex , Kurcyus Katarzyna , Shdo Suzanne M. , Allen Isabel , Sturm Virginia E. , Cobigo Yann , Borghesani Valentina , Battistella Giovanni , Gorno-Tempini Maria Luisa , Rankin Katherine P. , Kramer Joel , Rosen Howard H. , Miller Bruce L. , Seeley William W. 
Published: July 2019

AbstractThe human anterior insula (aINS) is a topographically organized brain region, in which ventral portions contribute to socio-emotional function through limbic and autonomic connections, whereas the dorsal aINS contributes to cognitive processes through frontal and parietal connections. Open questions remain, however, regarding how aINS connectivity varies over time. We implemented a novel approach combining seed-to-whole-brain sliding-window functional connectivity MRI and k-means clustering to assess time-varying functional connectivity of aINS subregions. We studied three independent large samples of healthy participants and longitudinal datasets to assess inter- and intra-subject stability, and related aINS time-varying functional connectivity profiles to dispositional empathy. We identified four robust aINS time-varying functional connectivity modes that displayed both “state” and “trait” characteristics: while modes featuring connectivity to sensory regions were modulated by eye closure, modes featuring connectivity to higher cognitive and emotional processing regions were stable over time and related to empathy measures.
Translation elongation factor 1A2 (eEF1A2) is encoded by one of four closely related eef1a genes and is dispensable for survival in zebrafish
Authors: Idigo Nwamaka J. , Soares Dinesh C. , Abbott Catherine M. 
Published: July 2019

AbstractZebrafish are valuable model organisms for the study of human single-gene disorders: they are genetically manipulable, their development is well understood, and mutant lines with measurable, disease-appropriate phenotypic abnormalities can be used for high throughput drug screening approaches. However, gene duplication events in zebrafish can result in redundancy of gene function, masking loss of function phenotypes and thus confounding this approach to disease modelling. Furthermore, recent studies have yielded contrasting results depending on whether specific genes are targeted using genome editing to make mutant lines, or whether morpholinos are used (morphants). De novo missense mutations in the human gene EEF1A2, encoding a tissue-specific translation elongation factor, cause severe neurodevelopmental disorders; there is a real need for a model system in which to study these disorders and we wanted to explore the possibility of a zebrafish model. We identified four eef1a genes and examined their developmental and tissue-specific expression patterns: eef1a1l1 is first to be expressed whilst eef1a2 is only detected later during development. We then determined the effects of introducing null mutations into eEF1A2 in zebrafish using CRISPR/Cas9 gene editing, in order to compare the results with previously described morphants, and with the severe neurodegenerative lethal phenotype of eEF1A2-null mice. In contrast with both earlier analysis in zebrafish using morpholinos and with the mouse eEF1A2-null mice, disruption of the eef1a2 gene in zebrafish is compatible with normal lifespan. The resulting lines, however, may provide a valuable platform for studying the effects of expression of mutant human eEF1A2 mRNA.
A new thalamo-cortical-amygdala circuit is involved in processing a natural auditory alarm cue
Authors: Pereira Ana G , Farias Matheus , Moita Marta A. 
Published: July 2019

ABSTRACTAnimals use auditory cues generated by defensive responses of others to detect impending danger. Here we identify a neural circuit in rats involved in the detection of one such auditory cue, the cessation of movement-evoked sound resulting from freezing. This circuit comprises the dorsal sub-nucleus of the medial geniculate body (MGD) and downstream areas, the ventral area of the auditory cortex (VA) and the lateral amygdala (LA). This study suggests a role for the auditory offset pathway in processing a natural sound cue of threat.
It’s the fiber, not the fat: Significant effects of dietary challenge on the gut microbiome
Authors: Morrison Kathleen E. , Jašarević Eldin , Howard Christopher D. , Bale Tracy L. 
Published: July 2019

AbstractBackgroundDietary effects on the gut microbiome has been shown to play a key role in the pathophysiology of behavioral dysregulation, inflammatory disorders, metabolic syndrome, and obesity. Often overlooked is that experimental diets vary significantly in the proportion and source of dietary fiber. Commonly, treatment comparisons are made between animals that are fed refined diets that lack soluble fiber and animals fed vivarium-provided chow diet that contain a rich source of soluble fiber. Despite the well-established role of soluble fiber on metabolism, immunity, and behavior via the gut microbiome, the extent to which measured outcomes may be driven by differences in dietary fiber is unclear. Further, the significant impact of sex and age in response to dietary challenge is likely important and should also be considered.ResultsWe compared the impact of transitioning young and aged male and female mice from a chow diet to a refined low soluble fiber diet on body weight and gut microbiota. Then, to determine the contribution of dietary fat, we examined the impact of transitioning a subset of animals from refined low fat to refined high fat diet. Serial tracking of body weights revealed that consumption of low fat or high fat refined diet increased body weight in young and aged adult male mice. Young adult females showed resistance to body weight gain, while high fat diet-fed aged females had significant body weight gain. Transition from a chow diet to low soluble fiber refined diet accounted for most of the variance in community structure and composition across all groups. This dietary transition was characterized by a loss of taxa within the phylum Bacteroidetes and a concurrent bloom of Clostridia and Proteobacteria in a sex- and age-specific manner. Most notably, no changes to gut microbiota community structure and composition were observed between mice consuming either low- or high-fat diet, suggesting that transition to the refined diet that lacks soluble fiber is the primary driver of gut microbiota alterations, with limited additional impact of dietary fat on gut microbiota.ConclusionCollectively, our results show that the choice of control diet has a significant impact on outcomes and interpretation related to body weight and gut microbiota. These data also have broad implications for rodent studies that draw comparisons between refined high fat diets and chow diets to examine dietary fat effects on metabolic, immune, behavioral, and neurobiological outcomes.
Effects of hydroperiod on growth, development, survival and immune defences in a temperate amphibian
Authors: Brannelly Laura A. , Ohmer Michel E. B. , Saenz Veronica , Richards‐Zawacki Corinne L. 
Published: July 2019

Abstract

The many and varied effects of human‐induced environmental change have the potential to threaten animal biodiversity and species abundance. Importantly, human land use and global climate change are predicted to reduce water availability, which might have negative consequences for freshwater organisms.

In this study, we tested for an effect of a shortened hydroperiod on larval growth and development, and post‐metamorphic survival and immune function in a temperate frog, Rana pipiens.

Animals developing under pond drying conditions metamorphosed at a smaller size and had lower survival after metamorphosis. We found sex‐specific differences in larval period in our fastest drying treatment, with males metamorphosing more quickly than females. Individuals that developed under drying conditions also showed reduced skin swelling after phytohaemagglutinin injection, indicating a compromised immune response. We found support for trade‐offs between growth, development and post‐metamorphic immune function across hydroperiod treatments. Whole blood from animals with shorter larval periods had lower bacterial killing ability, and small‐bodied juveniles had lower antibody titres.

Overall, our results indicate that a shortened hydroperiod can affect the rate of larval amphibian growth and development, and might negatively impact the condition of species that rely on freshwater for development. Our work improves understanding of the complex impacts that environmental stressors might have on the health of animal populations.
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