bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-coding Somatic Mutations Converge on the PAX8 Pathway in Epithelial Ovarian Cancer
Authors: Corona Rosario I. , Seo Ji-Heui , Lin Xianzhi , Hazelett Dennis J. , Reddy Jessica , Abassi Forough , Lin Yvonne G. , Mhawech-Fauceglia Paulette Y. , Lester Jenny , Shah Sohrab P. , Huntsman David G. , Gusev Alexander , Karlan Beth Y. , Berman Benjamin P. , Freedman Matthew L. , Gayther Simon A. , Lawrenson Kate
Published: February 2019

Transcriptional regulation is highly disease and cell-type specific. We performed H3K27ac chromatin immunoprecipitation and transcriptomic sequencing in primary tumors for the four different subtypes of invasive epithelial ovarian cancer (OC). Histotype-specific regulatory elements (REs) were enriched in enhancers (P<0.001).In silicoprediction of putative target genes for histotype-specific REs identified genes (WFDC2, P=5.5×10-5) and pathways (PI3K-Akt signaling, P<0.002) known to be involved in OC development. Some genes (e.g.PAX8andCA125) are associated with super-enhancers (SEs) in all OCs, while others are histotype-specific, includingPPP1R3Bwhich is associated with SEs specific to clear cell OC. Integrated analysis of active chromatin landscapes with somatic single nucleotide variants (SNVs) from whole genome sequencing (WGS) of 232 primary OCs identified frequently mutated REs, including theKLF6promoter (P=8.2×10-8) and a putative enhancer at chromosome 6p22.1 (P<0.05). In high-grade serous OCs, somatic SNVs clustered in binding sites for the PAX8 binding partner TEAD4 (P=6×10-11), while the collection ofcisregulatory elements associated withPAX8was the most frequently mutated set of enhancers in OC (P=0.003). Functional analyses supported our findings: Knockdown ofPPP1R3Bin clear cell OC cells significantly reduced intracellular glycogen content, a signature feature of this histotype; and stable knockout of a 635 bp region in the 6p22.1 enhancer induced downregulation of two predicted target genes,ZSCAN16andZSCAN12(P=6.6 x 10-4and P=0.02). In summary, we have characterized histotype-specific epigenomic and transcriptomic landscapes in OC and defined likely functional REs based on somatic mutation analysis of ovarian tumors.
Evidence accumulation during perceptual decision-making is sensitive to the dynamics of attentional selection
Authors: Rangelov Dragan , Mattingley Jason B.
Published: February 2019

The ability to select and combine multiple sensory inputs in support of accurate decisions is a hallmark of adaptive behaviour. Attentional selection is often needed to prioritize stimuli that are task-relevant and to attenuate potentially distracting sources of sensory information. As most studies of perceptual decision-making to date have made use of task-relevant stimuli only, relatively little is known about how attention modulates decision making. To address this issue, we developed a novel ‘integrated’ decision-making task, in which participants judged the average direction of successive target motion signals while ignoring concurrent and spatially overlapping distractor motion signals. In two experiments that varied the role of attentional selection, we used linear regression to quantify the influence of target and distractor stimuli on behaviour. Using electroencephalography, we characterised the neural correlates of decision making, attentional selection and feature-specific responses to target and distractor signals. While targets strongly influenced perceptual decisions and associated neural activity, we also found that concurrent and spatially coincident distractors exerted a measurable bias on both behaviour and brain activity. Our findings suggest that attention operates as a real-time but imperfect filter during perceptual decision-making by dynamically modulating the contributions of task-relevant and irrelevant sensory inputs.
Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets
Authors: Ozaki Haruka , Hayashi Tetsutaro , Umeda Mana , Nikaido Itoshi
Published: February 2019

Background

Read coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly “full-length” ones, provide read coverage of many individual cells and have the potential to reveal cellular heterogeneity in RNA transcription and processing. However, visualization tools suited to highlighting cell-to-cell heterogeneity in read coverage are still lacking.

Results

Here, we have developed Millefy, a tool for visualizing read coverage of scRNA-seq data in genomic contexts. Millefy is designed to show read coverage of all individual cells at once in genomic contexts and to highlight cell-to-cell heterogeneity in read coverage. By visualizing read coverage of all cells as a heat map and dynamically reordering cells based on diffusion maps, Millefy facilitates discovery of “local” region-specific, cell-to-cell heterogeneity in read coverage, including variability of transcribed regions.

Conclusions

Millefy simplifies the examination of cellular heterogeneity in RNA transcription and processing events using scRNA-seq data. Millefy is available as an R package (https://github.com/yuifu/millefy) and a Docker image to help use Millefy on the Jupyter notebook (https://hub.docker.com/r/yuifu/datascience-notebook-millefy).
Mechanical activation of TRPV4 channels controls albumin reabsorption by proximal tubule cells
Authors: Gualdani Roberta , Seghers François , Yerna Xavier , Schakman Olivier , Tajeddine Nicolas , Achouri Younès , Tissir Fadel , Devuyst Olivier , Gailly Philippe
Published: February 2019

The proximal tubule (PT) mediates the endocytosis of essential substances filtered through the glomerulus, including albumin and a large variety of low molecular weight proteins that would otherwise be lost in urine. Variations in the amount of ultrafiltrate delivered to the PT modulate protein endocytosis. Here we show that TRPV4 ion channel is expressed at the basolateral side of PT cells. Mechanical activation of TRPV4 by cell stretching induces an entry of Ca2+into the cytosol, which promotes endocytosis.Trpv4−/-mice present only a mild PT dysfunction in basal conditions but they exhibit a much more severe proteinuria thanTrpv4+/+mice when the permeability of glomerular filter is altered by systemic delivery of angiotensin II or antibodies against the glomerular basement membrane. These results emphasize the importance of TRPV4 channel in PT pressure sensing and provide insights into the mechanisms controlling protein reabsorption and potential targets for treating tubular proteinuria.

The proximal tubule (PT) mediates the endocytosis of albumin and low molecular weight proteins. Gualdani et al. report that variations in the amount of ultrafiltrate delivered to the PT activate TRPV4 ion channel expressed at the basolateral side of PT cells, which modulates protein endocytosis.
Trajectory of brain maturation in adolescent individuals at familial risk of mood disorder
Authors: de Nooij Laura , Harris Mathew A. , Hawkins Emma L. , Shen Xueyi , Clarke Toni-Kim , Chan Stella W.Y. , Ziermans Tim B. , McIntosh Andrew M. , Whalley Heather C.
Published: February 2019

Background

Accelerated biological ageing has been proposed as a mechanism underlying mood disorder, but has been predominantly studied cross-sectionally in adult populations. It remains unclear whether differential ageing/maturation trajectories emerge earlier in life, in particular during the neurodevelopmental period of adolescence, and whether they are associated with onset of mood disorder and/or presence of familial risk.

Methods

Participants were young individuals (16-25 years) from the prospective longitudinal Scottish Bipolar Family Study (SBFS) with and without family history of mood disorder. All were well at time of recruitment. Implementing a structural MRI-based brain age prediction model, individual maturational trajectories were captured by the difference between predicted brain age and chronological age (brain-PAD) at baseline and two-year follow-up. Based on clinical assessment at follow-up, individuals were categorised into three groups: (i) controls who remained well (C-well,n=94), (ii) high familial risk who remained well (HR-well,n=73) and (iii) high familial risk who developed a mood disorder (HR-MD,n=38).

Results

Results showed no differences in brain-PAD between groups at baseline or follow-up. However, we found negative trajectories of brain-PAD for HR-MD versus C-well (β= −0.68 years,p<.001) and versus HR-well (β= −0.38 years,p=.01), and for HR-well versus C-well (β= −0.30 years,p=.03).

Conclusions

These findings suggest that within young individuals, onset of mood disorder and familial risk may be associated with a deceleration in brain maturation trajectory. However, without significantly differential status of brain maturation at follow-up, extended longitudinal research will need to show whether this marks the emergence of maturational lag.
Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences
Authors: Schneider Thomas D. , Jejjala Vishnu
Published: February 2019

Restriction enzymes recognize and bind to specific sequences on invading bacteriophage DNA. Like a key in a lock, these proteins require many contacts to specify the correct DNA sequence. Using information theory we develop an equation that defines the number of independent contacts, which is the dimensionality of the binding. We show that EcoRI, which binds to the sequence GAATTC, functions in 24 dimensions. Information theory represents messages as spheres in high dimensional spaces. Better sphere packing leads to better communications systems. The densest known packing of hyperspheres occurs on the Leech lattice in 24 dimensions. We suggest that the single protein EcoRI molecule employs a Leech lattice in its operation. Optimizing density of sphere packing explains why 6 base restriction enzymes are so common.
Assessing graph-based read mappers against a novel baseline approach highlights strengths and weaknesses of the current generation of methods
Authors: Grytten Ivar , Rand Knut D. , Nederbragt Alexander J. , Sandve Geir K.
Published: February 2019

Graph-based reference genomes have become popular as they allow read mapping and follow-up analyses in settings where the exact haplotypes underlying a high-throughput sequencing experiment are not precisely known. Two recent papers show that mapping to graph-based reference genomes can improve accuracy as compared to methods using linear references. Both of these methods index the sequences for most paths up to a certain length in the graph in order to enable direct mapping of reads containing common variants. However, the combinatorial explosion of possible paths through nearby variants also leads to a huge search space and an increased chance of false positive alignments to highly variable regions.

We here assess two prominent graph-based read mappers against a novel hybrid baseline approach that combines an initial path determination with a tuned linear read mapping method. We show, using a previously proposed benchmark, that this simple approach is able to improve accuracy of read-mapping to graph-based reference genomes.

Our method is implemented in a tool, Two-step Graph Mapper, which is available at https://github.com/uio-bmi/two_step_graph_mapper along with data and scripts for reproducing the experiments.
Pleiotropic effects ofebonyandtanon pigmentation and cuticular hydrocarbon composition inDrosophila melanogaster
Authors: Massey J. H. , Akiyama N. , Bien T. , Dreisewerd K. , Wittkopp P. J. , Yew J.Y. , Takahashi A.
Published: February 2019

Pleiotropic genes are genes that affect more than one trait. For example, many genes required for pigmentation in the fruit flyDrosophila melanogasteralso affect traits such as circadian rhythms, vision, and mating behavior. Here, we present evidence that two pigmentation genes,ebonyandtan, which encode enzymes catalyzing reciprocal reactions in the melanin biosynthesis pathway, also affect cuticular hydrocarbon (CHC) composition inD. melanogasterfemales. More specifically, we report thatebonyloss-of-function mutants have a CHC profile that is biased toward long (>25C) chain CHCs, whereastanloss-of-function mutants have a CHC profile that is biased toward short (<25C) chain CHCs. Moreover, pharmacological inhibition of dopamine synthesis, a key step in the melanin synthesis pathway, reversed the changes in CHC composition seen inebonymutants, making the CHC profiles similar to those seen intanmutants. These observations suggest that genetic variation affectingebonyand/ortanactivity might cause correlated changes in pigmentation and CHC composition in natural populations. We tested this possibility using theDrosophilaGenetic Reference Panel (DGRP) and found that CHC composition covaried with pigmentation as well as levels ofebonyandtanexpression in newly eclosed adults in a manner consistent with theebonyandtanmutant phenotypes. These data suggest that the pleiotropic effects ofebonyandtanmight contribute to covariation of pigmentation and CHC profiles inDrosophila.
Genetically Increased Telomere Length and Aging-related Physical and Cognitive Traits in the UK Biobank
Authors: Demanelis Kathryn , Tong Lin , Pierce Brandon L.
Published: February 2019

Background

Telomere length (TL) shortens over time in most human cell types and is a potential biomarker aging. However, the causal impact of TL on physical and cognitive phenotypes that decline with age has not been extensively examined. Using a Mendelian randomization (MR) approach, we utilized genetically increased TL (GI-TL) to estimate the impact of TL on aging-related traits among UK Biobank (UKB) participants.

Methods

We manually curated >50 aging-related traits from UKB and restricted to unrelated participants of British ancestry (n=337,522). We estimated GI-TL as a linear combination of nine TL-associated SNPs, each weighted by its previously-reported association with leukocyte TL. Regression models were used to assess the associations between GI-TL and each trait. We obtained MR estimates using the two-sample inverse variance weighted (IVW) approach.

Results

We identified 5 age-related traits associated with GI-TL (Bonferroni-corrected threshold p<0.001): pulse pressure (PP) (p=5.2×10−14), systolic blood pressure (SBP) (p=2.9×10−15), diastolic blood pressure (DBP) (p=5.5×10−6), forced expiratory volume (FEV1) (p= p=0.0001), and forced vital capacity (FVC) (p=3.8×10−6). Under MR assumptions, one standard deviation increase in TL (∼1200 base pairs) increased PP, SBP, and DBP by 1.5, 2.3, and 0.8 mmHg, respectively, while FEV1 and FVC increased by 34.7 and 52.2 mL, respectively. The observed associations appear unlikely to be due to selection bias based on analyses including inverse probability weights and analyses of simulated data.

Conclusions

These findings suggest that longer TL increases pulmonary function and blood pressure traits. Further research is necessary to evaluate TL in cardiovascular and pulmonary age-related decline.

KEY MESSAGES

Telomere length (TL) is a potential biomarker and cause of aging, however, the causal relationship between TL and aging-related traits has not been thoroughly examined using a Mendelian randomization (MR) approach.

We evaluated genetically increased TL (GI-TL) and its association with over 50 aging-related traits in the UK Biobank cohort using regression models and MR approaches.

Pulmonary function (FEV1 and FVC) and blood pressure (SBP, DBP, and PP) traits were positively associated with GI-TL in the expected and unexpected direction, respectively.

Using inverse probability weights to account for the non-representativeness of the UKB, our observed associations for GI-TL with blood pressure traits and pulmonary function persisted.

Using simulated data to examine study selection as a potential source of collider bias, we concluded that selection bias was unlikely to explain the observed associations.
A Stomata Classification and Detection System in Microscope Images of Maize Cultivars
Authors: Aono Alexandre Hild , Nagai James Shiniti , Mendonça Dickel Gabriella da Silva , Marinho Rafaela Cabral , Macedo de Oliveira Paulo Eugênio Alves , Papa João Paulo , Faria Fabio Augusto
Published: February 2019

Research on stomata, i.e., morphological structures of plants, has increased in popularity in the last years. These structures (pores) are in charge of the interaction between the internal plant system and the environment, working on different processes such as photosynthesis and transpiration stream. Besides, a better understanding of the pore mechanism plays a significant role when exploring the evolution process, as well as the behavior of plants. Although the study of stomata in dicots species of plants has advanced considerably in the past years, there is little information about stomata of cereal grasses. Also, automated detection of these structures have been considered in the literature, but some gaps are still uncovered. This fact is motivated by high morphological variation of stomata and the presence of noise from the image acquisition step. In this work, we propose a new methodology for automatic stomata classification and a new detection system in microscope images for maize cultivars. We have achieved an approximated accuracy of 97.1% in the identification of stomata regions using classifiers based on deep learning features, which figures out as a nearly perfect classification system.
Drug-like Fragments Inhibit agr-Mediated Virulence Expression in Staphylococcus aureus
Authors: Bezar Ian F. , Mashruwala Ameya A. , Boyd Jeffrey M. , Stock Ann M.
Published: February 2019

In response to the increasingly problematic emergence of antibiotic resistance, novel strategies for combating pathogenic bacteria are being investigated. Targeting the agr quorum sensing system, which regulates expression of virulence in Staphylococcus aureus, is one potentially useful approach for combating drug-resistant pathogens that has not yet been fully explored. A previously published study of a fragment screen resulted in the identification of five compound fragments that interact with the DNA-binding domain of the response regulator AgrA from S. aureus. We have analyzed the ability of these compounds to affect agr-mediated virulence gene expression in S. aureus cells. Three of the compounds demonstrated the ability to reduce agr-driven transcription of at the P2 and P3 promoters of the agr operon and increase biofilm formation, and two of these compounds also showed the ability to reduce levels of secreted toxins. The finding that the compounds tested were able to reduce agr activity suggests that they could be useful tools for probing the effects of agr inhibition.

Furthermore, the characteristics of compound fragments make them good starting materials for the development of compound libraries to iteratively improve the inhibitors.
Phantom limb pain intensity is associated with generalized hyperalgesia
Authors: Fuchs Xaver , Diers Martin , Trojan Jörg , Kirsch Pinar , Milde Christopher , Bekrater-Bodmann Robin , Rance Mariela , Foell Jens , Andoh Jamila , Becker Susanne , Flor Herta
Published: February 2019

After limb amputation, most amputees suffer from phantom limb pain (PLP). The mechanisms underlying this condition are complex and insufficiently understood. Altered somatosensory sensitivity (either heightened or lowered) might contribute to PLP. Recent studies have tested this assumption but mainly focused on the residual limb. However, altered somatosensation in PLP might be generalized. In this study, we applied quantitative sensory testing to 37 unilateral upper-limb amputees (23 with PLP, 14 without PLP) and 19 healthy controls. We assessed thresholds to heat pain (HPT), pressure pain (PPT), warmth detection (WDT), and two-point discrimination (2PDT) at the residual limb, a homologous point and the thenar of the intact limb, and both corners of the mouth. We did not find significant differences in any of the thresholds between the groups. However, higher PLP intensity was significantly related to lower HPT at all measured body sites except for the residual limb. At the residual limb, lower HPT were observed in more distal amputations and in amputees showing a higher degree of prosthesis use. Although WDT did by itself not significantly correlate with PLP intensity at any of the body sites, multiple regression analysis showed the highest multiple correlations with PLP intensity for a combination of high WDT and low HPT at the corners of the mouth. In this model, the combination of HPT and WDT shared 58% of the variance with PLP intensity. Other factors of potential importance, especially residual limb pain, were not significantly associated to any sensory threshold. We conclude that the intensity, but not the presence of PLP is positively associated with higher heat pain sensitivity. Since this association was observed at various, distributed body sites, we suggest that central mechanisms might be underlying such generalized hyperalgesia.
GIT2 is dispensable for normal learning and memory function due to a predominant brain GIT2 splice variant that evades GIT/PIX complexes
Authors: Toth Krisztian , Martyn Amanda C. , Bastrikova Natalia , Kim Woojoo , Rodriguiz Ramona M. , Ahmed Umer , Schmalzigaug Robert , Dudek Serena M. , Wetsel William C. , Premont Richard T.
Published: February 2019

G protein-coupled receptor kinase-interacting protein 2 (GIT2) and GIT1 are highly similar, sharing the same domain structure and many binding partners. The most important GIT partners are the p21-activated protein kinase-interacting exchange factor (PIX) proteins, since through homomeric and heteromeric interactions, GIT and PIX proteins form oligomeric GIT/PIX complexes. Oligomeric GIT/PIX complexes function both as regulators of small GTP-binding proteins and as scaffolds for signalling molecules, including p21-activated protein kinases (PAKs). Deficits in learning and memory have been demonstrated in GIT1 knockout mice, and it has been assumed that GIT2 also would affect learning and memory. Unexpectedly, we find that GIT2-deficient mice respond normally in multiple tests of learning and memory, and have normal hippocampal long-term potentiation. Further, we find no evidence that GIT2 regulates ADHD-like phenotypes. To investigate why GIT2 and GIT1 differ so markedly in the brain, we identified the major isoform of GIT2 in the brain as a previously uncharacterized splice variant, GIT2(ΔBCE). This variant cannot dimerize or form oligomeric complexes with PIX proteins, and is thus incapable of regulating PAK in synapses, compared to oligomeric GIT1/PIX complexes. Because localized activation of PAK in synapses is required for structural plasticity underlying cognitive performance, loss of monomeric GIT2(ΔBCE) in the brain does not influence these responses.
Screening for neurotoxic potential of 15 flame retardants using freshwater planarians
Authors: Zhang Siqi , Ireland Danielle , Sipes Nisha S. , Behl Mamta , Collins Eva-Maria S.
Published: February 2019

Asexual freshwater planarians are an attractive invertebrate model for high-throughput neurotoxicity screening, because they possess multiple quantifiable behaviors to assess distinct neuronal functions. Planarians uniquely allow direct comparisons between developing and adult animals to distinguish developmentally selective effects from general neurotoxicity. In this study, we used our automated planarian screening platform to compare the neurotoxicity of 15 flame retardants (FRs), consisting of representative phased-out brominated (BFRs) and replacement organophosphorus FRs (OPFRs). OPFRs have emerged as a proposed safer alternative to BFRs; however, limited information is available on their health effects. We found 11 of the 15 FRs (3/6 BFRs, 7/8 OPFRs, and Firemaster 550) caused adverse effects in both adult and developing planarians with similar nominal lowest-effect-levels for BFRs and OPFRs. This suggests that replacement OPFRs are comparably neurotoxic to the phased-out compounds. BFRs were primarily systemically toxic, whereas OPFRs, except Tris(2-chloroethyl) phosphate, shared a behavioral phenotype in response to noxious heat at sublethal concentrations, indicating specific neurotoxic effects. By directly comparing effects on adult and developing planarians, we further found that one BFR (3,3’,5,5’-Tetrabromobisphenol A) caused a developmental selective defect. Together, these results demonstrate that our planarian screening platform yields high content data resulting from assaying various behavioral and morphological endpoints, allowing us to distinguish selective neurotoxic effects and effects specific to the developing nervous system. Ten of these 11 bioactive FRs were previously found to be bioactive in other models, including cell culture and alternative animal models (nematodes and zebrafish). This level of concordance across different platforms emphasizes the urgent need for further evaluation of OPFRs in mammalian systems.
Spontaneous whole-genome duplication restores fertility in interspecific hybrids
Authors: Charron Guillaume , Marsit Souhir , Hénault Mathieu , Martin Hélène , Landry Christian R.
Published: February 2019

Interspecies hybrids often show advantages over parents but suffer from reduced fertility, which can sometimes be overcome through sexual reproduction that sorts out incompatibilities. Sex is however inefficient due to the low viability or fertility of hybrid offspring and thus limits their evolutionary potential. Mitotic cell division could be an alternative to fertility recovery in facultative sexual species. To test this, we evolved under relaxed selection more than 600 diploid yeast hybrids between species that span 100,000 to 15 M years of divergence. We find that hybrids can recover fertility spontaneously and rapidly through whole-genome duplication. These events occurred in both hybrids between young and well-established species. Our results show that the instability of hybrid ploidy is a spontaneous path to fertility recovery.

One Sentence Summary

Ploidy changes potentiate hybrid speciation by leading to fertility recovery.
Task errors drive memories that improve sensorimotor adaptation
Authors: Leow Li-Ann , Marinovic Welber , de Rugy Aymar , Carroll Timothy J
Published: February 2019

Traditional views on how humans adapt movements to perturbations of sensory feedback emphasize a fundamental role for automatic, implicit correction of sensory prediction errors. However, it is now clear that adaptive behaviour also involves deliberate, strategic movement corrections. Such strategic processes have recently been argued to underlie the latent retention of sensorimotor adaptation, evident in improved adaptation to previously encountered perturbations; a phenomenon termed “savings”. It remains unclear, however, whether savings results from prior experience of sensory prediction errors, task errors, or both. Here, we used perturbations of target locations and hand position feedback during reaching to dissociate the contributions of task and sensory prediction errors to latent sensorimotor memory. We show that prior learning to correct for task errors is required to improve adaptation to rotated hand position feedback, whereas a history of sensory prediction errors is neither sufficient nor obligatory for savings. A history of correcting for task errors, induced by experimentally perturbing the target location instead of perturbing sensory feedback of movement, improved adaptation to visuomotor perturbations that were never before encountered. Limiting movement preparation time further showed that this learning consists of two distinct components: 1) a strategic component that is flexible enough to facilitate corrective responses in the opposite direction, but that requires substantial preparation time, and 2) a set of inflexible, cached, stimulus-response associations between targets and reach directions, that can be expressed under time-pressure when similar task conditions are experienced. The results emphasise that adaptive responses to sensorimotor perturbations take multiple forms.
Effect of flow rate and freezing on cyanocobalamin recovery using a commercial solid phase extraction cartridge
Authors: Lees Lauren , Bland Alison M. , DiTullio Giacomo R. , Janech Michael G. , Lee Peter A.
Published: February 2019

Analysis of vitamin B12 in sea water is laborious, time consuming, and often requires storage of relatively large-volume water samples. Alleviating these major limitations will increase the throughput of samples and, as a consequence, improve our understanding of the distribution and role of vitamin B12 in the oceans. Previous studies have indicated that target analyte recovery is negatively affected at flow rates exceeding 1 mL min−1 using home-made C18 Solid Phase Extraction (SPE) cartridges. In this study, the effect of flow rate on recovery of vitamin B12 was tested across a range of flow rates between 1 and 37 mL min−1 using a commercial SPE cartridge containing surface-modified styrene divinylbenzene. Recovery of vitamin B12 at flow rates up to the maximum rate tested did not statistically differ from 1 mL min 1. A second study was conducted to determine whether storage of the SPE cartridges at −20°C had a negative impact on vitamin B12 recovery. Recovery of vitamin B12 from SPE cartridges stored up to 13 days did not differ from unfrozen SPE cartridges. These data suggest that rapid extraction and cold storage of vitamin B12 on commercial SPE cartridges does not negatively affect recovery and offers an economical alternative to field studies.
Contextual cues as modifiers of cTBS effects on indulgent eating
Authors: Safati Adrian B. , Hall Peter A.
Published: February 2019

Background

Prior studies have found that continuous theta burst stimulation (cTBS) targeting the left dlPFC results in reliable increases in consumption of calorie-dense food items. However, it is not known to what extent such effects are modified by cues in the immediate eating environment. Tempting environments (i.e., those saturated with appetitive eating cues) may lead to more reliance on cognitive control networks involving the dlPFC, thereby enhancing cTBS on eating.

Objective/Hypothesis

The objective was to examine the extent to which cTBS effects on eating would be modified by contextual cues. It was hypothesized that cTBS effects on eating would be stronger in the presence of facilitating cues.

Methods

Using a between-subjects factorial design, 107 adults were randomly assigned to one of four conditions: 1) active cTBS + facilitating cues, 2) sham cTBS + facilitating cues, 3) active cTBS + inhibiting cues, 4) sham cTBS + inhibiting cues. Following stimulation participants completed a flanker paradigm and a taste test during which quantity consumed was assessed surreptitiously.

Results

Findings revealed a significant interaction between stimulation and cue type (F(1,102)=6.235, p=.014), such that the effects of cTBS were stronger for those in the facilitating cue condition.

Conclusions

The effects of cTBS on eating are strengthened in the presence of facilitating cues. Methodologically speaking, facilitating cues may be a functional prerequisite for exploring cTBS effects on eating in the laboratory. Substantively, the findings also suggest that facilitating cues in the eating environment may amplify counter-intentional food indulgence in everyday life via cognitive control failure.
The Evolutionary Dynamics of Cooperation in Collective Search
Authors: Tump Alan N. , Wu Charley M. , Bouhlel Imen , Goldstone Robert L.
Published: February 2019

How does cooperation arise in an evolutionary context? We approach this problem using a collective search paradigm where interactions are dynamic and there is competition for rewards. Using evolutionary simulations, we find that the unconditional sharing of information can be an evolutionary advantageous strategy without the need for conditional strategies or explicit reciprocation. Shared information acts as a recruitment signal and facilitates the formation of a self-organized group. Thus, the improved search efficiency of the collective grants byproduct benefits to the original sharer by altering the interaction structure. A key mechanism is a visibility radius, where individuals have access to information about neighbors within a limited distance. Our results show that for a variety of initial conditions and across both static and dynamic fitness landscapes, there is strong selection pressure for unconditional sharing.
Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells
Authors: Moudgil Arnav , Wilkinson Michael N. , Chen Xuhua , He June , Cammack Alex J. , Vasek Michael J. , Lagunas Tomas , Qi Zongtai , Morris Samantha A. , Dougherty Joseph D. , Mitra Robi D.
Published: February 2019

In situ measurements of transcription factor (TF) binding are confounded by cellular heterogeneity and represent averaged profiles in complex tissues. Single cell RNA-seq (scRNA-seq) is capable of resolving different cell types based on gene expression profiles, but no technology exists to directly link specific cell types to the binding pattern of TFs in those cell types. Here, we present self-reporting transposons (SRTs) and their use in single cell calling cards (scCC), a novel assay for simultaneously capturing gene expression profiles and mapping TF binding sites in single cells. First, we show how the genomic locations of SRTs can be recovered from mRNA. Next, we demonstrate that SRTs deposited by the piggyBac transposase can be used to map the genome-wide localization of the TFs SP1, through a direct fusion of the two proteins, and BRD4, through its native affinity for piggyBac. We then present the scCC method, which maps SRTs from scRNA-seq libraries, thus enabling concomitant identification of cell types and TF binding sites in those same cells. As a proof-of-concept, we show recovery of cell type-specific BRD4 and SP1 binding sites from cultured cells. Finally, we map Brd4 binding sites in the mouse cortex at single cell resolution, thus establishing a new technique for studying TF biology in situ.
Causes and consequences of cellulose production byPseudomonas fluorescensSBW25 at the air-liquid interface
Authors: Ardré Maxime , Rainey Paul B
Published: February 2019

Cellulose over-producing wrinkly spreader mutants ofPseudomonas fluorescensSBW25 have been the focus of much investigation, but conditions promoting the production of cellulose in ancestral SBW25, its effects and consequences have escaped investigation through lack ofin vitrophenotype. Here, using a custom built device, we reveal that in static broth microcosms ancestral SBW25 encounters environmental signals at the air-liquid interface that activate, via three diguanylate cyclase-encoding pathways (Wsp, Aws and Mws), production of cellulose. Secretion of the polymer at the meniscus leads to modification of the environment and growth of numerous micro-colonies that extend out from the surface. Accumulation of cellulose and associated microbial growth leads to Rayleigh-Taylor instability resulting in bioconvection and rapid transport of water-soluble products over tens of millimetres. Drawing upon data we build a mathematical model that recapitulates experimental results and captures the interactions between biological, chemical and physical processes.

IMPORTANCE

This work reveals a new bacterial behaviour that manifests at the air-liquid interface, which depends on production of cellulose, and hints to hitherto unrecognised dimensions to bacterial life at surfaces. Additionally, the study links activation of known diguanylate cyclase-encoding pathways to cellulose expression and to signals encountered at the air-liquid interface. Further significance stems from recognition of the consequences of fluid instabilities arising from surface production of cellulose for transport of water-soluble products over large distances.
Treatment of human cells with 5-aza-dC induces formation of PARP1-DNA covalent adducts at genomic regions targeted by DNMT1
Authors: Kiianitsa Kostantin , Maizels Nancy
Published: February 2019

The nucleoside analog 5-aza-2’-deoxycytidine (5-aza-dC) is used to treat some hematopoietic malignancies. The mechanism of cell killing depends upon DNMT1, but is otherwise not clearly defined. Here we show that PARP1 forms covalent DNA adducts in human lymphoblast or fibroblasts treated with 5-aza-dC. Some adducts recovered from 5-aza-dC-treated cells have undergone cleavage by apoptotic caspases 3/7. Mapping of PARP1-DNA adducts, by a new method, “Adduct-Seq”, demonstrates adduct enrichment at CpG-dense genomic locations that are targets of maintenance methylation by DNMT1. Covalent protein-DNA adducts can arrest replication and induce apoptosis, and these results raise the possibility that induction of PARP1-DNA adducts may contribute to cell killing in response to treatment with 5-aza-dC.
Necessary Conditions for Reliable Representation of Asynchronous Spikes Through a Single-layered Feedforward Network
Authors: Lankarany Milad
Published: February 2019

Reliable propagation of firing rate – specifically slow modulation of asynchronous spikes in fairly short time windows [20-500]ms across multiple layers of a feedforward network (FFN) receiving background synaptic noise has proven difficult to capture in spiking models. We, in this paper, explore how information of asynchronous spikes disrupted in the first layer of a typical FFN, and which factors can enable reliable information representation. Our rationale is that the reliable propagation of information across layers of a FFN is likely if that information can be preserved in the first layer of the FFN. In a typical FFN, each layer comprises a certain number (network size) of excitatory neurons – leaky integrate and fire (LIF) model neuron in this paper – receiving correlated input (common stimulus from the upstream layer) plus independent background synaptic noise. We develop a reduced network model of FFN which captures main features of a conventional all-to-all connected FFN. Exploiting the reduced network model, synaptic weights are calculated using a closed-form optimization framework that minimizes the mean squared error between reconstructed stimulus (by spikes of the first layer of FFN) and the original common stimulus. We further explore how representation of asynchronous spikes in a FFN changes with respect to other factors like the network size and the level of background synaptic noise while synaptic weights are optimized for each scenario. We show that not only synaptic weights but also the network size and the level of background synaptic noise are crucial to preserve a reliable representation of asynchronous spikes in the first layer of a FFN. This work sheds light in better understanding of how information of slowly time-varying fluctuations of the firing rate can be transmitted in multi-layered FFNs.
SynQuant: An Automatic Tool to Quantify Synapses from Microscopy Images
Authors: Wang Yizhi , Wang Congchao , Ranefall Petter , Broussard Gerard , Wang Yinxue , Shi Guilai , Wang Yue , Tian Lin , Yu Guoqiang
Published: February 2019

Motivation

Synapses are essential to neural signal transmission. Therefore, quantification of synapses and related neurites from images is vital to gain insights into the underlying pathways of brain functionality and diseases. Despite the wide availability of synapse imaging data, several issues prevent satisfactory quantification of these structures by current tools. First, the antibodies used for labeling synapses are not perfectly specific to synapses. These antibodies may exist in neurites or other cell compartments. Second, the brightness for different neurites and synapses is heterogeneous due to the variation of antibody concentration and synapse-intrinsic differences. Third, images often have low signal to noise ratio (SNR) due to constraints of experiments and availability of sensitive antibodies. The combination of these issues makes the detection of synapses challenging and necessitates developing a new tool to accurately and reliably quantify synapses.

Results

We present an automatic probability-principled synapse detection algorithm and integrate it into our synapse quantification tool SynQuant. Derived from the theory of order statistics, our method controls the false discovery rate and improves the power of detecting synapses. Through extensive experiments on both synthetic and real images in the presence of severe antibody diffusion, high heterogeneity, and large noise, our method was demonstrated to outperform peer specialized synapse detection tools as well as generic spot detection methods by a large margin. Finally, we show SynQuant reliably uncovers statistically significant differences between disease and control conditions in a neuron-astrocyte co-culture based model of Down Syndrome.

Availability

The Java source code, Fiji plug-in, and test data are available at https://github.com/yu-lab-vt/SynQuant.

Contact

yug@vt.edu
Genetic variation associated with infection and the environment in the accidental pathogenBurkholderia pseudomallei
Authors: Chewapreecha Claire , Mather Alison E. , Harris Simon R , Hunt Martin , Holden Matthew T. G. , Chaichana Chutima , Wuthiekanun Vanaporn , Dougan Gordon , Day Nicholas PJ , Limmathurotsakul Direk , Parkhill Julian , Peacock Sharon J
Published: February 2019

The environmental bacteriumBurkholderia pseudomalleicauses melioidosis, an endemic disease in tropical and sub-tropical countries. This bacterium occupies broad ecological niches ranging from soil, contaminated water, single-cell microbes and plants to human infection. Here, we performed genome-wide association studies for genetic determinants of environmental and human adaptation using a combined dataset of 1,011 whole genome sequences ofB. pseudomalleifrom Northeast Thailand (discovery cohort, number of clinical isolates = 325, environmental isolates =428) and Australia (validation cohort, number of clinical isolates = 185, environmental isolates = 73), representing two major global disease hotspots. With these data, we (i) identified 47 genes from 26 distinct loci associated with clinical or environmental isolates from Thailand and replicated 13 loci in an independent Australian cohort; (ii) outlined the selective pressures on the genetic loci (dN/dS) and the frequency at which they had been gained or lost throughout their evolutionary history, reflecting the bacterial adaptability to a wide range of ecological niches; and (iii) highlighted loci implicated in human disease.
Potential role of extracellular ATP released by bacteria in bladder infection and contractility
Authors: Abbasian Behnam , Shair Aidan , O’Gorman David B. , Pena-Diaz Ana M. , Engelbrecht Kathleen , Koenig David W. , Reid Gregor , Burton Jeremy P.
Published: February 2019

Urgency urinary incontinence (UUI), the result of conditions such as overactive bladder (OAB), could potentially be influenced by both commensal and urinary tract infection-associated bacteria. The sensing of bladder filling involves interplay between various parts of the nervous system eventually resulting in contraction of the detrusor muscle during micturition. Here we model host responses to various urogenital bacteria, firstly by using urothelial bladder cell lines and then with myofibroblast contraction assays. To measure responses, we examined calcium influx, gene expression and alpha smooth muscle actin deposition assays. We found that organisms such as Escherichia coli and Gardnerella vaginalis strongly induced calcium influx and contraction, whereas, Lactobacillus crispatus and L. gasseri did not induce this response. Additionally, supernatants from lactobacilli impeded influx-and contraction induced by the uropathogens. Upon further investigation of factors associated with the purinergic signaling pathways, we found that influx and contraction of cells correlated to the amount of extracellular ATP produced by E. coli. Certain lactobacilli appear to mitigate this response by utilizing extracellular ATP or producing inhibitory compounds which can act as a receptor agonist or calcium channel blocker. These findings suggest that members of the urinary microbiota may be influencing UUI.
First Crystal Structure of a Non-Structural Hepatitis E Viral Protein Identifies a Putative Novel Zinc-Binding Protein
Authors: Proudfoot Andrew , Hyrina Anastasia , Holdorf Meghan , Frank Andreas O. , Bussiere Dirksen
Published: February 2019

Hepatitis E virus (HEV) is a 7.2 kb positive-sense, single-stranded RNA virus containing three partially overlapping reading frames, ORF 1-3. All non-structural proteins required for viral replication are encoded by ORF1 and are transcribed as a single transcript. Computational analysis of the complete ORF1 polyprotein identified a previously uncharacterized region of predicted secondary structure bordered by two disordered regions coinciding partially with a region predicted as a putative cysteine protease. Following successful cloning, expression and purification of this region, the crystal structure of the identified protein was determined and identified to have considerable structural homology to a fatty acid binding domain. Further analysis of the structure revealed a metal binding site, shown unambiguously to specifically bind zinc via a non-classical, potentially catalytic zinc-binding motif. We present analysis for the first time of this identified non-structural protein, expanding the knowledge and understanding of the complex mechanisms of HEV biology.

Importance

Hepatitis E virus (HEV) is an emerging virus found predominately in developing countries causing an estimated 20 million infections, which result in approximately 57,000 deaths a year. Although it is known that the non-structural proteins of the HEV ORF1 are expressed as a single transcript, there is debate as to whether ORF1 functions as a single polyprotein or if it is processed into separate domains via a viral or endogenous cellular protease. In the following paper, we present the first structural and biophysical characterization of a HEV non-structural protein using a construct that has partially overlapping boundaries with the predicted putative cysteine protease. Based on the structural homology of the HEV protein with known structures, along with the presence of a catalytic zinc-binding motif, it is possible that the identified protein corresponds to the HEV protease, which could require activation or repression through the binding of a fatty acid. This represents a significant step forward in the characterization and the understanding of the molecular mechanisms of the HEV genome.