bluuebunny/crossref_metadata_2025 huggingface dataset:
From Anticipation to the Experience of Pain: The Importance of Visceral Versus Somatic Pain Modality in Neural and Behavioral Responses to Pain-Predictive Cues
Authors: Koenen Laura Ricarda , Icenhour Adriane , Forkmann Katarina , Theysohn Nina , Forsting Michael , Bingel Ulrike , Elsenbruch Sigrid
Published: June 2018

Objective

The aim of this study was to compare behavioral and neural anticipatory responses to cues predicting either somatic or visceral pain in an associative learning paradigm.

Methods

Healthy women (N = 22) underwent functional magnetic resonance imaging. During an acquisition phase, two different visual cues repeatedly signalled either experimental visceral or somatic pain. In a subsequent extinction phase, identical cues were presented without pain. Before and after each phase, cue valence and contingency awareness were assessed on visual analog scales.

Results

Visceral compared to somatic pain–predictive cues were rated as more unpleasant after acquisition (visceral, 32.18 ± 13.03 mm; somatic, −18.36 ± 10.36 mm; p = .021) with similarly accurate cue-pain contingencies. After extinction, cue valence returned to baseline for both modalities (visceral, 1.55 ± 9.81 mm; somatic, −18.45 ± 7.12; p = .41). During acquisition, analyses of cue-induced neural responses revealed joint neural activation engaging areas associated with attention processing and cognitive control. Enhanced deactivation of posterior insula to visceral cues was observed, which correlated with enhanced responses within the salience network (anterior cingulate cortex, anterior insula) during visceral compared to somatic pain stimulation. During extinction, both pain modalities induced anticipatory neural activation in the extinction and salience network (all p
FWE values < .05).

Conclusions

Conditioned emotional responses to pain-predictive cues are modality specific and enhanced for the visceral modality, suggesting that pain anticipation is shaped by the salience of painful stimuli. Common but also modality-specific neural mechanisms are involved during cue-pain learning, whereas extinction of cued responses seems unaffected by modality. Future research should examine potential implications for the pathophysiology of chronic pain conditions, especially chronic visceral pain.
Shared Leadership in Healthcare Action Teams: A Systematic Review
Authors: Janssens Sarah , Simon Robert , Beckmann Michael , Marshall Stuart
Published: June 2018

Objectives

The aims of this review were to consolidate the reported literature describing shared leadership in healthcare action teams (HCATs) and to review the reported outcomes related to leadership sharing in healthcare emergencies.

Methods

A systematic search of the English language literature before November 2017 was performed using PsycINFO, MEDLINE, PubMed, CINAHL, and EMBASE. Articles describing sharing of leadership functions in HCATs were included. Healthcare teams performing routine work were excluded. Studies were reviewed for type of leadership sharing and sharing-related outcomes.

Results

Thirty-three articles met the inclusion criteria. A variety of shared leadership models were described across the following three categories: spontaneous collaboration, intuitive working relations, and institutionalized practices. While leadership sharing has the potential for both positive and negative influences on team performance, only six articles reported outcomes potentially attributable to shared leadership.

Conclusions

Despite strong evidence for a positive relationship between shared leadership and team performance in other domains, there is limited literature describing shared leadership models in HCATs. The association between shared leadership and team performance in HCATs is a rich area for further investigation.
Assessment of Interstitial Lung Disease Using Lung Ultrasound Surface Wave Elastography
Authors: Clay Ryan , Bartholmai Brian J. , Zhou Boran , Karwoski Ronald , Peikert Tobias , Osborn Thomas , Rajagopalan Srinivasan , Kalra Sanjay , Zhang Xiaoming
Published: June 2018

Purpose:

Optimal strategies to detect early interstitial lung disease (ILD) are unknown. ILD is frequently subpleural in distribution and affects lung elasticity. Lung ultrasound surface wave elastography (LUSWE) is a noninvasive method of quantifying superficial lung tissue elastic properties. In LUWSE a handheld device applied at the intercostal space vibrates the chest at a set frequency, and the lung surface wave velocity is measured by an ultrasound probe 5 mm away in the same intercostal space. We explored LUWSE’s ability to detect ILD and correlated LUSWE velocity with physiological, quantitative, and visual radiologic features of subjects with known ILD and of healthy controls.

Materials and Methods:

Seventy-seven subjects with ILD, mostly caused by connective tissue disease, and 19 healthy controls were recruited. LUSWE was performed on all subjects in 3 intercostal lung regions bilaterally. Comparison of LUSWE velocities pulmonary function testing, visual assessment, and quantitative analysis of recent computed tomographic imaging with Computer-Aided Lung Informatics for Pathology Evaluation and Rating (CALIPER) software.

Results:

Sonographic velocities were higher in all lung regions for cases, with the greatest difference in the lateral lower lung. Median velocity in m/s was 5.84 versus 4.11 and 5.96 versus 4.27 (P<0.00001) for cases versus controls, left and right lateral lower lung zones, respectively. LUSWE velocity correlated negatively with vital capacity and positively with radiologist and CALIPER-detected interstitial abnormalities.

Conclusions:

LUSWE is a safe and noninvasive technique that shows high sensitivity to detect ILD and correlated with clinical, physiological, radiologic, and quantitative assessments of ILD. Prospective study in detecting ILD is indicated.
Endovascular Perfusion Augmentation for Critical Care: Partial Aortic Occlusion for Treatment of Severe Ischemia–Reperfusion Shock
Authors: Johnson M. Austin , Tibbits Emily M. , Hoareau Guillaume L. , Simon Meryl A. , Davidson Anders J. , DeSoucy Erik S. , Faulconer E. Robert , Grayson J. Kevin , Neff Lucas P. , Williams Timothy K.
Published: June 2018

Background:

The resuscitation of patients in shock is materially intensive and many patients are refractory to maximal therapy. We hypothesized that partial inflation of an intra-aortic balloon, termed Endovascular Perfusion Augmentation for Critical Care (EPACC), would minimize material requirements while improving physiologic metrics.

Methods:

Swine underwent a 25% controlled bleed and 45 min of complete aortic occlusion to create a severe ischemia–reperfusion shock state. Animals received either standardized critical care (SCC) composed of IV fluids and norepinephrine delivered through an algorithmically controlled platform or EPACC in addition to SCC. Physiologic parameters were collected, and blood was sampled for analysis. Primary outcomes were total IV fluids and average MAP during the critical care phase. Differences (P < 0.05) were measured with t test (continuous data) and Wilcoxon rank-sum test (ordinal data).

Results:

There were no differences in baseline characteristics. There were no differences in the maximum lactate; however, animals in the EPACC group had a higher average MAP (EPACC 65 mmHg, 95% confidence interval [CI], 65–66; SCC 60 mmHg, 95% CI, 57–63; P < 0.01) and remained within goal MAP for a greater period of time (EPACC 95.3%, 95% CI, 93.2–97.4; SCC 51.0%, 95% CI, 29.5–72.6; P < 0.01). EPACC animals required less IV fluids when compared with the SCC group (EPACC 21 mL/kg, 95% CI, 0–42; SCC 96 mL/kg, 95% CI, 76–117; P < 0.01). There were no differences in final lactate. Animals in the EPACC group had a higher final creatinine (EPACC 2.3 mg/dL, 95% CI, 2.1–2.5; SCC 1.7 mg/dL, 95% CI, 1.4–2.0; P < 0.01), but there were no differences in renal cellular damage on histology (P = 0.16).

Conclusion:

Using a swine model of severe shock, the addition of EPACC to SCC significantly reduced fluid resuscitation requirements and improved blood pressure. This is the first description of a new therapy for patients in refractory shock or in resource-limited settings.
SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data
Authors: Epping Lennard , van Tonder Andries J. , Gladstone Rebecca A. ,   The Global Pneumococcal Sequencing Consortium, Bentley Stephen D. , Page Andrew J. , Keane Jacqueline A.
Published: June 2018

Streptococcus pneumoniae is responsible for 240 000–460 000 deaths in children under 5 years of age each year. Accurate identification of pneumococcal serotypes is important for tracking the distribution and evolution of serotypes following the introduction of effective vaccines. Recent efforts have been made to infer serotypes directly from genomic data but current software approaches are limited and do not scale well. Here, we introduce a novel method, SeroBA, which uses a k-mer approach. We compare SeroBA against real and simulated data and present results on the concordance and computational performance against a validation dataset, the robustness and scalability when analysing a large dataset, and the impact of varying the depth of coverage on sequence-based serotyping. SeroBA can predict serotypes, by identifying the cps locus, directly from raw whole genome sequencing read data with 98 % concordance using a k-mer-based method, can process 10 000 samples in just over 1 day using a standard server and can call serotypes at a coverage as low as 15–21×. SeroBA is implemented in Python3 and is freely available under an open source GPLv3 licence from: https://github.com/sanger-pathogens/seroba
A systems biology approach to explore the impact of maple tree dormancy release on sap variation and maple syrup quality
Authors: N’guyen Guillaume , Martin Nathalie , Jain Mani , Lagacé Luc , Landry Christian R , Filteau Marie
Published: June 2018

Maple sap is a complex nutrient matrix collected during Spring to produce maple syrup. The characteristics of sap change over the production period and its composition directly impacts syrup quality. This variability could in part be attributed to changes in tree metabolism following dormancy release, but little is known about these changes in deciduous trees. Therefore, understanding the variation in sap composition associated with dormancy release could help pinpoint the causes of some defects in maple syrup. In particular, a defect known as “buddy”, is an increasing concern for the industry. This off-flavor appears around the time of bud burst, hence its name. To investigate sap variation related to bud burst and the buddy defect, we monitored sap variation with respect to a dormancy release index (Sbb) and syrup quality. First, we looked at variation in amino acid content during this period. We observed a shift in amino acid relative proportions associated with dormancy release and found that most of them increase rapidly near the point of bud burst, correlating with changes in syrup quality. Second, we identified biological processes that respond to variation in maple sap by performing a competition assay using the barcodedSaccharomyces cerevisiaeprototroph deletion collection. This untargeted approach revealed that the organic sulfur content may be responsible for the development of the buddy off-flavor, and that dormancy release is necessary for the appearance of the defect, but other factors such as microbial activity may also be contributing.
Sense-antisense gene overlap causes evolutionary retention of the few introns in Giardia genome and the implications
Authors: Xue Min , Chen Bing , Ye Qingqing , Shao Jingru , Lyu Zhangxia , Wen Jianfan
Published: June 2018

Background

It is widely accepted that the last eukaryotic common ancestor (LECA) and early eukaryotes were intron-rich and intron loss dominated subsequent evolution, thus the presence of only very few introns in some modern eukaryotes must be the consequence of massive loss. But it is striking that few eukaryotes were found to have completely lost introns. Despite extensive research, the causes of massive intron losses remain elusive, and actually the reverse question – how the few introns are retained under the pressure of loss is equally significant but was rarely studied, except that it was conjectured that the essential functions of some introns prevent their loss. The extremely few (eight) spliceosome-mediated cis-spliced introns in the relatively simple genome of Giardia lamblia provide an excellent opportunity to explore this question.

Results

Our investigation of the intron-containing genes and introns in Giardia found three types of intron distribution patterns: ancient intron in ancient gene, relatively new intron in ancient gene, and relatively new intron in relatively new gene, which can reflect to some extent the dynamic evolution of introns in Giardia. Not finding any special features or functional importance of these introns responsible for the retention, we noticed and experimentally verified that some intron-containing genes form sense-antisense gene pairs with functional genes on their complementary strands, and that the introns just reside in the overlapping regions.

Conclusions

In Giardia’s evolution, despite constant pressure of intron loss, intron gain can still occur in both ancient and newly-evolved genes, but only a few introns have been retained; the evolutionary retention of introns is most likely not due to the functional constraint of the introns themselves but the causes outside of introns, such as the constraints imposed by other genomic functional elements overlapping with the introns. These findings can not only provide some clues to find new genomic functional elements -- in the areas overlapping with introngs, but suggest that “functional constraint” of introns may not be necessarily directly associated with intron loss and gain, or that the real functions or the way of functioning of introns are probably still outside of our current knowledge.
Exposure to unpredictable trips and slips while walking can improve balance recovery responses with minimum predictive gait alterations
Authors: Okubo Yoshiro , Brodie Matthew A , Sturnieks Daina L , Hicks Cameron , Carter Hilary , Toson Barbara , Lord Stephen R
Published: June 2018

INTRODUCTION

This study aimed to determine if repeated exposure to unpredictable trips and slips while walking can improve balance recovery responses when predictive gait alterations (e.g. slowing down) are minimised.

METHODS

Ten young adults walked on a 10-m walkway that induced slips and trips in fixed and random locations. Participants were exposed to a total of 12 slips, 12 trips and 6 non-perturbed walks in three conditions: 1) right leg fixed location, 2) left leg fixed location and 3) random leg and location. Kinematics during non-perturbed walks and previous and recovery steps were analysed.

RESULTS

Throughout the three conditions, participants walked with similar gait speed, step length and cadence(p>0.05). Participants’ extrapolated centre of mass (XCoM) was anteriorly shifted immediately before slips at the fixed location (p<0.01), but this predictive gait alteration did not transfer to random perturbation locations. Improved balance recovery from trips in the random location was indicated by increased margin of stability and step length during recovery steps (p<0.05). Changes in balance recovery from slips in the random location was shown by reduced backward XCoM displacement and reduced slip speed during recovery steps (p<0.05).

CONCLUSIONS

Even in the absence of most predictive gait alterations, balance recovery responses to trips and slips were improved through exposure to repeated unpredictable perturbations. A common predictive gait alteration to lean forward immediately before a slip was not useful when the perturbation location was unpredictable. Training balance recovery with unpredictable perturbations may be beneficial to fall avoidance in everyday life.
No support for the sexy-sperm hypothesis in the seed beetle: sons of monandrous females fare better in post-copulatory competition
Authors: Hook Kristin A.
Published: June 2018

The sexy-sperm hypothesis posits that polyandrous females derive an indirect fitness benefit from multi-male mating because they increase the probability their eggs are fertilized by males whose sperm have high fertilizing efficiency, which is assumed to be heritable and conferred on their sons. However, whether this process occurs is contentious because father-to-son heritability may be constrained by the genetic architecture underlying traits important in sperm competition within certain species. Previous empirical work has revealed such genetic constraints in the seed beetle,Callosobruchus maculatus, a model system in sperm competition studies in which female multi-male mating is ubiquitous. Using the seed beetle, I tested a critical prediction of the sexy-sperm hypothesis that polyandrous females produce sons that are on average more successful under sperm competition than sons from monandrous females. Contrary to the prediction of the sexy-sperm hypothesis, I found that sons from monandrous females had significantly higher relative paternity in competitive double matings. Moreover, post-hoc analyses revealed that these sons produced significantly larger ejaculates when second to mate, despite being smaller. This study is the first to provide empirical evidence for post-copulatory processes favoring monandrous sons and discusses potential explanations for the unexpected bias in paternity.
Functional and Anatomical Specificity in a Higher Olfactory Centre
Authors: Frechter Shahar , Bates Alexander S. , Tootoonian Sina , Dolan Michael-John , Manton James D. , Jamasb Arian , Kohl Johannes , Bock Davi , Jefferis Gregory S. X. E.
Published: June 2018

Most sensory systems are organized into parallel neuronal pathways that process distinct aspects of incoming stimuli. For example, in insects, second order olfactory projection neurons target both the mushroom body, which is required for learning, and the lateral horn (LH), which has been proposed to mediate innate olfactory behavior. Mushroom body neurons encode odors in a sparse population code, which does not appear stereotyped across animals. In contrast the functional principles of odor coding in the LH remain poorly understood. We have carried out a comprehensive anatomical analysis of the Drosophila LH, counting ~1400 neurons; combining genetic driver lines, anatomical and functional criteria, we identify 165 LHN cell types. We then show that genetically labeled LHNs have stereotyped odor responses across animals for 33 of these cell types. LHN tuning can be ultra-sparse (1/40 odors tested), but on average single LHNs respond to three times more odors than single projection neurons. This difference can be rationalized by our observation that LHNs are better odor categorizers, likely due to pooling of input projection neurons responding to different odors of the same category. Our results reveal some of the principles by which a higher sensory processing area can extract innate behavioral significance from sensory stimuli.
Novel tumor suppressor roles forGZMAandRASGRP1in dissemination of bothTheileria annulata-transformed macrophages and human B-lymphoma cells
Authors: Rchiad Zineb , Haidar Malak , Ansari Hifzur Rahman , Tajeri Shahin , Mfarrej Sara , Rached Fathia Ben , Kaushik Abhinav , Langsley Gordon , Pain Arnab
Published: June 2018

Theileria annulatais a tick-transmitted apicomplexan parasite that infects and transforms bovine leukocytes into disseminating tumors that cause a disease called tropical theileriosis. Using comparative transcriptomics we identified genes transcriptionally perturbed duringTheileria-induced transformation. Dataset comparisons highlighted a small set of genes associated withTheileria-transformed leukocyte dissemination. The roles of Granzyme A (GZMA) and RAS guanyl-releasing protein 1 (RASGRP1) were verified by CRISPR/Cas9-mediated knock-down. Knocking down ofGZMAandRASGRP1in attenuated macrophages led to a regain in their dissemination in Rag2/γC mice confirming their role as dissemination suppressorsin vivo. We further evaluated the roles ofGZMAandRASGRP1in human B-lymphoma cells by comparing the transcriptome of 934 human cancer cell lines to that ofTheileria-transformed bovine host cells. We confirmed dampened dissemination potential of human B-lymphoma cells that overexpressGZMAandRASGRP1. Our results provide evidence thatGZMAandRASGRP1have a novel tumor suppressor function in bothT. annulata-infected bovine host cells and in human B-lymphomas.

We compared the transcriptomes ofTheileria annulatatransformed B-lymphocytes to 934 human cancer cell lines and provide functional evidence for shared tumor suppressor roles for GZMA and RASGRP1 in controlling the dissemination phenotype of both human B lymphomas and Theileria-transformed leukocytes.
Predicting onset, progression, and clinical subtypes of Parkinson disease using machine learning
Authors: Faghri Faraz , Hashemi Sayed Hadi , Leonard Hampton , Scholz Sonja W. , Campbell Roy H. , Nalls Mike A. , Singleton Andrew B.
Published: June 2018

Background

The clinical manifestations of Parkinson disease are characterized by heterogeneity in age at onset, disease duration, rate of progression, and constellation of motor versus nonmotor features. Due to these variable presentations, counseling of patients about their individual risks and prognosis is limited. There is an unmet need for predictive tests that facilitate early detection and characterization of distinct disease subtypes as well as improved, individualized predictions of the disease course. The emergence of machine learning to detect hidden patterns in complex, multi-dimensional datasets provides unparalleled opportunities to address this critical need.

Methods and Findings

We used unsupervised and supervised machine learning approaches for subtype identification and prediction. We used machine learning methods on comprehensive, longitudinal clinical data from the Parkinson Disease Progression Marker Initiative (PPMI) (n=328 cases) to identify patient subtypes and to predict disease progression. The resulting models were validated in an independent, clinically well-characterized cohort from the Parkinson Disease Biomarker Program (PDBP) (n=112 cases). Our analysis distinguished three distinct disease subtypes with highly predictable progression rates, corresponding to slow, moderate and fast disease progressors. We achieved highly accurate projections of disease progression four years after initial diagnosis with an average Area Under the Curve of 0.93 (95% CI: 0.96 ± 0.01 for PDvec1, 0.87 ± 0.03 for PDvec2, and 0.96 ± 0.02 for PDvec3). We have demonstrated robust replication of these findings in the independent validation cohort.

Conclusions

These data-driven results enable clinicians to deconstruct the heterogeneity within their patient cohorts. This knowledge could have immediate implications for clinical trials by improving the detection of significant clinical outcomes that might have been masked by cohort heterogeneity. We anticipate that machine learning models will improve patient counseling, clinical trial design, allocation of healthcare resources and ultimately individualized clinical care.
Trio deep-sequencing does not reveal unexpected mutations in Cas9-edited monkeys
Authors: Luo Xin , He Yaoxi , Zhang Chao , He Xiechao , Yan Lanzhen , Li Min , Hu Ting , Hu Yan , Jiang Jin , Meng Xiaoyu , Ji Weizhi , Zhao Xudong , Zheng Ping , Xu Shuhua , Su Bing
Published: June 2018

CRISPR-Cas9 is a widely-used genome editing tool, but its off-target effect remains a concern, especially in view of future clinical applications. Non-human primates (NHPs) share close genetic and physiological similarities with humans, making them an ideal preclinical model for developing Cas9-based therapies. However, no comprehensive in vivo off-target assessment has been conducted in NHPs. Here we performed whole genome trio sequencing of Cas9-treated monkeys. We found they only carried a small number of de novo mutations that can be explained by expected spontaneous mutations, and no unexpected mutations were detected.
Gamma-Band Correlations in Primary Visual Cortex
Authors: Liu Xiaochen Morning , Sanz-Leon Paula , Robinson P. A.
Published: June 2018

Neural field theory is used to quantitatively analyze the two-dimensional spatiotemporal correlation properties of gamma-band (30 - 70 Hz) oscillations evoked by stimuli arriving at the primary visual cortex (V1), and modulated by patchy connectivities that depend on orientation preference (OP). Correlation functions are derived analytically under different stimulus and measurement conditions. The predictions reproduce a range of published experimental results, including the existence of two-point oscillatory temporal cross-correlations with zero time-lag between neurons with similar OP, the influence of spatial separation of neurons on the strength of the correlations, and the effects of differing stimulus orientations.
A long-non-coding RNA, LINC00473, confers the human adipose tissue thermogenic phenotype through enhanced cAMP responsiveness
Authors: Tran Khanh-Van , Nandrup-Bus Cecilie , DeSouza Tiffany , Soares Ricardo , Jespersen Naja Zenius , Min So Yun , Rojas-Rodriguez Raziel , Willenbrock Hanni , Juhlin Therese , Severinsen Mai Charlotte Krogh , Malka Kimberly , Pedersen Bente Klarlund , Fitzgibbons Timothy , Scheele Camilla , Corvera Silvia , Nielsen Søren
Published: June 2018

Specialized adipocytes localized in distinct depots mediate the many physiological functions of adipose tissue. In humans, paucity of thermogenic adipocytes correlates with high metabolic disease risk, raising much interest in the mechanisms by which these cells arise. Here we report molecular signatures associated with adipocyte development in different human depots and identify a long non-coding RNA, LINC00473, as the transcript most closely associated with enrichment of thermogenic adipocytes. LINC00473 expression is low in subjects with obesity or type-2 diabetes and is highly correlated with cAMP signaling and mitochondrial oxidative phosphorylation pathways. LINC00473 is localized in the nucleus and the cytoplasm, and its knockdown impairs induction of UCP1 and mitochondrial respiration. These results reveal that depot-enriched genes that modulate responsiveness to external stimuli, specifically LINC00473, are important determinants of the adipose tissue thermogenic phenotype, and potential targets for metabolic disease therapy.
Simultaneous representation of sensory and mnemonic information in human visual cortex
Authors: Rademaker R. L. , Chunharas C. , Serences J. T.
Published: June 2018

Traversing sensory environments requires keeping relevant information in mind while simultaneously processing new inputs. Visual information is kept in working memory via feature selective responses in early visual cortex, but recent work had suggested that new sensory inputs wipe out this information. Here we show region-wide multiplexing abilities in classic sensory areas, with population-level response patterns in visual cortex representing the contents of working memory concurrently with new sensory inputs.
Targeted Molecular Dynamics Simulations Suggest Direct Ligand Competition as a Plausible Efflux Inhibition Mechanism in the Multidrug Resistance Pump AcrB
Authors: Silva Lande , da Silva Pedro Eduardo Almeida , Machado Karina S. , Dutra Nelson , Lybrand Terry P.
Published: June 2018

We report computer simulation results using the Targeted Molecular Dynamics technique to explore possible transport mechanisms in the multidrug efflux pump AcrB for two substrates, ethidium bromide and a tetrahydropyridine derivative. These studies revealed structural elements, including specific α-helices, β-strands and flexible loops that define a physically plausible pathway for substrates to the extracellular environment. These calculation results can be used to plan future biophysical experiments and may suggest interesting drug design possibilities to address drug resistance due to AcrB function.

Importance

Addressing the issue of antimicrobial resistance mediated by efflux, this study presents possible binding sites and structures in the AcrB MDR pump that could be molecular targets for drugs. Targeted molecular dynamics simulations suggested that these sites and structures seem vital for a successful efflux. The AcrB is proposed to be divided into three distinct zones, with loops, sheets and helices mediating the passage of molecules from one zone to another. We also described possible capture sites on the outer part of the protein and access ways to its interior. Finally, we proposed that ligand competition for same pathways could be thought as an efflux inhibitory mechanism, thus assisting to conceive new ways of designing efflux pump inhibitors.
Connecting the dots between mechanosensitive channel abundance, osmotic shock, and survival at single-cell resolution
Authors: Chure Griffin , Lee Heun Jin , Phillips Rob
Published: June 2018

Rapid changes in extracellular osmolarity are one of many insults microbial cells face on a daily basis. To protect against such shocks,Escherichia coliand other microbes express several types of transmembrane channels which open and close in response to changes in membrane tension. InE. coli, one of the most abundant channels is the mechanosensitive channel of large conductance (MscL). While this channel has been heavily characterized through structural methods, electrophysiology, and theoretical modeling, our understanding of its physiological role in preventing cell death by alleviating high membrane tension remains tenuous. In this work, we examine the contribution of MscL alone to cell survival after osmotic shock at single cell resolution using quantitative fluorescence microscopy. We conduct these experiments in anE. colistrain which is lacking all mechanosensitive channel genes save for MscL whose expression is tuned across three orders of magnitude through modifications of the Shine-Dalgarno sequence. While theoretical models suggest that only a few MscL channels would be needed to alleviate even large changes in osmotic pressure, we find that between 500 and 700 channels per cell are needed to convey upwards of 80% survival. This number agrees with the average MscL copy number measured in wild-typeE. colicells through proteomic studies and quantitative Western blotting. Furthermore, we observe zero survival events in cells with less than 100 channels per cell. This work opens new questions concerning the contribution of other mechanosensitive channels to survival as well as regulation of their activity.
Heterologous Expression ofPseudomonas putidaMethyl-Accepting Chemotaxis Proteins YieldsEscherichia coliChemotactic to Aromatic Compounds
Authors: Roggo Clémence , Clerc Estelle Emilie , Hadadi Noushin , Carraro Nicolas , Stocker Roman , van der Meer Jan Roelof
Published: June 2018

Escherichia coli, commonly used in chemotaxis studies, is attracted mostly by amino acids, sugars and peptides. We envisioned modifying chemotaxis specificity ofE. coliby expressing heterologous chemoreceptors fromPseudomonas putidaenabling attraction either to toluene or benzoate. ThemcpTgene encoding the type 40H methyl-accepting chemoreceptor for toluene fromPseudomonas putidaMT53 and thepcaYgene for the type 40H receptor for benzoate and related molecules fromP. putidaF1 were expressed from thetrgpromoter on a plasmid in motile wild-typeE. coliMG1655.E. colicells expressing McpT accumulated in chemoattraction assays to sources with 60–200 μM toluene; less strongly than the response to 100 μM serine, but statistically significantly stronger than to sources without any added attractant. An McpT-mCherry fusion protein was detectably expressed inE. coliand yielding weak but distinguishable membrane and polar foci in 1% of cells.E. coliexpressing PcaY showed weak attraction to 0.1–1 mM benzoate but 50–70% of cells localized the PcaY-mCherry fusion to their membrane. We conclude that implementing heterologous receptors in theE. colichemotaxis network is possible and, upon improvement of the compatibility of the type 40H chemoreceptors, may bear interest for biosensing.

IMPORTANCE

Bacterial chemotaxis might be harnessed for the development of rapid biosensors, in which chemical availability is deduced from cell accumulation to chemoattractants over time. Chemotaxis ofEscherichia colihas been well-studied, but the bacterium is not attracted to chemicals of environmental concern, such as aromatic solvents. We show here that heterologous chemoreceptors for aromatic compounds fromPseudomonas putidaat least partly functionally complement theE. colichemotaxis network, yielding cells attracted to toluene or benzoate. Complementation was still inferior to native chemoattractants like serine, but our study demonstrates the potential for obtaining selective sensing for aromatic compounds inE. coli.
TGFβ1-induced cell motility is mediated through Cten in colorectal cancer
Authors: Asiri Abdulaziz , Raposo Teresa Pereira , Alfahed Abdulaziz , Ilyas Mohammad
Published: June 2018

Cten is a tensin which promotes epithelial-mesenchymal transition (EMT) and cell motility. The precise mechanisms regulating Cten are unknown, although Cten could be regulated by several cytokines and growth factors. Since Transforming growth factor beta 1 (TGF-β1) regulates integrin function and promotes EMT / cell motility, we investigated whether this happens through Cten signalling in colorectal cancer (CRC).

TGF-β1 signalling was modulated by either stimulation or knockdown in the CRC cell lines SW620 and HCT116. The effect of this modulation on expression of Cten, EMT markers and cellular function was tested. Cten role as a direct mediator of TGF-β1 signalling was investigated in a CRC cell line with a deleted Cten gene (SW620ΔCten).

When TGF-β1 was stimulated or inhibited, this resulted in, respectively, upregulation and downregulation of Cten expression and EMT markers. Cell migration and invasion were significantly increased following TGF-β1 stimulation and lost by TGF-β1 knockdown. TGF-β1 stimulation in SW620ΔCten resulted in selective loss of the effect of TGF-β1 signalling on EMT and cell motility whilst the stimulatory effect on cell proliferation was retained.

These data suggested Cten may play an essential role in mediating TGF-β1-induced EMT and cell motility and may play a role in metastasis in CRC.
Unified Analysis of Global and Focal Aspects of Absence Epilepsy via Neural Field Theory of the Corticothalamic System
Authors: Yang Dong-Ping , Robinson P. A.
Published: June 2018

A physiology-based corticothalamic model is investigated with focal spatial heterogeneity, to unify global and focal aspects of absence epilepsy. Numerical and analytical calculations are employed to investigate the emergent spatiotemporal dynamics induced by focal activity as well as their underlying dynamical mechanisms. The spatiotemporal dynamics can be categorized into three scenarios: suppression, localization, and generalization of the focal activity, as summarized from a phase diagram vs. focal width and characteristic axon range. The corresponding temporal frequencies and spatial extents of wave activity during seizure generalization and localization agree well with experimental observations of global and focal aspects of absence epilepsy, respectively. The emergent seizure localization provide a biophysical explanation of the temporally higher frequency but spatially more localized cortical waves observed in genetic rat models that display characteristics of human absence epilepsy. Predictions are also presented for further experimental test.

Author Summary

Absence epilepsy is characterized by a sudden paroxysmal loss of consciousness accompanied by oscillatory activity propagating over many brain areas. Although primary generalized absence seizures are supported by the global corticothalamic system, converging experimental evidence supports a focal theory of absence epilepsy. Here we propose a dynamical mechanism to unify the global and focal aspects of absence epilepsy, with focal absence seizures associated with seizure localization, and the global ones associated with seizure generalization. Our corticothalamic model is used to investigate how seizure rhythms and spatial extents are related in these two different aspects of absence epilepsy. The results account for the difference of the experimentally observed seizure rhythms and spatial extents between humans and genetic rat models, which has previously been used to argue against the validity of such rats as animal models of absence epilepsy in humans.
A cumulative inertia phenomenon explains anomalous long-distance transport in eukaryotic cells
Authors: Fedotov Sergei , Korabel Nickolay , Waigh Thomas A. , Han Daniel , Allan Victoria J.
Published: June 2018

We demonstrate the phenomenon of cumulative inertia in intracellular transport involving multiple motor proteins in human epithelial cells by measuring the empirical survival probability of cargoes on the microtubule and their detachment rates. We found the longer a cargo moves along a microtubule, the less likely it detaches from it. As a result, the movement of cargoes is non-Markovian and involves a memory. We observe memory effects on the scale of up to 2 seconds. We provide a theoretical link between the measured detachment rate and the super-diffusive Levy walk-like cargo movement.
Physical and transcriptional organisation of the bread wheat intracellular immune receptor repertoire
Authors: Steuernagel Burkhard , Witek Kamil , Krattinger Simon G. , Ramirez-Gonzalez Ricardo H. , Schoonbeek Henk-jan , Yu Guotai , Baggs Erin , Witek Agnieszka I. , Yadav Inderjit , Krasileva Ksenia V. , Jones Jonathan D. G. , Uauy Cristobal , Keller Beat , Ridout Christopher J. ,   The International Wheat Genome Sequencing Consortium, Wulff Brande B. H.
Published: June 2018

Disease resistance genes encoding intracellular immune receptors of the nucleotide-binding and leucine-rich repeat (NLR) class of proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR encoding genes. The availability of the hexaploid wheat cultivar Chinese Spring reference genome now allows a detailed study of its NLR complement. However, low NLR expression as well as high intra-family sequence homology hinders their accurate gene annotation. Here we developed NLR-Annotator forin silicoNLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. Applying our tool to wheat and combining it with a transcript-validated subset of genes from the reference gene annotation, we characterized the structure, phylogeny and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci of which 1,540 were confirmed as complete genes. NLRs with integrated domains mostly group in specific sub-clades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains suggesting a paired helper-function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts), which may be tissue-specific and/or induced by biotic stress. As a case study for applying our tool to the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease resistant varieties.
Amylasecopy number analysis in several mammalian lineages reveals convergent adaptive bursts shaped by diet
Authors: Pajic Petar , Pavlidis Pavlos , Dean Kirsten , Neznanova Lubov , Daugherity Erin , Romano Rose-Anne , Garneau Danielle , Globig Anja , Ruhl Stefan , Gokcumen Omer
Published: June 2018

The amylase gene (AMY), which codes for a starch-digesting enzyme in animals, underwent several gene copy number gains in humans1, dogs2, and mice3, presumably along with increased starch consumption during the evolution of these species. Here we present evidence for additionalAMYcopy number expansions in several mammalian species, most of which also consume starch-rich diets. We also show that these independentAMYcopy number gains are often accompanied by a gain in enzymatic activity of amylase in saliva. We used multi-species coalescent modeling to provide further evidence that these recurrentAMYgene copy number expansions were adaptive. Our findings underscore the overall importance of gene copy number amplification as a flexible and fast adaptive mechanism in evolution that can independently occur in different branches of the phylogeny.
Whole-brain imaging and characterization ofDrosophilabrains based on one-, two-, and three-photon excitations
Authors: Hsu Kuo-Jen , Lin Yen-Yin , Chiang Ann-Shyn , Chu Shi-Wei
Published: June 2018

To study functional connectome, optical microscopy provides the advantages ofin vivoobservation, molecular specificity, high-speed acquisition, and sub-micrometer spatial resolution. Now, the most complete single-neuron-based anatomical connectome is built uponDrosophila; thus it will be a milestone to achieve whole-brain observation with sub-cellular resolution in livingDrosophila.Surprisingly, two-photon microscopy cannot penetrate through the 200-μm-thick brain, due to the extraordinarily strong aberration/scattering from tracheae. Here we achieve whole-Drosophila-brain observation by degassing the brain or by using three-photon microscopy at 1300-nm, while only the latter providesin vivofeasibility, reduced aberration/scattering and exceptional optical sectioning capability. Furthermore, by comparing one-photon (488-nm), two-photon (920-nm), and three-photon (1300-nm) excitations in the brain, we not only demonstrate first quantitative reduction of both scattering and aberration in trachea-filled tissues, but unravel that the contribution of aberration exceeds scattering at long wavelengths. Our work paves the way toward constructing functional connectome in a livingDrosophila.
CalmAn: An open source tool for scalable Calcium Imaging data Analysis
Authors: Giovannucci Andrea , Friedrich Johannes , Gunn Pat , Kalfon Jérémie , Koay Sue Ann , Taxidis Jiannis , Najafi Farzaneh , Gauthier Jeffrey L. , Zhou Pengcheng , Tank David W. , Chklovskii Dmitri , Pnevmatikakis Eftychios A.
Published: June 2018

Advances in fluorescence microscopy enable monitoring larger brain areasin-vivowith finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. Here we present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good performance on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn we collected a corpus of ground truth annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.
Separation and Loss of Centrioles From Primordidal Germ Cells to Mature Oocytes in the Mouse
Authors: Simerly Calvin , Manil-Ségalen Marion , Castro Carlos , Hartnett Carrie , Kong Dong , Verlhac Marie-Hélène , Loncarek Jadranka , Schatten Gerald
Published: June 2018

Oocytes, including those from mammals, lack centrioles, but neither the mechanism by which mature eggs lose their centrioles nor the exact stage at which centrioles are destroyed during oogenesis is known. To answer questions raised by centriole disappearance during oogenesis, using a transgenic mouse expressing GFP-centrin-2 (GFP CETN2), we traced their presence from e11.5 primordial germ cells (PGCs) through oogenesis and their ultimate dissolution in mature oocytes. We show tightly coupled CETN2 doublets in PGCs, oogonia, and pre-pubertal oocytes. Beginning with follicular recruitment of incompetent germinal vesicle (GV) oocytes, through full oocyte maturation, the CETN2 doublets separate within the pericentriolar material (PCM); concomitantly, a rise in single CETN2 pairs is identified. CETN2 dissolution accelerates following meiosis resumption. Remarkably, a single CETN2 pair is retained in the PCM of most meiotic metaphase-I and -II spindle poles. Partial dissolution of the CETN2 foci occurs even as other centriole markers, like Cep135, a protein necessary for centriole duplication, are maintained at the PCM. Furthermore, live imaging demonstrates that the link between the two centrioles breaks as meiosis resumes and that centriole association with the PCM is progressively lost. Microtubule inhibition shows that centriole dissolution is uncoupled from microtubule dynamics. Thus, centriole doublets, present in early G2-arrested meiotic prophase oocytes, begin partial reduction during follicular recruitment and meiotic resumption, much later than previously thought.
Revealing heterogeneity of brain imaging phenotypes in Alzheimer’s disease based on unsupervised clustering of blood marker profiles
Authors: Martí-Juan Gerard , Sanroma Gerard , Piella Gemma ,   for the Alzheimer’s Disease Neuroimaging Initiative and the Alzheimer’s Disease Metabolomics Consortium
Published: June 2018

Alzheimer’s disease (AD) affects millions of people and is a major rising problem in health care worldwide. Recent research suggests that AD could have different subtypes, presenting differences in how the disease develops. Characterizing those subtypes could be key to deepen the understanding of this complex disease. In this paper, we used a multivariate, non-supervised clustering method over blood-based markers to find subgroups of patients defined by distinctive blood marker profiles. Our analysis on ADNI database identified 4 possible subgroups, each with a different blood profile. More importantly, we show that subgroups with different profiles have a different relationship between brain phenotypes detected in magnetic resonance imaging and disease condition.
Tandem repeats drive variation of intrinsically disordered regions in budding yeast
Authors: Babokhov Michael , Reinfeld Bradley I. , Hackbarth Kevin , Bentov Yotam , Fuchs Stephen M.
Published: June 2018

Copy-number variation in tandem repeat coding regions is more prevalent in eukaryotic genomes than current literature suggests. We have reexamined the genomes of nearly 100 yeast strains looking to map regions of repeat variation. From this analysis we have identified that length variation is highly correlated to intrinsically disordered regions (IDRs). Furthermore, the majority of length variation is associated with tandem repeats. These repetitive regions are rich in homopolymeric amino acid sequences but nearly half of the variation comes from longer-repeating motifs. Comparisons of repeat copy number and sequence between strains of budding yeast as well as closely related fungi suggest selection for and conservation of IDR-related tandem repeats. In some instances, repeat variation has been demonstrated to mediate binding affinity, aggregation, and protein stability. With this analysis, we can identify proteins for which repeat variation may play conserved roles in modulating protein function.