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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 57,506 bioRxiv papers from 264,779 authors.

Most downloaded bioRxiv papers, since beginning of last month

56,052 results found. For more information, click each entry to expand.

46701: Rapid genome sequencing for outbreak analysis of the emerging human fungal pathogen Candida auris
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Posted to bioRxiv 13 Oct 2017

Rapid genome sequencing for outbreak analysis of the emerging human fungal pathogen Candida auris
11 downloads epidemiology

Johanna Rhodes, Alireza Abdolrasouli, Rhys A Farrer, Christina A Cuomo, David M Aanensen, Darius Armstrong-James, Matthew Fisher, Silke Schelenz

Background: Candida auris was first described in 2009, and has since caused nosocomial outbreaks, invasive infections and fungaemia across 11 countries in five continents. An outbreak of C. auris occurred in a specialised cardiothoracic London hospital between April 2015 and November 2016, which to date has been the largest outbreak reported worldwide, involving a total of 72 patients. Methods: To understand the epidemiology of C. auris infection within this hospital, we sequenced the genomes of outbreak isolates using Oxford Nanopore Technologies and Illumina in order to type antifungal resistance alleles and to explore the outbreak within its local and global context. Findings: Phylogenomic analysis placed the UK outbreak in the India/Pakistan clade, demonstrating an Asian origin. The outbreak showed similar diversity to that of the entire clade and limited local spatiotemporal clustering was observed. One isolate displayed resistance to both echinocandins and 5-flucytosine; the former was associated with a serine to tyrosine amino acid substitution in the gene FKS1, and the latter was associated with a phenylalanine to isoleucine substitution in the gene FUR1. These mutations are novel for this pathogen. Interpretation: Multiple differential episodic selection of antifungal resistant genotypes has occurred within a genetically heterogenous population across this outbreak, creating a resilient pathogen and making it difficult to define local-scale patterns of transmission as well as implementing outbreak control measures. Funding: Antimicrobial Research Collaborative, Imperial College London

46702: A Mathematical Modeling Approach to The Cort-Fitness Hypothesis
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Posted to bioRxiv 27 Dec 2018

A Mathematical Modeling Approach to The Cort-Fitness Hypothesis
11 downloads animal behavior and cognition

Fadoua El Moustaid, Samuel Lane, Ignacio Moore, Leah Johnson

The Cort-Fitness hypothesis has generated much interest from investigators integrating field endocrinology with evolutionary biology, ecology, and conservation. The hypothesis was developed on the assumption that if glucocorticoid levels increase with environmental challenges and fitness decreases with environmental challenges, then there should be a negative relationship between glucocorticoid levels and fitness. However, studies across diverse taxa have found that the relationship between glucocorticoid levels and fitness is not consistent: some studies show a positive relationship, others negative, and some show no correlation. Hence, support for the hypothesis is not consistent and thus a deeper understanding of the mechanisms underlying the relationship between glucocorticoid levels, environmental pressures, and fitness is needed. We propose a mathematical model representing the links between glucocorticoid levels, environmental challenges, and fitness. Our model explores how variation in the predictability and intensity of environmental challenges, reproductive strategies, and fitness metrics can all contribute to the variability observed in empirical tests of the Cort-Fitness hypothesis. We provide qualitative results showing the Cort-Fitness relationship for different environmental scenarios and discuss how the model can be used to inform future Cort-Fitness studies.

46703: Vesicular delivery of the antifungal antibiotics of Lysobacter enzymogenes C3
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Posted to bioRxiv 12 Jun 2018

Vesicular delivery of the antifungal antibiotics of Lysobacter enzymogenes C3
11 downloads microbiology

Paul Meers, Carol Liu, Rensa Chen, William Bartos, Julianne Davis, Nicole Dziedzic, Jason Orciuolo, Szymon Kutyla, Maria Jose Pozo, Deepti Mithrananda, Dominick Panzera, Shu Wang

Lysobacter enzymogenes C3 is a predatory strain of gram-negative gliding bacteria that produces antifungal antibiotics by the polyketide synthetic pathway. Outer membrane vesicles (OMV) are formed as a stress response and can deliver virulence factors to host cells. The production of OMV by C3 and their role in antifungal activity are reported here. Vesicles in the range of 130-150 nm in diameter were discovered in the cell-free supernatants of C3 cultures. These OMV contain molecules characteristic of bacterial outer membranes, such as lipopolysaccharide and phospholipids. In addition, they contain chitinase activity and essentially all of the heat stable antifungal activity in cell supernatants. We show here that C3 OMV can directly inhibit growth of the yeast Saccharomyces cerevisiae as well as the filamentous fungus Fusarium subglutinans. The activity is dependent on physical contact between OMV and the cells. Furthermore, fluorescent lipid labeling of C3 OMV demonstrated transfer of the membrane-associated probe to yeast cells, suggesting the existence of a mechanism of delivery for membrane-associated molecules. Mass spectrometric analysis of C3 OMV extracts indicates the presence of molecules with molecular weights identical to some of the previously identified antifungal products of C3. These data together suggest that OMV act as an important remote mobile component of predation by Lysobacter.

46704: Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly
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Posted to bioRxiv 23 Feb 2016

Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly
11 downloads biochemistry

John M A Grime, James F Dama, Barbie K Ganser-Pornillos, Cora L Woodward, Grant J Jensen, Mark J Yeager, Gregory A Voth

The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies.

46705: When is selection effective?
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Posted to bioRxiv 30 Oct 2014

When is selection effective?
11 downloads genetics

Simon Gravel

Deleterious alleles are more likely to reach high frequency in small populations because of chance fluctuations in allele frequency. This may lead, over time, to reduced average fitness in the population. In that sense, selection is more ‘effective’ in larger populations. Many recent studies have considered whether the different demographic histories across human populations have resulted in differences in the number, distribution, and severity of deleterious variants, leading to an animated debate. This article seeks to clarify some terms of the debate by identifying differences in definitions and assumptions used in these studies and providing an intuitive explanation for the observed similarity in genetic load among populations. The intuition is verified through analytical and numerical calculations. First, even though rare variants contribute to load, they contribute little to load differences across populations. Second, the accumulation of non-recessive load after a bottleneck is slow for the weakly deleterious variants that contribute much of the long-term variation among populations. Whereas a bottleneck increases drift instantly, it affects selection only indirectly, so that fitness differences can keep accumulating long after a bottleneck is over. Third, drift and selection tend to have opposite effects on load differentiation under dominance models. Because of this competition, load differences across populations depend sensitively and intricately on past demographic events and on the distribution of fitness effects. A given bottleneck can lead to increased or decreased load for variants with identical fitness effects, depending on the subsequent population history. Because of this sensitivity, both classical population genetic intuition and detailed simulations are required to understand differences in load across populations.

46706: Triggering mechanisms for motor actions: A mini meta-analysis and experimental data.
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Posted to bioRxiv 03 Jul 2018

Triggering mechanisms for motor actions: A mini meta-analysis and experimental data.
11 downloads neuroscience

Li-Ann Leow, Aya Uchida, Jamie-Lee Egberts, Stephan Riek, Ottmar Lipp, James Tresilian, Welber Marinovic

Motor actions can be released much sooner than normal when the go-signal is of very high intensity (> 100dBa). Although statistical evidence from individual studies has been mixed, it has been assumed that sternocleidomastoid (SCM) muscle activity could be used to distinguish between two neural circuits involved in movement triggering. We summarized meta-analytically the available evidence for this hypothesis, comparing the difference in premotor reaction time (RT) of actions where SCM activity was elicited (SCM+ trials) by loud acoustic stimuli against trials in which it was absent (SCM- trials). We found ten studies, all reporting comparisons between SCM+ and SCM- trials. Our mini meta-analysis showed that premotor RTs are faster in SCM+ than in SCM- trials. We also present experimental data showing the effects of foreperiod predictability can induce differences in RT that would be of similar size to those attributed to the activation of different neurophysiological pathways to trigger prepared actions. We discuss plausible physiological mechanisms that would explain differences in premotor RTs between SCM+ and SCM- trials.

46707: The evolution of tumour composition during fractionated radiotherapy: implications for outcome
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Posted to bioRxiv 13 Aug 2017

The evolution of tumour composition during fractionated radiotherapy: implications for outcome
11 downloads cancer biology

Thomas D. Lewin, Philip K Maini, Eduardo G. Moros, Heiko Enderling, Helen M Byrne

Current protocols for delivering radiotherapy are based primarily on tumour stage and nodal and metastases status, even though it is well known that tumours and their microenvironments are highly heterogeneous. It is well established that the local oxygen tension plays an important role in radiation-induced cell death, with hypoxic tumour regions responding poorly to irradiation. Therefore, to improve radiation response, it is important to understand more fully the spatiotemporal distribution of oxygen within a growing tumour before and during fractionated radiation. To this end, we have extended a spatially-resolved mathematical model of tumour growth first proposed by Greenspan (Stud. Appl. Math., 1972) to investigate the effects of oxygen heterogeneity on radiation-induced cell death. In more detail, cell death due to radiation at each location in the tumour, as determined by the well-known linear-quadratic model, is assumed also to depend on the local oxygen concentration. The oxygen concentration is governed by a reaction-diffusion equation that is coupled to an integro-differential equation that determines the size of the assumed spherically-symmetric tumour. We combine numerical and analytical techniques to investigate radiation response of tumours with different intratumoral oxygen distribution profiles. Model simulations reveal a rapid transient increase in hypoxia upon re-growth of the tumour spheroid post-irradiation. We investigate the response to different radiation fractionation schedules and identify a tumour-specific relationship between inter-fraction time and dose per fraction to achieve cure. The rich dynamics exhibited by the model suggest that spatial heterogeneity may be important for predicting tumour response to radiotherapy for clinical applications.

46708: OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances reprogramming to epithelial lineages
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Posted to bioRxiv 14 Mar 2019

OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances reprogramming to epithelial lineages
11 downloads cell biology

Kazuhide Watanabe, Ye Liu, Shuhei Noguchi, Madeleine Murray, Jen-Chien Chang, Mami Kishima, Hajime Nishimura, Kosuke Hashimoto, Aki Minoda, Harukazu Suzuki

Mesenchymal-to-epithelial transition (MET) is an important step in cell reprogramming from fibroblasts (a cell type frequently used for this purpose) to various epithelial cell types. However, the mechanism underlying MET induction in fibroblasts remains to be understood. The present study aimed to identify the transcription factors (TFs) that efficiently induce MET in dermal fibroblasts. OVOL2 was identified as a potent inducer of key epithelial genes, and OVOL2 cooperatively enhanced MET induced by HNF1A, TP63, and KLF4, which are known reprogramming TFs to epithelial lineages. In TP63/KLF4-induced keratinocyte-like cell-state reprogramming, OVOL2 greatly facilitated the activation of epithelial and keratinocyte-specific genes. This was accompanied by enhanced changes in chromatin accessibility across the genome. Mechanistically, motif enrichment analysis revealed that the target loci of KLF4 and TP63 become accessible upon induction of TFs, whereas the OVOL2 target loci become inaccessible. This indicates that KLF4 and TP63 positively regulate keratinocyte-associated genes whereas OVOL2 suppresses fibroblast-associated genes. The exogenous expression of OVOL2 therefore disrupts fibroblast lineage identity and facilitates fibroblast cell reprogramming into epithelial lineages cooperatively with tissue-specific reprogramming factors. Identification of OVOL2 as a MET inducer and an epithelial reprogramming enhancer in fibroblasts provides new insights into cellular reprogramming improvement for future applications.

46709: Excess Mortality Related To Chikungunya Epidemics In The Context Of Co-circulation Of Other Arboviruses In Brazil
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Posted to bioRxiv 25 May 2017

Excess Mortality Related To Chikungunya Epidemics In The Context Of Co-circulation Of Other Arboviruses In Brazil
11 downloads epidemiology

Andre R. R. Freitas, Luciano P. G. Cavalcanti, Andrea P. B. von Zuben, M. Rita Donalisio

Chikungunya is an emerging arbovirus that reached the Western Hemisphere at the end of 2013. Studies conducted in Indic Ocean and India suggest that many of deaths associated with chikungunya cannot be recognized by passive surveillance system. The occurrence of these deaths can be inferred by an increase in the overall mortality observed during chikungunya epidemics. To evaluate the mortality associated with chikungunya epidemics in Brazil, we studied monthly mortality by age group comparing the pre-chikungunya period with the chikungunya epidemic period in the most affected states of Brazil. We obtained official data from National System of Notifiable Diseases (SINAN) and Mortality Information System (SIM), both maintained by the Ministry of Health. It was possible to identify a significant increase in all-cause mortality rate during chikungunya epidemics, there was no similar mortality in previous years, even during dengue epidemics. We estimated an excess of 4,842 deaths in Pernambuco during the chikungunya epidemics (51.4/100,000 inhabitants), the most affected age groups were the elderly and under 1 year of age, the same pattern occurred in all states. Further studies at other sites are needed to confirm the association between increased mortality and chikungunya epidemics. If these findings are confirmed, it will be necessary to revise guidelines to recognize the real mortality associated with chikungunya and to improve therapeutic approaches and protective measures in the most vulnerable groups.

46710: Precise Timing Of Sensory Modulations Coupled To Eye Movements During Active Vision
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Posted to bioRxiv 31 May 2017

Precise Timing Of Sensory Modulations Coupled To Eye Movements During Active Vision
11 downloads neuroscience

Christ Devia, Rodrigo Montefusco-Siegmund, Jose Ignacio Egana, Pedro E. Maldonado

Perception is the result of ongoing brain activity combined with sensory stimuli. In natural vision, changes in the visual input typically occur as the result of self-initiated eye movements. Nonetheless, in most studies, stimuli are flashed, and natural eye movements are avoided or restricted. As a consequence, the neural sensory processing associated with active vision is poorly understood. Here, we show that occipital event-related potentials (ERP) to eye movements during free exploration of natural images exhibited different amplitudes, time course and motor dependency than that from the same flashed stimuli. We found that the ERP to visual fixations doubles in P1 magnitude and does not show a late component, which is classically seen with flashed stimuli. In addition, we discovered that the ERP to the saccade onset was as large as the ERP to fixations onset, with an early component that preceded the visual input, suggesting that a motor modulation was associated with the saccades. Furthermore, the use of different visual scenes revealed that both the ERP amplitude and time course were dependent on the type of image explored. Our results demonstrated that during active vision, the nervous system engages a mechanism of sensory modulation that is precisely timed to the self-initiated stimulus changes. This mechanism could help coordinate neural activity across different cortical areas and, by extension, serve as a general mechanism for the global coordination of neural networks.

46711: The CD11a and EPCR marker combination simplifies and improves the purification of mouse hematopoietic stem cells
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Posted to bioRxiv 13 Nov 2017

The CD11a and EPCR marker combination simplifies and improves the purification of mouse hematopoietic stem cells
11 downloads immunology

Alborz Karimzadeh, Vanessa Scarfone, Connie Chao, Karin Grathwohl, John W. Fathman, David Fruman, Thomas Serwold, Matthew A Inlay

Hematopoietic stem cells (HSCs) are the self-renewing multipotent progenitors to all blood cell types. Identification and isolation of HSCs for study has depended on the expression of combinations of surface markers on HSCs that reliably distinguish it from other cell types. However, the increasing number of markers required to isolate HSCs has made it tedious, expensive, and difficult for newcomers, suggesting the need for a simpler panel of HSC markers. We previously showed that phenotypic HSCs could be separated based on expression of CD11a, and that only the CD11a negative fraction contained true HSCs. Here, we show that CD11a and another HSC marker, EPCR, can be used to effectively identify and purify HSCs. We introduce a new two-color HSC sorting method that can highly enrich for HSCs with efficiencies comparable to the gold standard combination of CD150 and CD48. Our results demonstrate that adding CD11a and EPCR to the HSC biologist's toolkit improves the purity of and simplifies isolation of HSCs.

46712: Anti-phage islands force their target phage to directly mediate island excision and spread
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Posted to bioRxiv 11 Nov 2017

Anti-phage islands force their target phage to directly mediate island excision and spread
11 downloads microbiology

Amelia C McKitterick, Kimberley Seed

To defend against their adversaries, bacteria and phage engage in cycles of adaptation and counter-adaptation that shape their mutual evolution. Vibrio cholerae, the causative agent of the diarrheal disease cholera, is antagonized by phages in the environment as well as in human hosts. The lytic phage ICP1 has been recovered from cholera patient stool and water samples over at least 12 years in Bangladesh and is consequently considered a persistent predator of epidemic V. cholerae in this region. In previous work, we demonstrated that mobile genetic elements called phage-inducible chromosomal island-like elements (PLEs) protect V. cholerae from ICP1 infection. PLEs initiate their anti-phage response by excising from the chromosome, however, the mechanism and molecular specificity underlying this response are not known. Here, we show that PLE 1 encodes a large serine recombinase, Int, that exploits an ICP1-specific protein, PexA, as a recombination directionality factor (RDF) to sense and excise in response to ICP1 infection. We validate the functionality and specificity of this unique recombination system, in which the recombinase and RDF are encoded in separate genomes. Additionally, we show that PexA is also hijacked to trigger excision in PLEs found in V. cholerae isolates recovered decades ago. Our results uncover an aspect of the molecular specificity underlying the longstanding conflict between a single predatory phage and V. cholerae PLE and contribute to our understanding of the molecular arms race that drives long-term evolution between combatting phage and their bacterial hosts in nature.

46713: Comparison of video-based and sensor-based head impact exposure
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Posted to bioRxiv 16 Dec 2017

Comparison of video-based and sensor-based head impact exposure
11 downloads bioengineering

Calvin Kuo, Lyndia C Wu, Jesus Loza, Daniel Senif, Scott Anderson, David B Camarillo

Previous research has sought to quantify head impact exposure using wearable kinematic sensors. However, many sensors suffer from poor accuracy in estimating impact kinematics and count, motivating the need for additional independent impact exposure quantification for comparison. Here, we equipped seven collegiate American football players with instrumented mouthguards, and video recorded practices and games to compare video-based and sensor-based exposure rates and impact location distributions. Over 50 player-hours, we identified 271 helmet contact periods in video, while the instrumented mouthguard sensor recorded 2,032 discrete head impacts. Matching video and mouthguard real-time stamps yielded 193 video-identified helmet contact periods and 217 sensor-recorded impacts. To compare impact locations, we binned matched impacts into frontal, rear, side, oblique, and top locations based on video observations and sensor kinematics. While both video-based and sensor-based methods found similar location distributions, our best method utilizing integrated linear and angular position only correctly predicted 81 of 217 impacts. Finally, based on the activity timeline from video assessment, we also developed a new exposure metric unique to American football quantifying number of cross-verified sensor impacts per player-play. We found significantly higher exposure during games (0.35, 95% CI: 0.29-0.42) than practices (0.20, 95% CI: 0.17-0.23) (p<0.05). In the traditional impacts per player-hour metric, we observed higher exposure during practices (4.7) than games (3.7) due to increased player activity in practices. Thus, our exposure metric accounts for variability in on-field participation. While both video-based and sensor-based exposure datasets have limitations, they can complement one another to provide more confidence in exposure statistics.

46714: Effectiveness of live attenuated monovalent human rotavirus vaccination in rural Ecuador, 2008-2013
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Posted to bioRxiv 30 Nov 2018

Effectiveness of live attenuated monovalent human rotavirus vaccination in rural Ecuador, 2008-2013
11 downloads epidemiology

Alicia N. M. Kraay, Edward L Ionides, Gwenyth O Lee, William F Cevallos Trujillo, Joseph N S Eisenberg

Background: While live attenuated monovalent human rotavirus vaccine (Rotarix) efficacy has been characterized through randomized studies, its effectiveness, especially in non-clinical settings, is unclear. In this study, we estimate direct, indirect, and overall effectiveness of Rotarix vaccination. Methods: We analyze 29 months of all-cause diarrhea surveillance from a child cohort (n=376) and ten years of serial population-based case-control lab-confirmed rotavirus data (n=2489) from rural Ecuador during which Rotarix vaccination was introduced. We estimate: 1) the direct effect of vaccination from a cohort of children born from 2008-2013 using Cox regression to compare time to first all-cause diarrhea case by vaccine status; and 2) the overall effect on all-cause diarrheal and symptomatic and asymptomatic rotavirus infection for all age groups, including indirect effects on adults, from the case-control data using weighted logistic regression. Results: Rotarix vaccination provided direct protection against all-cause diarrhea among children 0.5 - 2 years (All-cause diarrhea reduction for receipt of 2 doses of Rotarix=57.1%, 95% CI: 16.6, 77.9%). Overall effectiveness against rotavirus infection was strong (Exposure to 100% coverage of Rotarix vaccination was associated with an 85.5% reduction, 95% CI: 61.1-94.6%) compared to 0% coverage. Indirect effects were observed among older, vaccine-ineligible children and adults (84.5% reduction, 95% CI: 48.2-95.4%). Vaccine effectiveness was high against both symptomatic (48.3% reduction,95% CI: 0.03-73.1%) and asymptomatic infection (90.1% reduction, 95% CI: 56.9-97.7%). Conclusions: Rotarix vaccination suppresses overall transmission. It is highly effective among children in a rural community setting and provides population-level benefits through indirect protection among adults.

46715: Exogenous putrescine alleviates photoinhibition caused by salt stress through increasing cyclic electron flow in cucumber
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Posted to bioRxiv 16 Apr 2018

Exogenous putrescine alleviates photoinhibition caused by salt stress through increasing cyclic electron flow in cucumber
11 downloads plant biology

Xinyi Wu, Sheng Shu, Yu Wang, Ruonan Yuan, Shirong Guo

When plants suffer from abiotic stresses, cyclic electron flow (CEF) is induced for photoprotection. Putrescine (Put), a main polyamine in chloroplasts, plays a critical role in stress tolerance. To elucidate the mechanism of Put regulating CEF for salt-tolerance in cucumber leaves, we measured chlorophyll fluorescence, P700 redox state, ATP and NADPH accumulation and so on. The maximum photochemical efficiency of PSII (Fv/Fm) was not influenced by NaCl and/or Put, but the activity of PSI reaction center (P700) was seriously inhibited by NaCl. Salt stress induced high level of CEF, moreover, NaCl and Put treated plants exhibited much higher CEF activity and ATP accumulation than single salt-treated plants to provide adequate ATP/NADPH ratio for plants growth. Furthermore, Put decreased the trans-membrane proton gradient (ΔpH), accompanied by reducing the pH-dependent non-photochemical quenching (qE) and increasing efficient quantum yield of PSII (Y(II)). The ratio of NADP+/NADPH in salt stressed leaves was significantly increased by Put, indicating that Put relieved over-reduction pressure at PSI accepter side. Taken together, our results suggest that exogenous Put enhances CEF to supply extra ATP for PSI recovery and CO2 assimilation, decreases ΔpH for electron transport related proteins staying active, and enable the non-photochemical quenching transformed into photochemical quenching.

46716: Epigenome-Wide Association Study Of Asthma And Wheeze In Childhood And Adolescence
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Posted to bioRxiv 09 May 2017

Epigenome-Wide Association Study Of Asthma And Wheeze In Childhood And Adolescence
11 downloads epidemiology

Ryan Arathimos, Matthew Suderman, Gemma C. Sharp, Kimberley Burrows, Raquel Granell, Kate Tilling, Tom Gaunt, John Henderson, Susan Ring, Rebecca Richmond, Caroline L Relton

Asthma heritability has only been partially explained by genetic variants and is known to be sensitive to environmental factors, implicating epigenetic modifications such as DNA methylation in its pathogenesis. Using data collected in the Avon Longitudinal Study of Parents and Children (ALSPAC), we assessed associations of asthma and wheeze with DNA methylation at 7.5 years and 16.5 years, at over 450,000 CpG sites in DNA from the peripheral blood of approx. 1000 participants. We used Mendelian randomization (MR), a method of causal inference that uses genetic variants as instrumental variables, to infer the direction of association between DNA methylation and asthma. We identified 302 CpGs associated with current asthma status (FDR-adjusted P-value <0.05) and 445 with current wheeze status at 7.5 years, with substantial overlap between the two. Genes annotated to the 302 associated CpGs were enriched for pathways related to movement of cellular/subcellular components, locomotion, interleukin-4 production and eosinophil migration. All associations attenuated when adjusted for eosinophil and neutrophil cell count estimates. At 16.5 years, two sites were associated with current asthma after adjustment for cell counts. The CpGs mapped to the AP2A2 and IL5RA genes, with a -2.32 [95% CI -1.47,-3.18] and -2.49 [95% CI -1.56,-3.43] change in percentage methylation in asthma cases respectively. Two-sample bi-directional MR indicated a causal effect of asthma on DNA methylation at several CpG sites at 7.5 years. However, associations did not persist after adjustment for multiple testing. There was no evidence of a causal effect of asthma on DNA methylation at either of the two CpG sites at 16.5 years. The majority of observed associations are driven by higher eosinophil cell counts in asthma cases, acting as an intermediate phenotype, with important implications for future studies of DNA methylation in atopic diseases.

46717: Mapping protein function with CRISPR/Cas9-mediated mutagenesis
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Posted to bioRxiv 23 Sep 2016

Mapping protein function with CRISPR/Cas9-mediated mutagenesis
11 downloads genomics

Katherine F Donovan, Mudra Hegde, Meagan Sullender, Emma W Vaimberg, Cory M Johannessen, David E Root, John G. Doench

CRISPR/Cas9 screening has proven to be a versatile tool for genomics research. We describe a CRISPR/Cas9-mediated approach to mutagenesis, exploiting the allelic diversity generated by error-prone non-homologous end-joining (NHEJ) to identify gain-of-function alleles of the MAPK signaling pathway genes MEK1 and BRAF. These results illustrate a scalable technique to easily generate cell populations containing thousands of endogenous allelic variants of any gene or genes to map variant functions.

46718: Sensorimotor memory for object weight is based on previous experience during lifting, not holding
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Posted to bioRxiv 07 Nov 2018

Sensorimotor memory for object weight is based on previous experience during lifting, not holding
11 downloads neuroscience

Vonne van Polanen, Marco Davare

To allow skilled object manipulation, the brain must generate a motor command specifically tailored to the object properties. For instance, in object lifting, the forces applied by the fingertips must be scaled to the object's weight. When lifting a series of objects, forces are usually scaled according to recent experience from previously lifted objects, an effect often referred to as sensorimotor memory. In this study, we investigated the specific time period during which stored information from previous object manipulation is used to mediate sensorimotor memory. More specifically, we examined whether sensorimotor memory was based on weight information obtained between object contact and lift completion (lifting phase) or during stable holding (holding phase). Participants lifted objects in virtual reality that could increase or decrease in weight after the object was lifted and held in the air. In this way, we could distinguish whether the force planning in the next lift was scaled depending on weight information gathered from either the dynamic lifting or static holding period. We found that force planning was based on the previous object weight experienced during the lifting, but not holding, phase. This suggest that the lifting phase, while merely lasting a few hundred milliseconds, is a key time period for building up internal object representations used for planning future hand-object interactions.

46719: Efficient enrichment cloning of TAL effector genes from Xanthomonas
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Posted to bioRxiv 30 Jan 2018

Efficient enrichment cloning of TAL effector genes from Xanthomonas
11 downloads microbiology

Tuan Tu Tran, Hinda Doucouré, Mathilde Hutin, Boris Szurek, Sebastien Cunnac, Ralf Koebnik

Many plant-pathogenic xanthomonads use a type III secretion system to translocate Transcription Activator-Like (TAL) effectors into eukaryotic host cells where they act as transcription factors. Target genes are induced upon binding of a TAL effector to double-stranded DNA in a sequence-specific manner. DNA binding is governed by a highly repetitive protein domain, which consists of an array of nearly identical repeats of ca. 102 base pairs. Many species and pathovars of Xanthomonas, including pathogens of rice, cereals, cassava, citrus and cotton, encode multiple TAL effectors in their genomes. Some of the TAL effectors have been shown to act as key pathogenicity factors, which induce the expression of susceptibility genes to the benefit of the pathogen. However, due to the repetitive character and the presence of multiple gene copies, high-throughput cloning of TAL effector genes remains a challenge. In order to isolate complete TAL effector gene repertoires, we developed an enrichment cloning strategy based on (i) genome-informed in silico optimization of restriction digestions, (ii) selective restriction digestion of genomic DNA, and (iii) size fractionation of DNA fragments. Our rapid, cheap and powerful method allows efficient cloning of TAL effector genes from xanthomonads, as demonstrated for two rice-pathogenic strains of Xanthomonas oryzae from Africa.

46720: Multiple QTL underlie milk phenotypes at the CSF2RB locus
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Posted to bioRxiv 12 Sep 2018

Multiple QTL underlie milk phenotypes at the CSF2RB locus
11 downloads genomics

Thomas J Lopdell, Kathryn Tiplady, Christine Couldrey, Thomas JJ Johnson, Michael Keehan, Stephen R Davis, Bevin L Harris, Richard J Spelman, Russell G Snell, Mathew D Littlejohn

Background: Bovine milk provides an important source of nutrition in much of the Western world, forming components of many food products. Over many years, artificial selection has substantially improved milk production by cows. However, the genes underlying milk production quantitative trait loci (QTL) remain relatively poorly characterised. Here, we investigate a previously-reported QTL located at the CSF2RB locus, for several milk production phenotypes, to better understand its underlying genetic and molecular causes. Results: Using a population of 29,350 taurine dairy cattle, we conducted association analyses for milk yield and composition traits, and identified highly significant QTL for milk yield, milk fat concentration, and milk protein concentration. Strikingly, protein concentration and milk yield appear to show co-located yet genetically distinct QTL. To attempt to understand the molecular mechanisms that might be mediating these effects, gene expression data were used to investigate eQTL for eleven genes in the broader interval. This analysis highlighted genetic impacts on CSF2RB and NCF4 expression that share similar association signatures to those observed for lactation QTL, strongly implicating one or both of these genes as the cause of these effects. Using the same gene expression dataset representing 357 lactating cows, we also identified 38 novel RNA editing sites in the 3' UTR of CSF2RB transcripts. The extent to which two of these sites were edited also appears to be genetically co-regulated with lactation QTL, highlighting a further layer of regulatory complexity implicating the CSF2RB gene. Conclusions: This chromosome 5 locus presents a diversity of molecular and lactation QTL, likely representing multiple overlapping effects that, at a minimum, highlight the CSF2RB gene as having a causal role in these processes.

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