bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chiral vortex dynamics on membranes is an intrinsic property of FtsZ, driven by GTP hydrolysis
Authors: Ramirez Diego , García-Soriano Daniela A. , Raso Ana , Feingold Mario , Rivas Germán , Schwille Petra 
Published: October 2016

AbstractThe primary protein of the bacterial Z ring guiding cell division, FtsZ, has recently been shown to engage in intriguing self-organization together with one of its natural membrane anchors, FtsA. When co-reconstituted on flat supported membranes, these proteins assemble into dynamic chiral vortices whose diameters resemble the cell circumference. These dynamics are due to treadmilling polar FtsZ filaments, supposedly destabilized by the co-polymerizing membrane adaptor FtsA, thus catalysing their turnover. Here we show that FtsA is in fact dispensable and that the phenomenon is an intrinsic property of FtsZ alone when supplemented with a membrane anchor. The emergence of these chiral dynamic patterns is critically dependent on GTP concentration and FtsZ surface densities, in agreement with theoretical predictions. The interplay of membrane tethering, GTP binding, and hydrolysis promotes both, the assembly and the destabilization of FtsZ polymers, leading to the observed treadmilling dynamics. Notably, the vortex chirality is defined by the position of the membrane targeting sequence (mts) and can be inverted when attaching it to the opposite end of FtsZ. This reveals a so far unknown vectorial character of these cytomotive filaments, comprising three orthogonal directions: Filament polarity, curvature, and membrane attachment.
A mathematical approach for secondary structure analysis can provide an eyehole to the RNA world
Authors: Konstantinides Nikolaos 
Published: October 2016

AbstractThe RNA pseudoknot is a conserved secondary structure encountered in a number of ribozymes, which assume a central role in the RNA world hypothesis. However, RNA folding algorithms could not predict pseudoknots until recently. Analytic combinatorics – a newly arisen mathematical field – has introduced a way of enumerating different RNA configurations and quantifying RNA pseudoknot structure robustness and evolvability, two features that drive their molecular evolution. I will present a mathematician’s viewpoint of RNA secondary structures, and explain how analytic combinatorics applied on RNA sequence to structure maps can represent a valuable tool for understanding RNA secondary structure evolution. Analytic combinatorics can be implemented for the optimization of RNA secondary structure prediction algorithms, the derivation of molecular evolution mathematical models, as well as in a number of biotechnological applications, such as biosensors, riboswitches etc. Moreover, it showcases how the integration of biology and mathematics can provide a different viewpoint into the RNA world.
Spatiotemporal patterns of desiccation tolerance in natural populations ofDrosophila melanogaster
Authors: Rajpurohit Subhash , Gefen Eran , Bergland Alan , Petrov Dmitri , Gibbs Allen G , Schmidt Paul S 
Published: October 2016

AbstractWater availability is a major environmental challenge to a variety of terrestrial organisms. In insects, desiccation tolerance varies predictably over various spatial and temporal scales and is an important physiological basis of fitness variation among natural populations. Here, we examine the dynamics of desiccation tolerance in North American populations ofDrosophila melanogasterusing: 1) natural populations sampled across latitudes and seasons in the eastern USA; 2) experimental evolution in the field in response to changing seasonal environments; 3) a sequenced panel of inbred lines (DGRP) to perform genome wide associations and examine whether SNPs/genes associated with variation in desiccation tolerance exhibit patterns of clinal and/or seasonal enrichment in pooled sequencing of populations. In natural populations we observed a shallow cline in desiccation tolerance, for which tolerance exhibited a positive association with latitude; the steepness of this cline increased with decreasing culture temperature, demonstrating a significant degree of thermal plasticity. No differences in desiccation tolerance were observed between spring and autumn collections from three mid-to-northern latitude populations, or as a function of experimental evolution to seasonality. Similarly, water loss rates did not vary significantly among latitudinal, seasonal or experimental evolution populations. However, changes in metabolic rates during prolonged exposure to dry conditions indicate increased tolerance in higher latitude populations. Genome wide association studies identified thirty-six SNPs in twenty-eight genes associated with sex-averaged drought tolerance. Among North American populations, genes associated with drought tolerance do not show increased signatures of spatially varying selection relative to the rest of the genome, whereas among Australian populations they do.
Behavior ofCaenorhabditis elegansin a nicotine gradient modulated by food
Authors: Sobkowiak Robert , Kaczmarek Piotr , Kowalski Mateusz , Kabaciński Rafał , Lesicki Andrzej 
Published: October 2016

AbstractNicotine decreases food intake, and smokers often report that they smoke to control their weight. To see whether similar phenomena could be observed in the model organismCaenorhabditis elegans, we challenged drug-naïve nematodes with a chronic low (0.01 mM) and high (1 mM) nicotine concentration for 55 h (from hatching to adulthood). After that, we recorded changes in their behavior in a nicotine gradient, where they could choose a desired nicotine concentration. By using a combination of behavioral and morphometric methods, we found that both nicotine and food modulate worm behavior. In the presence of food the nematodes adapted to the low nicotine concentration, when placed in the gradient, chose a similar nicotine concentration likeC. elegansadapted to the high nicotine concentration. However, in the absence of food, the nematodes adapted to the low nicotine concentration, when placed in the gradient of this alkaloid, chose a similar nicotine concentration like naïve worms. The nematodes growing up in the presence of high concentrations of nicotine had a statistically smaller body size, compared to the control condition, and the presence of food did not cause any enhanced slowing movement. These results provide a platform for more detailed molecular and cellular studies of nicotine addiction and food intake in this model organism.
Collider Scope: When selection bias can substantially influence observed associations
Authors: Munafò Marcus R. , Tilling Kate , Taylor Amy E. , Evans David M. , Davey Smith George 
Published: October 2016

AbstractLarge-scale cross-sectional and cohort studies have transformed our understanding of the genetic and environmental determinants of health outcomes. However, the representativeness of these samples may be limited – either through selection into studies, or by attrition from studies over time. Here we explore the potential impact of this selection bias on results obtained from these studies, from the perspective that this amounts to conditioning on a collider (i.e., a form of collider bias). While it is acknowledged that selection bias will have a strong effect on representativeness and prevalence estimates, it is often assumed that it should not have a strong impact on estimates of associations. We argue that because selection can induce collider bias (which occurs when two variables independently influence a third variable, and that third variable is conditioned upon), selection can lead to substantially biased estimates of associations. In particular, selection related to phenotypes can bias associations with genetic variants associated with those phenotypes. In simulations, we show that even modest influences on selection into, or attrition from, a study can generate biased and potentially misleading estimates of both phenotypic and genotypic associations. Our results highlight the value of knowing which population your study sample is representative of. If the factors influencing selection and attrition are known, they can be adjusted for. For example, having DNA available on most participants in a birth cohort study offers the possibility of investigating the extent to which polygenic scores predict subsequent participation, which in turn would enable sensitivity analyses of the extent to which bias might distort estimates.Key MessagesSelection bias (including selective attrition) may limit the representativeness of large-scale cross-sectional and cohort studies.This selection bias may induce collider bias (which occurs when two variables independently influence a third variable, and that variable is conditioned upon).This may lead to substantially biased estimates of associations, including of genetic associations, even when selection / attrition is relatively modest.
PoGo: Jumping from Peptides to Genomic Loci
Authors: Schlaffner Christoph N. , Pirklbauer Georg , Bender Andreas , Choudhary Jyoti S. 
Published: October 2016

AbstractCurrent tools for visualization and integration of proteomics with other omics datasets are inadequate for large-scale studies and capture only basic sequence identity information. We developed PoGo for mapping peptides identified through mass spectrometry to a reference genome to overcome these limitations. PoGo exhibited superior performance over other tools on benchmarking with large-scale human tissue and cancer phosphoproteome datasets. Additionally, extended functionality enables representation of single nucleotide variants, post-translational modifications and quantitative features.
Genomic Comparison of Campylobacter spp. and Their Potential for Zoonotic Transmission between Birds, Primates, and Livestock
Authors: Weis Allison M. , Storey Dylan B. , Taff Conor C. , Townsend Andrea K. , Huang Bihua C. , Kong Nguyet T. , Clothier Kristin A. , Spinner Abigail , Byrne Barbara A. , Weimer Bart C. 
Published: October 2016

ABSTRACT

Campylobacter
is the leading cause of human gastroenteritis worldwide. Wild birds, including American crows, are abundant in urban, suburban, and agricultural settings and are likely zoonotic vectors of
Campylobacter
. Their proximity to humans and livestock increases the potential spreading of
Campylobacter
via crows between the environment, livestock, and humans. However, no studies have definitively demonstrated that crows are a vector for pathogenic
Campylobacter
. We used genomics to evaluate the zoonotic and pathogenic potential of
Campylobacter
from crows to other animals with 184 isolates obtained from crows, chickens, cows, sheep, goats, humans, and nonhuman primates. Whole-genome analysis uncovered two distinct clades of
Campylobacter jejuni
genotypes; the first contained genotypes found only in crows, while a second genotype contained “generalist” genomes that were isolated from multiple host species, including isolates implicated in human disease, primate gastroenteritis, and livestock abortion. Two major β-lactamase genes were observed frequently in these genomes (
oxa-184
, 55%, and
oxa-61
, 29%), where
oxa-184
was associated only with crows and
oxa-61
was associated with generalists. Mutations in
gyrA
, indicative of fluoroquinolone resistance, were observed in 14% of the isolates. Tetracycline resistance (
tetO
) was present in 22% of the isolates, yet it occurred in 91% of the abortion isolates. Virulence genes were distributed throughout the genomes; however,
cdtC
alleles recapitulated the crow-only and generalist clades. A specific
cdtC
allele was associated with abortion in livestock and was concomitant with
tetO
. These findings indicate that crows harboring a generalist
C. jejuni
genotype may act as a vector for the zoonotic transmission of
Campylobacter
.

IMPORTANCE
This study examined the link between public health and the genomic variation of
Campylobacter
in relation to disease in humans, primates, and livestock. Use of large-scale whole-genome sequencing enabled population-level assessment to find new genes that are linked to livestock disease. With 184
Campylobacter
genomes, we assessed virulence traits, antibiotic resistance susceptibility, and the potential for zoonotic transfer to observe that there is a “generalist” genotype that may move between host species.
Genetic Diversity and Origins of the Homoploid-Type Hybrid
Phytophthora ×alni
Authors: Aguayo Jaime , Halkett Fabien , Husson Claude , Nagy Zoltán Á. , Szigethy András , Bakonyi József , Frey Pascal , Marçais Benoit 
Published: October 2016

ABSTRACT

Assessing the process that gives rise to hybrid pathogens is central to understanding the evolution of emerging plant diseases.
Phytophthora ×alni
, a pathogen of alder, results from the homoploid hybridization of two related species,
Phytophthora uniformis
and
Phytophthora
×
multiformis
. Describing the genetic characteristics of
P
. ×
alni
should help us understand how reproductive mechanisms and historical processes shaped the population structure of this emerging hybrid pathogen. The population genetic structure of
P
. ×
alni
and the relationship with its parental species were investigated using 12 microsatellites and one mitochondrial DNA (mtDNA) marker on a European collection of 379 isolates. Populations of
P
. ×
alni
were dominated by one multilocus genotype (MLG). The frequency of this dominant MLG increased after the disease emergence together with a decline in diversity, suggesting that it was favored by a genetic mechanism such as drift or selection. Combined microsatellite and mtDNA results confirmed that
P
. ×
alni
originated from multiple hybridization events that involved different genotypes of the progenitors. Our detailed analyses point to a geographic structure that mirrors that observed for
P. uniformis
in Europe. The study provides more insights on the contribution of
P. uniformis
, an invasive species in Europe, to the emergence of
Phytophthora
-induced alder decline.

IMPORTANCE
Our study describes an original approach to assess the population genetics of polyploid organisms using microsatellite markers. By studying the parental subgenomes present in the interspecific hybrid
P. ×alni
, we were able to assess the geographical and temporal structure of European populations of the hybrid, shedding new light on the evolution of an emerging plant pathogen. In turn, the study of the parental subgenomes permitted us to assess some genetic characteristics of the parental species of
P. ×alni
,
P. uniformis
, and
P
. ×
multiformis
, which are seldom sampled in nature. The subgenomes found in
P. ×alni
represent a picture of the “fossilized” diversity of the parental species.
The Surface-Associated Exopolysaccharide of Bifidobacterium longum 35624 Plays an Essential Role in Dampening Host Proinflammatory Responses and Repressing Local T
H
17 Responses
Authors: Schiavi Elisa , Gleinser Marita , Molloy Evelyn , Groeger David , Frei Remo , Ferstl Ruth , Rodriguez-Perez Noelia , Ziegler Mario , Grant Ray , Moriarty Thomas Fintan , Plattner Stephan , Healy Selena , O'Connell Motherway Mary , Akdis Cezmi A. , Roper Jennifer , Altmann Friedrich , van Sinderen Douwe , O'Mahony Liam 
Published: October 2016

ABSTRACT

The immune-modulating properties of certain bifidobacterial strains, such as
Bifidobacterium longum
subsp.
longum
35624 (
B. longum
35624), have been well described, although the strain-specific molecular characteristics associated with such immune-regulatory activity are not well defined. It has previously been demonstrated that
B. longum
35624 produces a cell surface exopolysaccharide (sEPS), and in this study, we investigated the role played by this exopolysaccharide in influencing the host immune response.
B. longum
35624 induced relatively low levels of cytokine secretion from human dendritic cells, whereas an isogenic exopolysaccharide-negative mutant derivative (termed sEPS
neg
) induced vastly more cytokines, including interleukin-17 (IL-17), and this response was reversed when exopolysaccharide production was restored in sEPS
neg
by genetic complementation. Administration of
B. longum
35624 to mice of the T cell transfer colitis model prevented disease symptoms, whereas sEPS
neg
did not protect against the development of colitis, with associated enhanced recruitment of IL-17
+
lymphocytes to the gut. Moreover, intranasal administration of sEPS
neg
also resulted in enhanced recruitment of IL-17
+
lymphocytes to the murine lung. These data demonstrate that the particular exopolysaccharide produced by
B. longum
35624 plays an essential role in dampening proinflammatory host responses to the strain and that loss of exopolysaccharide production results in the induction of local T
H
17 responses.

IMPORTANCE
Particular gut commensals, such as
B. longum
35624, are known to contribute positively to the development of mucosal immune cells, resulting in protection from inflammatory diseases. However, the molecular basis and mechanisms for these commensal-host interactions are poorly described. In this report, an exopolysaccharide was shown to be decisive in influencing the immune response to the bacterium. We generated an isogenic mutant unable to produce exopolysaccharide and observed that this mutation caused a dramatic change in the response of human immune cells
in vitro
. In addition, the use of mouse models confirmed that lack of exopolysaccharide production induces inflammatory responses to the bacterium. These results implicate the surface-associated exopolysaccharide of the
B. longum
35624 cell envelope in the prevention of aberrant inflammatory responses.
Sulfur-oxidizing bacteria prior to the Great Oxidation Event from the 2.52 Ga Gamohaan Formation of South Africa
Authors: Czaja Andrew D. , Beukes Nicolas J. , Osterhout Jeffrey T. 
Published: October 2016

Abstract
The first 2 b.y. of Earth’s history was an important time for life when microbes evolved and diversified into essentially all of the metabolic forms that now exist. Because of feedbacks between biology and the surface environment, understanding Earth’s biological history can help us understand the evolution of Earth itself. The morphological and geochemical evidence for this ancient biological history is sparse but is increasing. Here we report evidence for 2.52 Ga exceptionally large, organic, smooth-walled, coccoidal microfossils preserved in a deep-water black chert in the Gamohaan Formation of the Kaapvaal craton of South Africa. These fossils occur mainly as compressed solitary coccoids that range in size from 20 to 265 µm but occasionally occur in short chains of cells. Morphologically these fossils are similar to Proterozoic and Phanerozoic acritarchs and to certain Archean fossils interpreted as possible cyanobacteria. However, their exceptionally large size, simple cell wall microstructure, and paleoecological setting, as well as multiple sulfur isotope systematics of pyrite within the unit, suggest that the Gamohaan Formation fossils were sulfur-oxidizing bacteria similar to those of the modern genus Thiomargarita, organisms that live in anoxic and sulfidic deep-water settings. These are the oldest reported fossil sulfur bacteria and reveal a diversity of life and ecosystems, previously only interpreted from geochemical proxies, just prior to the Great Oxidation Event, a time of major atmospheric evolution.
Dimensions of tinnitus-related complaints reported by patients and their significant others: protocol for a systematic review
Authors: Haider Haúla , Fackrell Kathryn , Kennedy Veronica , Hall Deborah A 
Published: October 2016

IntroductionOver 70 million people in Europe and >50 million people in the USA are reported to experience tinnitus (the sensation of noise in the absence of any corresponding sound source). Tinnitus is a multidimensional concept. Individual patients may report different profiles of tinnitus-related symptoms which may each require a tailored management approach and an appropriate measure of therapeutic benefit. This systematic review concerns the patient perspective and has the purpose to find what symptoms are reported by people who experience tinnitus and by their significant others.Methods and analysisThis protocol lays out the methodology to define what dimensions of tinnitus-related symptoms patients and their significant others report as being a problem. Methods are defined according to the Preferred Reporting Items for Systematic reviews and Meta-analyses for Protocols (PRISMA-P) 2015 and data will be collated in a narrative synthesis. Findings will contribute to the eventual establishment of a Core Domain Set for clinical trials of tinnitus.Ethics and disseminationNo ethical issues are foreseen. Findings will be reported at national and international ENT and audiology conferences and in a peer-reviewed journal.Trial registration numberCRD42015020629.
Community-randomised controlled trial embedded in the Anishinaabek Cervical Cancer Screening Study: human papillomavirus self-sampling versus Papanicolaou cytology
Authors: Zehbe Ingeborg , Jackson Robert , Wood Brianne , Weaver Bruce , Escott Nicholas , Severini Alberto , Krajden Mel , Bishop Lisa , Morrisseau Kyla , Ogilvie Gina , Burchell Ann N , Little Julian 
Published: October 2016

ObjectivesThe incidence of cervical cancer is up to 20-fold higher among First Nations women in Canada than the general population, probably due to lower participation in screening. Offering human papillomavirus (HPV) self-sampling in place of Papanicolaou (Pap) testing may eventually increase screening participation and reduce cervical cancer rates in this population.DesignA community-randomised controlled screening trial.SettingFirst Nations communities in Northwest Ontario, Canada.ParticipantsWomen aged between 25 and 69, living in Robinson Superior Treaty First Nations. The community was the unit of randomisation.InterventionsWomen were asked to complete a questionnaire and have screening by HPV self-sampling (arm A) or Pap testing (arm B).Primary outcome measuresThe number of women who participated in cervical screening.RandomisationCommunity clusters were randomised to include approximately equivalent numbers of women in each arm.Results6 communities were randomised to arm A and 5 to arm B. One community withdrew, leaving 5 communities in each group (834 eligible women). Participation was <25%. Using clustered intention-to-treat (ITT) analysis, initial and cumulative averaged uptakes in arm A were 1.4-fold (20% vs 14.3%, p=0.628) and 1.3-fold (20.6% vs 16%, p=0.694) higher compared to arm B, respectively. Corresponding per protocol (PP) analysis indicates 2.2-fold (22.9% vs 10.6%, p=0.305) and 1.6-fold (22.9% vs 14.1%, p=0.448) higher uptakes in arm A compared to arm B. Screening uptake varied between communities (range 0–62.1%). Among women who completed a questionnaire (18.3% in arm A, 21.7% in arm B), the screening uptake was 1.8-fold (ITT; p=0.1132) or 3-fold (PP; p<0.01) higher in arm A versus arm B.ConclusionsPap and HPV self-sampling were compared in a marginalised, Canadian population. Results indicated a preference for self-sampling. More research on how to reach underscreened Indigenous women is necessary.Trial registration numberISRCTN84617261.