bluuebunny/crossref_metadata_2025_split huggingface dataset:
A survey of DNA methylation polymorphism identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome
Authors: Garg Paras , Joshi Ricky S. , Watson Corey , Sharp Andrew J. 
Published: September 2017

ABSTRACTWhile studies such as the 1000 Genomes Projects have resulted in detailed maps of genetic variation in humans, to date there are few robust maps of epigenetic variation. We defined sites of common epigenetic variation, termed Variably Methylated Regions (VMRs) in five purified cell types. We observed that VMRs occur preferentially at enhancers and 3’ UTRs. While the majority of VMRs have high heritability, a subset of VMRs within the genome show highly correlated variation intrans, forming co-regulated networks that have low heritability, differ between cell types and are enriched for specific transcription factor binding sites and biological pathways of functional relevance to each tissue. For example, in T cells we defined a network of 72 co-regulated VMRs enriched for genes with roles in T-cell activation; in fibroblasts a network of 21 coregulated VMRs comprising all fourHOXgene clusters enriched for control of tissue growth; and in neurons a network of 112 VMRs enriched for roles in learning and memory. By culturing genetically-identical fibroblasts under varying conditions of nutrient deprivation and cell density, we experimentally demonstrate that some VMR networks are responsive to environmental conditions, with methylation levels at these loci changing in a coordinated fashion intransdependent on cellular growth. Intriguingly these environmentally-responsive VMRs showed a strong enrichment for imprinted loci (p<10−94), suggesting that these are particularly sensitive to environmental conditions. Our study provides a detailed map of common epigenetic variation in the human genome, showing that both genetic and environmental causes underlie this variation.
Development and characterization of 24 microsatellite markers in Primula tosaensis, an endangered primrose, using MiSeq
Authors: Yamamoto Masaya , Handa Yoshihiro , Aihara Hiroki , Setoguchi Hiroaki 
Published: September 2017

AbstractPrimula tosaensis (Primulaceae) is an endangered primrose endemic to Japan. In this study, 24 novel microsatellite markers were developed using Illumina MiSeq sequencing to facilitate conservation of this endangered species. The genetic diversity and polymorphisms of these novel markers were measured in 32 individuals from a wild P. tosaensis population. The number of alleles and expected heterozygosities ranged from 2 to 5 (mean = 2.8) and from 0.119 to 0.724 (mean = 0.395), respectively. All loci were in Hardy–Weinberg equilibrium. The markers developed in this study will provide a powerful and practical tool for investigating the population structure and genetic diversity of P. tosaensis.
Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the South China Sea
Authors: Xie Zhang‐Xian , Chen Feng , Zhang Shu‐Feng , Wang Ming‐Hua , Zhang Hao , Kong Ling‐Fen , Dai Min‐Han , Hong Hua‐Sheng , Lin Lin , Wang Da‐Zhi 
Published: September 2017

SummaryViral concentrates (VCs), containing bioinformative DNA and proteins, have been used to study viral diversity, viral metagenomics and virus–host interactions in natural ecosystems. Besides viruses, VCs also contain many noncellular biological components including diverse functional proteins. Here, we used a shotgun proteomic approach to characterize the proteins of VCs collected from the oligotrophic deep chlorophyll maximum (DCM) of the South China Sea. Proteins of viruses infecting picophytoplankton, that is, cyanobacteria and prasinophytes, and heterotrophic bacterioplankton, such as SAR11 and SAR116, dominated the viral proteome. Almost no proteins from RNA viruses or known gene transfer agents were detected, suggesting that they were not abundant at the sampling site. Remarkably, nonviral proteins made up about two thirds of VC proteins, including overwhelmingly abundant periplasmic transporters for nutrient acquisition and proteins for diverse cellular processes, that is, translation, energy metabolism and one carbon metabolism. Interestingly, three 56 kDa selenium‐binding proteins putatively involved in peroxide reduction from gammaproteobacteria were abundant in the VCs, suggesting active removal of peroxide compounds at DCM. Our study demonstrated that metaproteomics provides a valuable avenue to explore the diversity and structure of the viral community and also the pivotal biological functions affiliated with microbes in the natural environment.
To Lube or not to Lube: The Effect of Intrapartum Lubricant use on Vaginal Microbiota
Authors: McElroy Katie Gresia , Regan Mary 
Published: September 2017

PurposeThis study aimed to characterize the composition of vaginal microbiota during labor and to investigate the effect of lubricant use on its bacterial composition.Research QuestionsWhat is the composition of vaginal microbiota in late pregnancy, throughout labor, and in the postpartum period? Does intrapartum lubricant use affect the composition of vaginal microbiota during labor?SignificanceThe composition of vaginal microbiota is critically important during pregnancy because maternal microbes transferred at birth form the basis of the neonate's microbiome. Vaginal dysbiosis, a disruption in composition, is linked with many biological and behavioral factors, including use of personal lubricants. Studies show that lubricants can alter microbial composition and damage the integrity of vaginal epithelium. These findings are concerning because similar lubricants are frequently used during labor. However, the effect of lubricant use on vaginal microbiota during labor has not been studied.MethodsThe prospective cohort study was nested within a federally‐funded study (R01NR014826). Fifteen participants collected mid‐vaginal specimens during pregnancy, labor, and in the postpartum period, and clinical labor data were extracted from medical records. 16S rRNA gene profiling was used for bacterial composition, and multiple linear regression was used to investigate the effect of intrapartum lubricant use.ResultsThe composition of vaginal microbiota varied among participants, with a notable high abundance of Lactobacillus iners and Gardnerella vaginalis. A significant bivariate negative correlation between lubricant use and relative abundance of L. crispatus disappeared when controlling for time since ruptured membranes. A trend between lubricant use and changes in the composition of vaginal microbiota as measured by the Jensen‐Shannon distance was noted but not significant.DiscussionThe study offers novel information about the composition of vaginal microbiota during labor and the effect of lubricant use on its composition. The potential relationship between increased lubricant use and decreased L. crispatus has important clinical significance for perinatal providers and can be used to begin to build evidence that supports a less invasive approach to perinatal practice. The study was limited by a small sample, a lack of control group, and the analysis of relative abundance, as opposed to absolute abundance. A larger study is needed to further elucidate the association between lubricant use and vaginal dysbiosis.
Modeling
the Deformation of the Elastin Network in the Aortic
Valve
Authors: Anssari-Benam Afshin , Bucchi Andrea 
Published: September 2017

Abstract
This paper is concerned with proposing a suitable structurally motivated strain energy function, denoted by Weelastin network, for modeling the deformation of the elastin network within the aortic valve (AV) tissue. The AV elastin network is the main noncollagenous load-bearing component of the valve matrix, and therefore, in the context of continuum-based modeling of the AV, the Weelastin network strain energy function would essentially serve to model the contribution of the “isotropic matrix.” To date, such a function has mainly been considered as either a generic neo-Hookean term or a general exponential function. In this paper, we take advantage of the established structural analogy between the network of elastin chains and the freely jointed molecular chain networks to customize a structurally motivated Weelastin network function on this basis. The ensuing stress–strain (force-stretch) relationships are thus derived and fitted to the experimental data points reported by (Vesely, 1998, “The Role of Elastin in Aortic Valve Mechanics,” J. Biomech., 31, pp. 115–123) for intact AV elastin network specimens under uniaxial tension. The fitting results are then compared with those of the neo-Hookean and the general exponential models, as the frequently used models in the literature, as well as the “Arruda–Boyce” model as the gold standard of the network chain models. It is shown that our proposed Weelastin network function, together with the general exponential and the Arruda–Boyce models provide excellent fits to the data, with R2 values in excess of 0.98, while the neo-Hookean function is entirely inadequate for modeling the AV elastin network. However, the general exponential function may not be amenable to rigorous interpretation, as there is no structural meaning attached to the model. It is also shown that the parameters estimated by the Arruda–Boyce model are not mathematically and structurally valid, despite providing very good fits. We thus conclude that our proposed strain energy function Weelastin network is the preferred choice for modeling the behavior of the AV elastin network and thereby the isotropic matrix. This function may therefore be superimposed onto that of the anisotropic collagen fibers family in order to develop a structurally motivated continuum-based model for the AV.
Potential of Rice Stubble as a Reservoir of Bradyrhizobial Inoculum in Rice-Legume Crop Rotation
Authors: Piromyou Pongdet , Greetatorn Teerana , Teamtisong Kamonluck , Tittabutr Panlada , Boonkerd Nantakorn , Teaumroong Neung 
Published: September 2017

ABSTRACT

Bradyrhizobium
encompasses a variety of bacteria that can live in symbiotic and endophytic associations with leguminous and nonleguminous plants, such as rice. Therefore, it can be expected that rice endophytic bradyrhizobia can be applied in the rice-legume crop rotation system. Some endophytic bradyrhizobial strains were isolated from rice (
Oryza sativa
L.) tissues. The rice biomass could be enhanced when supplementing bradyrhizobial strain inoculation with KNO
3
, NH
4
NO
3
, or urea, especially in
Bradyrhizobium
sp. strain SUTN9-2. In contrast, the strains which suppressed rice growth were photosynthetic bradyrhizobia and were found to produce nitric oxide (NO) in the rice root. The expression of genes involved in NO production was conducted using a quantitative reverse transcription-PCR (qRT-PCR) technique. The
nirK
gene expression level in
Bradyrhizobium
sp. strain SUT-PR48 with nitrate was higher than that of the
norB
gene. In contrast, the inoculation of SUTN9-2 resulted in a lower expression of the
nirK
gene than that of the
norB
gene. These results suggest that SUT-PR48 may accumulate NO more than SUTN9-2 does. Furthermore, the
nifH
expression of SUTN9-2 was induced in treatment without nitrogen supplementation in an endophytic association with rice. The indole-3-acetic acid (IAA) and 1-amino-cyclopropane-1-carboxylic acid (ACC) deaminase produced
in planta
by SUTN9-2 were also detected. Enumeration of rice endophytic bradyrhizobia from rice tissues revealed that SUTN9-2 persisted in rice tissues until rice-harvesting season. The mung bean (
Vigna radiata
) can be nodulated after rice stubbles were decomposed. Therefore, it is possible that rice stubbles can be used as an inoculum in the rice-legume crop rotation system under both low- and high-organic-matter soil conditions.

IMPORTANCE
This study shows that some rice endophytic bradyrhizobia could produce IAA and ACC deaminase and have a nitrogen fixation ability during symbiosis inside rice tissues. These characteristics may play an important role in rice growth promotion by endophytic bradyrhizobia. However, the NO-producing strains should be of concern due to a possible deleterious effect of NO on rice growth. In addition, this study reports the application of endophytic bradyrhizobia in rice stubbles, and the rice stubbles were used directly as an inoculum for a leguminous plant (mung bean). The degradation of rice stubbles leads to an increased number of SUTN9-2 in the soil and may result in increased mung bean nodulation. Therefore, the persistence of endophytic bradyrhizobia in rice tissues can be developed to use rice stubbles as an inoculum for mung bean in a rice-legume crop rotation system.
Succinate Transport Is Not Essential for Symbiotic Nitrogen Fixation by Sinorhizobium meliloti or Rhizobium leguminosarum
Authors: Mitsch Michael J. , diCenzo George C. , Cowie Alison , Finan Turlough M. 
Published: September 2017

ABSTRACT

Symbiotic nitrogen fixation (SNF) is an energetically expensive process performed by bacteria during endosymbiotic relationships with plants. The bacteria require the plant to provide a carbon source for the generation of reductant to power SNF. While C
4
-dicarboxylates (succinate, fumarate, and malate) appear to be the primary, if not sole, carbon source provided to the bacteria, the contribution of each C
4
-dicarboxylate is not known. We address this issue using genetic and systems-level analyses. Expression of a malate-specific transporter (MaeP) in
Sinorhizobium meliloti
Rm1021
dct
mutants unable to transport C
4
-dicarboxylates resulted in malate import rates of up to 30% that of the wild type. This was sufficient to support SNF with
Medicago sativa
, with acetylene reduction rates of up to 50% those of plants inoculated with wild-type
S. meliloti
.
Rhizobium leguminosarum
bv. viciae 3841
dct
mutants unable to transport C
4
-dicarboxylates but expressing the
maeP
transporter had strong symbiotic properties, with
Pisum sativum
plants inoculated with these strains appearing similar to plants inoculated with wild-type
R. leguminosarum
. This was despite malate transport rates by the mutant bacteroids being 10% those of the wild type. An RNA-sequencing analysis of the combined
P. sativum
-
R. leguminosarum
nodule transcriptome was performed to identify systems-level adaptations in response to the inability of the bacteria to import succinate or fumarate. Few transcriptional changes, with no obvious pattern, were detected. Overall, these data illustrated that succinate and fumarate are not essential for SNF and that, at least in specific symbioses,
l
-malate is likely the primary C
4
-dicarboxylate provided to the bacterium.

IMPORTANCE
Symbiotic nitrogen fixation (SNF) is an economically and ecologically important biological process that allows plants to grow in nitrogen-poor soils without the need to apply nitrogen-based fertilizers. Much research has been dedicated to this topic to understand this process and to eventually manipulate it for agricultural gains. The work presented in this article provides new insights into the metabolic integration of the plant and bacterial partners. It is shown that malate is the only carbon source that needs to be available to the bacterium to support SNF and that, at least in some symbioses, malate, and not other C
4
-dicarboxylates, is likely the primary carbon provided to the bacterium. This work extends our knowledge of the minimal metabolic capabilities the bacterium requires to successfully perform SNF and may be useful in further studies aiming to optimize this process through synthetic biology approaches. The work describes an engineering approach to investigate a metabolic process that occurs between a eukaryotic host and its prokaryotic endosymbiont.
CmeABC Multidrug Efflux Pump Contributes to Antibiotic Resistance and Promotes Campylobacter jejuni Survival and Multiplication in Acanthamoeba polyphaga
Authors: Vieira Ana , Ramesh Amritha , Seddon Alan M. , Karlyshev Andrey V. 
Published: September 2017

ABSTRACT

Campylobacter jejuni
is a foodborne pathogen that is recognized as the leading cause of human bacterial gastroenteritis. The widespread use of antibiotics in medicine and in animal husbandry has led to an increased incidence of antibiotic resistance in
Campylobacter
. In addition to a role in multidrug resistance (MDR), the
Campylobacter
CmeABC resistance-nodulation-division (RND)-type efflux pump may be involved in virulence. As a vehicle for pathogenic microorganisms, the protozoan
Acanthamoeba
is a good model for investigations of bacterial survival in the environment and the molecular mechanisms of pathogenicity. The interaction between
C. jejuni
81-176 and
Acanthamoeba polyphaga
was investigated in this study by using a modified gentamicin protection assay. In addition, a possible role for the CmeABC MDR pump in this interaction was explored. Here we report that this MDR pump is beneficial for the intracellular survival and multiplication of
C. jejuni
in
A. polyphaga
but is dispensable for biofilm formation and motility.

IMPORTANCE
The endosymbiotic relationship between amoebae and microbial pathogens may contribute to persistence and spreading of the latter in the environment, which has significant implications for human health. In this study, we found that
Campylobacter jejuni
was able to survive and to multiply inside
Acanthamoeba polyphaga
; since these microorganisms can coexist in the same environment (e.g., on poultry farms), the latter may increase the risk of infection with
Campylobacter
. Our data suggest that, in addition to its role in antibiotic resistance, the CmeABC MDR efflux pump plays a role in bacterial survival within amoebae. Furthermore, we demonstrated synergistic effects of the CmeABC MDR efflux pump and TetO on bacterial resistance to tetracycline. Due to its role in both the antibiotic resistance and the virulence of
C. jejuni
, the CmeABC MDR efflux pump could be considered a good target for the development of antibacterial drugs against this pathogen.
The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies
Authors: Spatafora Joseph W. , Aime M. Catherine , Grigoriev Igor V. , Martin Francis , Stajich Jason E. , Blackwell Meredith 
Published: September 2017

ABSTRACTThe kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.
Incidence of retinopathy of prematurity (ROP) and ROP treatment in Switzerland 2006–2015: a population-based analysis
Authors: Gerull Roland , Brauer Viviane , Bassler Dirk , Laubscher Bernard , Pfister Riccardo E , Nelle Mathias , Müller Béatrice , Gerth-Kahlert Christina , Adams Mark 
Published: September 2017

BackgroundRetinopathy of prematurity (ROP) is a severe complication of preterm birth and can lead to severe visual impairment or even blindness if untreated. The incidence of ROP requiring treatment is increasing in some developed countries in conjunction with higher survival rates at the lower end of gestational age (GA).Material and methodsThe incidence of ROP and severe ROP (sROP) requiring treatment in Switzerland was analysed using the SwissNeoNet registry. We conducted a retrospective cohort analysis of very preterm infants with a GA below 32 weeks who were born between 2006 and 2015 in Switzerland. Patient characteristics were stratified according to GA.Results9.3% and 1.8% of very preterm infants in Switzerland developed ROP of any stage and sROP, respectively. The incidence of ROP treatment was 1.2%. Patients with 24 and 25 weeks GA had the highest proportion of ROP treatment at 14.5% and 7.3%, respectively, whereas the proportion of treated infants at or above a GA of 29 weeks was 0.06%. Similarly, the risk of sROP declined strongly with increasing GA. During the observation period of 10 years, the incidence of ROP treatment ranged between 0.8% and 2.0%. Incidences of sROP or ROP treatment did not increase over time.ConclusionThe incidence of ROP treatment in Switzerland is low and was stable over the analysed period. The low incidence of sROP in patients with a GA of 29 weeks or more leaves room for a redefinition of ROP screening criteria.
Reproductive, maternal, neonatal and child health in conflict: a case study on Syria using Countdown indicators
Authors: DeJong Jocelyn , Ghattas Hala , Bashour Hyam , Mourtada Rima , Akik Chaza , Reese-Masterson Amelia 
Published: September 2017

IntroductionWomen and children account for a disproportionate morbidity burden among conflict-affected populations, and yet they are not included in global accountability frameworks for women’s and children’s health. We use Countdown to 2015 (Millennium Development Goals) health indicators to provide an up-to-date review and analysis of the best available data on Syrian refugees in Jordan, Lebanon and Turkey and internally displaced within Syria and explore data challenges in this conflict setting.MethodsWe searched Medline, PubMed, Scopus, Popline and Index Medicus for WHO Eastern Mediterranean Region Office and relevant development/humanitarian databases in all languages from January 2011 until December 2015. We met in person or emailed relevant key stakeholders in Lebanon, Jordan, Syria and Turkey to obtain any unpublished or missing data. We convened a meeting of experts working with these populations to discuss the results.ResultsThe following trends were found based on available data for these populations as compared with preconflict Syria. Birth registration in Syria and in host neighbouring countries decreased and was very low in Lebanon. In Syria, the infant mortality rate and under-five mortality rate increased, and coverage of antenatal care (one visit with a skilled attendant), skilled birth attendance and vaccination (except for DTP3 vaccine) declined. The number of Syrian refugee women attending more than four antenatal care visits was low in Lebanon and in non-camp settings in Jordan. Few data were available on these indicators among the internally displaced. In conflict settings such as that of Syria, coverage rates of interventions are often unknown or difficult to ascertain because of measurement challenges in accessing conflict-affected populations or to the inability to determine relevant denominators in this dynamic setting.ConclusionResearch, monitoring and evaluation in humanitarian settings could better inform public health interventions if findings were more widely shared, methodologies were more explicit and globally agreed definitions and indicators were used consistently.