bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic tools and plant genes to mitigate impacts of climate change and extreme environments.
Authors: De Pace C. 
Published: April 2016

Abstract
This review outlines a conceptual framework that links climate-related risk components (hazard, exposure and vulnerability) to the genetics and genomics tools used for developing new crop varieties to promote adaptation to extreme weather events and to mitigate risks related to the effects of climate change. The establishment of templates for identifiable features or markers on the genome to refine genetic maps for monogenic traits - especially those related to stress resistance in plant model species - has benefited plant genome projects from early on. Genomics has facilitated the discovery of genes affecting quantitative, or continuous, traits for enhancing yield in low-input sustainable agriculture. Genomics and genomic tools developed in model species favour translational approaches when searching for orthologous genes in diploid crop species or diploid relatives of polyploid crop species. Discovering genetic variation through focused identification of germplasm from extreme environments, and generating genetic variation by mutagenesis and 'genome editing', will facilitate targeted induction of new alleles and adaptation to the effects of climate change. Genetic marker-aided transfer and shuffling alleles by introgression breeding and publically accepted plant transformation methodologies, will accelerate precise breeding and release of crop cultivars that will greatly benefit adaptation to and mitigation of risks related to climate change.
Prevention of enterotoxigenic
Escherichia coli
infections in pigs by dairy-based nutrition.
Authors: Sugiharto S. , Jensen B. B. , Jensen K. H. , Lauridsen C. 
Published: April 2016

Abstract

Postweaning diarrhoea (PWD) is a significant enteric disease causing considerable economic losses for the pig industry. Among several aetiological risk factors, enterotoxigenic
Escherichia coli
(ETEC) is considered to be a major cause. After being routinely used for several decades to control bacterial disease outbreaks in piglets, the use of antibiotics at subtherapeutic concentrations has been banned in the European Union because of the increasing prevalence of resistance to antibiotics in pigs. The removal of in-feed antibiotics from piglet diets has negative economic consequences as it dramatically increases the rate of morbidity and mortality due to ETEC as well as the use of antibiotics for therapeutic purposes. Other than subtherapeutic antibiotics, zinc oxide (ZnO) has been reported to ameliorate and/or prevent the development of PWD in piglets, but its excretion may have negative impacts on the environment. Thus, other alternatives that can control ETEC infections in piglets postweaning will be of great advantage. A number of nutritional strategies have been proposed as alternative means of preventing ETEC infections, of which feeding dairy-based products to piglets could be one of such strategies. It is apparent that colostrum, milk and milk fractions such as whey and casein contain several biologically active compounds with anti-microbial and immunomodulatory properties. Recently, these dairy products and their isolated compounds such as lactoferrin and oligosaccharides have been employed as anti-infective agents against ETEC infections in piglets postweaning. The dairy by-products (e.g. whey or whey permeate) may also be fermented to further improve the anti-infective potential of the products. Overall, the anti-infective activities of dairy-based products against ETEC could be attributed to the improvement of the intestinal barrier functions, microbial ecosystem and immunity of the piglets.
Comparison of the measurement standards of the length unit in the field of roundness deviations measurements
Authors: Lysenko V G , Kupko V S , Makarevich V B 
Published: April 2016

A trilateral comparison has been performed in the subject field of roundness measurement. The comparison was pilot by VNIIMS, Russia and took place between February 2014 and August 2014. The circulated standards were a roundness transfer standard in the form of a glass hemisphere and a magnification standard often referred to as a 'Flick' standard. Data from the roundness standard were processed using a Gaussian filter and a bandpass up to 50 undulations per revolution to provide a measured value of Roundness Deviation (RONt). For the magnification standard, data were also filtered and the fitted element was the circumscribed circle together with the deviation of the valleys (RONv). The results of comparisons show the correspondence of measurement uncertainties to the declared values and the compared measurement standards are equivalent.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCL, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Redox potential as a master variable controlling pathways of metal reduction byGeobacter sulfurreducens
Authors: Levar Caleb E. , Hoffman Colleen L. , Dunshee Aubrey J. , Toner Brandy M. , Bond Daniel R. 
Published: April 2016

AbstractGeobacter sulfurreducensuses at least two different pathways to transport electrons out of the inner membrane quinone pool before reducing acceptors beyond the outer membrane. When growing on electrodes poised at oxidizing potentials, the CbcL-dependent pathway operates at or below redox potentials of −0.10 V vs. the Standard Hydrogen Electrode (SHE), while the ImcH-dependent pathway operates only above this value. Here, we provide evidence thatG. sulfurreducensalso requires different electron transfer proteins for reduction of a wide range of Fe(III)- and Mn(IV)- (oxyhydr)oxides, and must transition from a high- to low-potential pathway during reduction of commonly studied soluble and insoluble metal electron acceptors. Freshly precipitated Fe(III)-(oxyhydr)oxides could not be reduced by mutants lacking the high potential pathway. Aging these minerals by autoclaving did not change their powder X-ray diffraction pattern, but restored reduction by mutants lacking the high-potential pathway. Mutants lacking the low-potential, CbcL-dependent pathway had higher growth yields with both soluble and insoluble Fe(III). Together, these data suggest that the ImcH-dependent pathway exists to harvest additional energy when conditions permit, and CbcL switches on to allow respiration closer to thermodynamic equilibrium conditions. With evidence of multiple pathways within a single organism, the study of extracellular respiration should consider not only the crystal structure or solubility of a mineral electron acceptor, but rather the redox potential, as this variable determines the energetic reward affecting reduction rates, extents, and final microbial growth yields in the environment.
Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences
Authors: Cheng Jiujun , Romantsov Tatyana , Engel Katja , Doxey Andrew C. , Rose David R. , Neufeld Josh D. , Charles Trevor 
Published: April 2016

AbstractA soil metagenomic library carried in pJC8 (an IncP cosmid) was used for functional complementation for β-galactosidase activity in bothα-Proteobacteria (Sinorhizobium meliloti)andγ-Proteobacteria (Escherichia coli).Oneβ-galactosidase, encoded by overlapping clones selected in both hosts, was identified as a member of glycoside hydrolase family 2. ORFs obviously encoding possible β-galactosidases were not identified in 19 other clones that were only able to complementS. meliloti.Based on low sequence similarity to known glycoside hydrolases but not β-galactosidases, three ORFs were examined further. Biochemical analysis confirmed that all encodedβ-galactosidase activity. Bioinformatic and structural modeling implied that Lac161_ORF10 protein represented a novel enzyme family with a five-bladed propeller glycoside hydrolase domain.
Order under uncertainty: robust differential expression analysis using probabilistic models for pseudotime inference
Authors: Campbell Kieran , Yau Christopher 
Published: April 2016

AbstractSingle cell gene expression profiling can be used to quantify transcriptional dynamics in temporal processes, such as cell differentiation, using computational methods to label each cell with a ‘pseudotime’ where true time series experimentation is too difficult to perform. However, owing to the high variability in gene expression between individual cells, there is an inherent uncertainty in the precise temporal ordering of the cells. Preexisting methods for pseudotime ordering have predominantly given point estimates precluding a rigorous analysis of the implications of uncertainty. We use probabilistic modelling techniques to quantify pseudotime uncertainty and propagate this into downstream differential expression analysis. We demonstrate that reliance on a point estimate of pseudotime can lead to inflated false discovery rates compared and that probabilistic approaches provide greater robustness and measures of the temporal resolution that can be obtained from pseudotime inference.
Impact of electrical heating on effective thermal Insulation of a multi-layered winter clothing system for optimal heating efficiency
Authors: Park Huiju , Hwang Soo-kyung , Lee Joo-Young , Fan Jintu , Jeong Youngjin 
Published: April 2016

Purpose
This paper investigated the impact of the distance of the heating unit from the body in a multi-layered winter clothing system on effective thermal insulation and heating efficiency.

Design/methodology/approach
To identify changes in the thermal insulation and heating efficiency of electrical heating in different layers inside a winter clothing ensemble, a series of thermal manikin tests was conducted. A multi-layered winter ensemble with and without activation of a heating unit was tested on the thermal manikin under two different ambient temperature conditions (10°C and -5°C).

Findings
Results show that the effective thermal insulation of test ensembles increased by 5-7% with the activation of the heating unit compared to that without the activation. The closer the heating unit to the body, the higher the effective thermal insulation was in both ambient temperature conditions. This trend was more significant at lower ambient temperature.

Research limitations/implications
The results of this study indicate that providing electric heating next to the skin is the most effective in increasing effective thermal insulation and decreasing body heat loss in both ambient temperature (-5°C and 10°C). This trend was more remarkable in colder environment at -5°C of ambient temperature as evidenced by sharp decrease in heating efficiency and effective thermal insulation with an increase in distance between the manikin skin and heating unit at -5°C of ambient temperature compared to at 10°C of ambient temperature.

Practical implications
Based on the results, it is expected that proximity heating next to the skin, in cold environment, may reduce the weight and size of the battery for the heating unit because of the higher efficiency of electric heating and the potentially immediate perception of warmth supported by the greatest increase in effective thermal insulation, as well as the lowest heat loss that comes with activation of heating on the first layer in cold environment.

Originality/value
The finding of this study provides guidelines to sportswear designers, textile scientists, sports enthusiasts, and civilians who consider electric heating benefits for improved thermal comfort and safety in cold environments, especially in the areas of outdoor and winter sports and in military service. The results of this study indicate that providing electric heating next to the skin is the most effective in increasing effective thermal insulation and decreasing body heat loss in both ambient temperature (-5°C and 10°C).
Constructing the female body: using female genital mutilation law to address genital-normalizing surgery on intersex children in the United States
Authors: Fraser Sylvan 
Published: April 2016

Purpose– The purpose of this paper is to explore the harms suffered by intersex children who are subjected to medically unnecessary genital-normalizing surgery (GNS) and the possible applicability of statutes prohibiting female genital mutilation (FGM) to certain cases of GNS to redress this harm in the USA.Design/methodology/approach– Consulting publications by medical researchers and intersex activists alike, this comment reviews the procedures undertaken as part of GNS (most commonly including clitoral reduction) and the reasons behind these procedures. It also parses the language of federal and state statutes prohibiting FGM in the USA.Findings– Surgical practices that include clitoral cutting when the procedure is not necessary to the health of the person on whom it is performed constitute FGM and are punishable under federal and certain state laws in the USA. GNS with clitoral reduction fits the definition of FGM because it is performed for cosmetic and social reasons, not medical necessity.Originality/value– Acknowledging GNS with clitoral reduction as FGM is a crucial strategy to ensure that female-assigned intersex children’s rights to bodily autonomy are protected to the same extent as non-intersex children’s rights. Intersex legal activists in the USA should press for enforcement of FGM statutes as to female-assigned intersex children until the medical practitioners who continue to defend and perform GNS see the procedures as illegal genital mutilation.
Singly Flagellated Pseudomonas aeruginosa Chemotaxes Efficiently by Unbiased Motor Regulation
Authors: Cai Qiuxian , Li Zhaojun , Ouyang Qi , Luo Chunxiong , Gordon Vernita D. 
Published: April 2016

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic human pathogen that has long been known to chemotax. More recently, it has been established that chemotaxis is an important factor in the ability of
P. aeruginosa
to make biofilms. Genes that allow
P. aeruginosa
to chemotax are homologous with genes in the paradigmatic model organism for chemotaxis,
Escherichia coli
. However,
P. aeruginosa
is singly flagellated and
E. coli
has multiple flagella. Therefore, the regulation of counterclockwise/clockwise flagellar motor bias that allows
E. coli
to efficiently chemotax by runs and tumbles would lead to inefficient chemotaxis by
P. aeruginosa
, as half of a randomly oriented population would respond to a chemoattractant gradient in the wrong sense. How
P. aeruginosa
regulates flagellar rotation to achieve chemotaxis is not known. Here, we analyze the swimming trajectories of single cells in microfluidic channels and the rotations of cells tethered by their flagella to the surface of a variable-environment flow cell. We show that
P. aeruginosa
chemotaxes by symmetrically increasing the durations of both counterclockwise and clockwise flagellar rotations when swimming up the chemoattractant gradient and symmetrically decreasing rotation durations when swimming down the chemoattractant gradient. Unlike the case for
E. coli
, the counterclockwise/clockwise bias stays constant for
P. aeruginosa
. We describe
P. aeruginosa
’s chemotaxis using an analytical model for symmetric motor regulation. We use this model to do simulations that show that, given
P. aeruginosa
’s physiological constraints on motility, its distinct, symmetric regulation of motor switching optimizes chemotaxis.

IMPORTANCE
Chemotaxis has long been known to strongly affect biofilm formation by the opportunistic human pathogen
P. aeruginosa
, whose essential chemotaxis genes have homologues in
E. coli
, which achieves chemotaxis by biasing the relative probability of counterclockwise and clockwise flagellar rotation. However, the physiological difference between multiflagellated
E. coli
and singly flagellated
P. aeruginosa
implies that biased motor regulation should prevent
P. aeruginosa
populations from chemotaxing efficiently. Here, we used experiments, analytical modeling, and simulations to demonstrate that
P. aeruginosa
uses unbiased, symmetric regulation of the flagellar motor to maximize its chemotaxis efficiency. This mode of chemotaxis was not previously known and demonstrates a new variant of a paradigmatic signaling system in an important human pathogen.
SpoVG Is a Conserved RNA-Binding Protein That Regulates Listeria monocytogenes Lysozyme Resistance, Virulence, and Swarming Motility
Authors: Burke Thomas P. , Portnoy Daniel A. 
Published: April 2016

ABSTRACT

In this study, we sought to characterize the targets of the abundant
Listeria monocytogenes
noncoding RNA Rli31, which is required for
L. monocytogenes
lysozyme resistance and pathogenesis. Whole-genome sequencing of lysozyme-resistant suppressor strains identified loss-of-expression mutations in the promoter of
spoVG
, and deletion of
spoVG
rescued lysozyme sensitivity and attenuation
in vivo
of the
rli31
mutant. SpoVG was demonstrated to be an RNA-binding protein that interacted with Rli31
in vitro.
The relationship between Rli31 and SpoVG is multifaceted, as both the
spoVG
-encoded protein and the
spoVG
5′-untranslated region interacted with Rli31. In addition, we observed that
spoVG
-deficient bacteria were nonmotile in soft agar and suppressor mutations that restored swarming motility were identified in the gene encoding a major RNase in Gram-positive bacteria, RNase J1. Collectively, these findings suggest that SpoVG is similar to global posttranscriptional regulators, a class of RNA-binding proteins that interact with noncoding RNA, regulate genes in concert with RNases, and control pleiotropic aspects of bacterial physiology.

IMPORTANCE
spoVG
is widely conserved among bacteria; however, the function of this gene has remained unclear since its initial characterization in 1977. Mutation of
spoVG
impacts various phenotypes in Gram-positive bacteria, including methicillin resistance, capsule formation, and enzyme secretion in
Staphylococcus aureus
and also asymmetric cell division, hemolysin production, and sporulation in
Bacillus subtilis
. Here, we demonstrate that
spoVG
mutant strains of
Listeria monocytogenes
are hyper-lysozyme resistant, hypervirulent, nonmotile, and misregulate genes controlling carbon metabolism. Furthermore, we demonstrate that SpoVG is an RNA-binding protein. These findings suggest that SpoVG has a role in
L. monocytogenes
, and perhaps in other bacteria, as a global gene regulator. Posttranscriptional gene regulators help bacteria adapt to various environments and coordinate differing aspects of bacterial physiology. SpoVG may help the organism coordinate environmental growth and virulence to survive as a facultative pathogen.
The CpxQ sRNA Negatively Regulates Skp To Prevent Mistargeting of β-Barrel Outer Membrane Proteins into the Cytoplasmic Membrane
Authors: Grabowicz Marcin , Koren Daria , Silhavy Thomas J. 
Published: April 2016

ABSTRACT

The promoter most strongly induced upon activation of the Cpx two-component envelope stress response is the
cpxP
promoter. The 3′ untranscribed region (UTR) of the
cpxP
transcript is shown to produce a small RNA (sRNA), CpxQ. We investigated the role of CpxQ in combating envelope stress. Remarkably, the two effectors specified by the transcript are deployed to combat distinct stresses in different cellular compartments. CpxP acts in both a regulatory negative-feedback loop and as an effector that combats periplasmic protein misfolding. We find that CpxQ combats toxicity at the inner membrane (IM) by downregulating the synthesis of the periplasmic chaperone Skp. Our data indicate that this regulation prevents Skp from inserting β-barrel outer membrane proteins (OMPs) into the IM, a lethal event that likely collapses the proton motive force. Our findings suggest that Skp can fold and directly insert OMPs into a lipid bilayer
in vivo
without the aid of the Bam complex.

IMPORTANCE
Skp is a well-characterized periplasmic chaperone that binds unfolded OMPs. Surprisingly, we find that Skp can catalyze the folding and mistargeting of OMPs into the inner membrane without the aid of the other cellular proteins that normally assemble OMPs. Several OMPs function as diffusion pores. Accordingly, their mistargeting is lethal because it depolarizes the inner membrane. We show that the most highly expressed transcript of the Cpx stress response produces an sRNA from the 3′ UTR, CpxQ, which combats this potential toxicity by downregulating Skp production. Defects in OMP assembly trigger the σ
E
response to upregulate factors, including Skp, that promote OMP folding. The Cpx response downregulates σ
E
. Our findings reveal that this heretofore puzzling hierarchy exists to protect the inner membrane.
Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia
Authors: Bacharach Eran , Mishra Nischay , Briese Thomas , Zody Michael C. , Kembou Tsofack Japhette Esther , Zamostiano Rachel , Berkowitz Asaf , Ng James , Nitido Adam , Corvelo André , Toussaint Nora C. , Abel Nielsen Sandra Cathrine , Hornig Mady , Del Pozo Jorge , Bloom Toby , Ferguson Hugh , Eldar Avi , Lipkin W. Ian 
Published: April 2016

ABSTRACT

Tilapia are an important global food source due to their omnivorous diet, tolerance for high-density aquaculture, and relative disease resistance. Since 2009, tilapia aquaculture has been threatened by mass die-offs in farmed fish in Israel and Ecuador. Here we report evidence implicating a novel orthomyxo-like virus in these outbreaks. The tilapia lake virus (TiLV) has a 10-segment, negative-sense RNA genome. The largest segment, segment 1, contains an open reading frame with weak sequence homology to the influenza C virus PB1 subunit. The other nine segments showed no homology to other viruses but have conserved, complementary sequences at their 5′ and 3′ termini, consistent with the genome organization found in other orthomyxoviruses.
In situ
hybridization indicates TiLV replication and transcription at sites of pathology in the liver and central nervous system of tilapia with disease.

IMPORTANCE
The economic impact of worldwide trade in tilapia is estimated at $7.5 billion U.S. dollars (USD) annually. The infectious agent implicated in mass tilapia die-offs in two continents poses a threat to the global tilapia industry, which not only provides inexpensive dietary protein but also is a major employer in the developing world. Here we report characterization of the causative agent as a novel orthomyxo-like virus, tilapia lake virus (TiLV). We also describe complete genomic and protein sequences that will facilitate TiLV detection and containment and enable vaccine development.