bluuebunny/crossref_metadata_2025_split huggingface dataset:
Manipulating Cx43 expression triggers gene reprogramming events in dermal fibroblasts from oculodentodigital dysplasia patients
Authors: Esseltine Jessica L. , Shao Qing , Huang Tao , Kelly John J. , Sampson Jacinda , Laird Dale W. 
Published: September 2015

Oculodentodigital dysplasia (ODDD) is primarily an autosomal dominant disorder linked to over 70 GJA1 gene [connexin43 (Cx43)] mutations. For nearly a decade, our laboratory has been investigating the relationship between Cx43 and ODDD by expressing disease-linked mutants in reference cells, tissue-relevant cell lines, 3D organ cultures and by using genetically modified mouse models of human disease. Although salient features of Cx43 mutants have been revealed, these models do not necessarily reflect the complexity of the human context. To further overcome these limitations, we have acquired dermal fibroblasts from two ODDD-affected individuals harbouring D3N and V216L mutations in Cx43, along with familial controls. Using these ODDD patient dermal fibroblasts, which naturally produce less GJA1 gene product, along with RNAi and RNA activation (RNAa) approaches, we show that manipulating Cx43 expression triggers cellular gene reprogramming. Quantitative RT-PCR, Western blot and immunofluorescent analysis of ODDD patient fibroblasts show unusually high levels of extracellular matrix (ECM)-interacting proteins, including integrin α5β1, matrix metalloproteinases as well as secreted ECM proteins collagen-I and laminin. Cx43 knockdown in familial control cells produces similar effects on ECM expression, whereas Cx43 transcriptional up-regulation using RNAa decreases production of collagen-I. Interestingly, the enhanced levels of ECM-associated proteins in ODDD V216L fibroblasts is not only a consequence of increased ECM gene expression, but also due to an apparent deficit in collagen-I secretion which may further contribute to impaired collagen gel contraction in ODDD fibroblasts. These findings further illuminate the altered function of Cx43 in ODDD-affected individuals and highlight the impact of manipulating Cx43 expression in human cells.
In vitro translation of mRNAs that are in their native ribonucleoprotein complexes
Authors: Panthu Baptiste , Mure Fabrice , Gruffat Henri , Ohlmann Theophile 
Published: September 2015

mRNA is bound to a complex network of hundreds of RNA-binding proteins (RBPs) which constitute the mature ribonucleoprotein (mRNP). Such a complex particle is initially scaffolded in the nucleus and stays associated throughout mRNA's journey to the cytoplasm, where it participates in translation. However, due to the size, complexity and variability of the mRNP, it remains technically challenging to assess its impact on translation. By designing a novel in vitro translational assay, we have been able to compare the translational efficiency of reporter mRNAs that are, or are not, associated with their cognate RBPs. This showed the strong impact of these RBPs on translational efficiency, and revealed intrinsic variations according to the structure of both the mRNA and its nuclear history, e.g. the use of intron-containing mRNA constructs showed that splicing strongly enhanced translation. The present study shows that nuclear and cytoplasmic gene expression steps in vitro are coupled in eukaryotes and this is determined from the very birth of the mRNA in the nucleus by a network of hundreds of RBPs.
Neighborhood effects on use of African-American Vernacular English
Authors: Rickford John R. , Duncan Greg J. , Gennetian Lisa A. , Gou Ray Yun , Greene Rebecca , Katz Lawrence F. , Kessler Ronald C. , Kling Jeffrey R. , Sanbonmatsu Lisa , Sanchez-Ordoñez Andres E. , Sciandra Matthew , Thomas Ewart , Ludwig Jens 
Published: September 2015

Significance
We provide, to our knowledge, the first experimental evidence of neighborhood effects on the use by low-income minority youth of African-American Vernacular English (AAVE). Rising U.S. residential economic segregation may be contributing to growing differences within the population in AAVE use, which has benefits to in-group solidarity and identity but is associated with discrimination in schools and workplaces and so may exacerbate the disadvantages of youth growing up in high-poverty areas. To the extent that the association between AAVE use and income represents a causal effect of AAVE use, our illustrative calculations suggest that neighborhood effects on speech could increase lifetime earnings by approximately $18,000 (∼3–4% of lifetime income).
Suburbanization, estrogen contamination, and sex ratio in wild amphibian populations
Authors: Lambert Max R. , Giller Geoffrey S. J. , Barber Larry B. , Fitzgerald Kevin C. , Skelly David K. 
Published: September 2015

Significance
We focus on a critical issue, the influence of human-derived contaminants on wildlife populations. Endocrine disrupting chemicals that act through hormonal pathways are capable of having large influences even when concentrations are relatively low. While there is evidence that such endocrine disruption can result from the application of agricultural pesticides and through exposure to wastewater effluent, we have identified a diversity of endocrine disrupting chemicals within suburban neighborhoods. Sampling populations of a local frog species, we found a strong association between the degree of landscape development and frog offspring sex ratio. Our study points to rarely studied contamination sources, like vegetation landscaping and impervious surface runoff, that may be associated with endocrine disruption environments around suburban homes.
Dissecting repulsion linkage in the dwarfing gene
Dw3
region for sorghum plant height provides insights into heterosis
Authors: Li Xin , Li Xianran , Fridman Eyal , Tesso Tesfaye T. , Yu Jianming 
Published: September 2015

Significance
Heterosis, the better performance of hybrids over their parents, holds great economic and biological significance. Different theories have been proposed, but specific examples with detailed dissection are limited. If close linkage of alleles with opposite effects exists, the superiority of hybrids over inbreds is observed and may appear as overdominance at a single locus. We present a case of pseudo-overdominance generated by repulsion linkage between two quantitative trait loci in sorghum plant height. A combination of approaches were used: linkage mapping under a defined genetic background, genome-wide association study with a diversity panel, computer simulation, and designed crosses with selected genetic stocks. Our findings provide insights into heterosis and a tool box for plant breeders to develop ideal cultivars.
Origami tubes assembled into stiff, yet reconfigurable structures and metamaterials
Authors: Filipov Evgueni T. , Tachi Tomohiro , Paulino Glaucio H. 
Published: September 2015

Significance
Origami, the ancient art of folding paper, has recently emerged as a method for creating deployable and reconfigurable engineering systems. These systems tend to be flexible because the thin sheets bend and twist easily. We introduce a new method of assembling origami into coupled tubes that can increase the origami stiffness by two orders of magnitude. The new assemblages can deploy through a single flexible motion, but they are substantially stiffer for any other type of bending or twisting movement. This versatility can be used for deployable structures in robotics, aerospace, and architecture. On a smaller scale, assembling thin sheets into these tubular assemblages can create metamaterials that can be deployed, stiffened, and tuned.
Rapid and transient palmitoylation of the tyrosine kinase Lck mediates Fas signaling
Authors: Akimzhanov Askar M. , Boehning Darren 
Published: September 2015

Significance
Protein palmitoylation has been proposed to mediate the recruitment of signaling proteins into lipid rafts. However, a significant shortcoming of this hypothesis is that the proposed kinetics of protein palmitoylation/depalmitoylation heretofore have been too slow to mediate very rapid signaling events. Using a combination of a highly sensitive palmitoylation assay with pulsed metabolic labeling, we were able to detect a population of the Src kinase Lck undergoing extremely rapid palmitoylation and depalmitoylation subsequent to Fas receptor stimulation. The rapid rise and fall in Lck palmitoylation was highly synchronized with other signaling events occurring during the first minutes after activation of the Fas pathway, suggesting the existence of a previously undescribed signal transduction mechanism.
Glass-to-cryogenic-liquid transitions in aqueous solutions suggested by crack healing
Authors: Kim Chae Un , Tate Mark W. , Gruner Sol M. 
Published: September 2015

Significance
For decades, physicists, physical chemists, and biologists have been tremendously intrigued by the unusual thermodynamic and kinetic properties of supercooled water. Theories have been proposed to account for the properties but these theories remain contentious for lack of experimental evidence. We investigated phase behavior of water at cryogenic temperatures and showed clear experimental evidence that the two cryogenic glassy states of water (high-density amorphous and low-density amorphous) undergo glass-to-cryogenic-liquid transitions and they are thermodynamically separated by a first-order phase transition. The results provide insight into the physical origin of the anomalous properties of supercooled water.
Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse
Authors: Perera Lalith , Freudenthal Bret D. , Beard William A. , Shock David D. , Pedersen Lee G. , Wilson Samuel H. 
Published: September 2015

Significance
DNA polymerases use a general two-metal ion mechanism for DNA synthesis. Recent time-lapse crystallographic studies identified additional adjunct metal ions in the polymerase active site. One of these ions correlates with appearance of pyrophosphate and was proposed to be involved in pyrophosphorolysis (reverse reaction of DNA synthesis). Because DNA polymerases can use pyrophosphorolysis to remove chain-terminating nucleotides during chemotherapies, a better understanding of this reaction is warranted. Through site-directed mutagenesis, pyrophosphorolysis measurements, and computational analysis, we examine the role of metal ions in the reverse reaction. The results indicate that the product-associated metal ion facilitates pyrophosphorolysis during the early stages of the reaction but deters the reaction at later stages, suggesting dynamic metal behavior that can modulate the chemical equilibrium.
Widespread convergence in toxin resistance by predictable molecular evolution
Authors: Ujvari Beata , Casewell Nicholas R. , Sunagar Kartik , Arbuckle Kevin , Wüster Wolfgang , Lo Nathan , O’Meally Denis , Beckmann Christa , King Glenn F. , Deplazes Evelyne , Madsen Thomas 
Published: September 2015

SignificanceConvergence has strong bearing on the fundamental debate about whether evolution is stochastic and unpredictable or subject to constraints. Here we show that, in certain circumstances, evolution can be highly predictable. We demonstrate that several lineages of insects, amphibians, reptiles, and mammals have utilized the same molecular solution, via the process of convergence, to evolve resistance to toxic cardiac glycosides produced defensively by plants and bufonid toads. The repeatability of this process across the animal kingdom demonstrates that evolution can be constrained to proceed along highly predictable pathways at molecular and functional levels. Our study has important implications for conservation biology by providing a predictive framework for assessing the vulnerability of native fauna to the introduction of invasive toxic toads.
Accelerating molecular simulations of proteins using Bayesian inference on weak information
Authors: Perez Alberto , MacCallum Justin L. , Dill Ken A. 
Published: September 2015

Significance
An important challenge has been to develop computer methods that can predict protein native structures from their sequences and satisfy the thermodynamic principle of Boltzmann's Law, which requires that the sampling method obey detailed balance. The latter is needed to study mechanisms and dynamics, which require an understanding of relative populations of states. These dual goals are met by atomistic model simulations, but they have been too expensive computationally. Here, we join together molecular dynamics (MD) with Bayesian inferences derived from loose insights (proteins have “hydrophobic cores” and “secondary structures”). We show that this method can speed up MD simulations by up to five orders of magnitude, allowing for the accurate predictions of small native protein structures with only atomistic potentials.
Balanced harvesting in fisheries: a preliminary analysis of management implications‡
Authors: Garcia S. M. , Rice J. , Charles A. 
Published: September 2015

AbstractBalanced harvest (BH) proposes to distribute a moderate mortality from fishing across the widest possible range of species, stocks, and sizes in an ecosystem, in proportion to their natural productivity so that the relative size and species composition are maintained, in line with the CBD requirement for sustainable use. This proposal has many and not always intuitive implications for fisheries management, e.g. in relation to selectivity, protection of juveniles and spawning sites, models of harvesting strategies, a focus on size and species, the impacts of discarding, aspects of emblematic species and ecosystem services, operational complexity, partial implementation, ecosystem rebuilding, and relations with broader management frameworks. The paper closes with a discussion of BH implementation, concluding that a logical step would be to integrate several separate initiatives to move fisheries into a more ecosystem-conscious context. Implementation challenges will be encountered, but there are lessons to be drawn from fishery ecosystems already close to BH, as in some tropical multispecies fisheries, and further, the implementation challenges are already being taken on in many well-managed fisheries and areas as management begins to address the realities of what ecosystem-based fishery management actually entails.
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach
Authors: Chauve Cedric , Ponty Yann , Peirera Zanetti João Paulo 
Published: September 2015

AbstractContextThe reconstruction of evolutionary scenarios for whole genomes in terms of genome rearrangements is a fundamental problem in evolutionary and comparative genomics. The DeCo algorithm, recently introduced by Bérardet al., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. However, as for many combinatorial optimization algorithms, there can exist many co-optimal, or slightly sub-optimal, evolutionary scenarios that deserve to be considered.ContributionWe extend the DeCo algorithm to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution, and also to compute Boltzmann probabilities for specific ancestral adjacencies.ResultsWe apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies.
Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three relatedPopulusspecies
Authors: Wang Jing , Street Nathaniel R , Scofield Douglas G , Ingvarsson Pär K 
Published: September 2015

AbstractA central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome re-sequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum and population-scaled recombination rates in three species ofPopulus:P. tremula, P. tremuloidesandP. trichocarpa. We find thatP. tremuloideshas the highest level of genome-wide variation, skewed allele frequencies and population-scaled recombination rates, whereasP. trichocarpaharbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, both due to purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination are largely explaining the disparate magnitudes and signatures of linked selection we observe among species. The present work provides the first phylogenetic comparative study at genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.
HacDivSel: Two new methods (haplotype-based and outlier-based) for the detection of divergent selection in pairs of populations
Authors: Carvajal-Rodríguez A. 
Published: September 2015

AbstractThe detection of genomic regions involved in local adaptation is an important topic in current population genetics. There are several detection strategies available depending on the kind of genetic and demographic information at hand. A common drawback is the high risk of false positives. In this study we introduce two complementary methods for the detection of divergent selection from populations connected by migration. Both methods have been developed with the aim of being robust to false positives. The first method combines haplotype information with inter-population differentiation (FST). Evidence of divergent selection is concluded only when both the haplotype pattern and theFSTvalue support it. The second method is developed for independently segregating markers i.e. there is no haplotype information. In this case, the power to detect selection is attained by developing a new outlier test based on detecting a bimodal distribution. The test computes theFSToutliers and then assumes that those of interest would have a different mode. We demonstrate the utility of the two methods through simulations and the analysis of real data. The simulation results showed power ranging from 60-95% in several of the scenarios whilst the false positive rate was controlled below the nominal level. The analysis of real samples consisted of phased data from the HapMap project and unphased data from intertidal marine snail ecotypes. The results illustrate that the proposed methods could be useful for detecting locally adapted polymorphisms. The software HacDivSel implements the methods explained in this manuscript.
Epigenetic Mutation of RAV6 Affects Leaf Angle and Seed Size in Rice
Authors: Zhang Xiangqian , Sun Jing , Cao Xiaofeng , Song Xianwei 
Published: September 2015

Abstract
Heritable epigenetic variants of genes, termed epialleles, can broaden genetic and phenotypic diversity in eukaryotes. Epialleles may also provide a new source of beneficial traits for crop breeding, but very few epialleles related to agricultural traits have been identified in crops. Here, we identified Epi-rav6, a gain-of-function epiallele of rice (Oryza sativa) RELATED TO ABSCISIC ACID INSENSITIVE3 (ABI3)/VIVIPAROUS1 (VP1) 6 (RAV6), which encodes a B3 DNA-binding domain-containing protein. The Epi-rav6 plants show larger lamina inclination and smaller grain size; these agronomically important phenotypes are inherited in a semidominant manner. We did not find nucleotide sequence variation of RAV6. Instead, we found hypomethylation in the promoter region of RAV6, which caused ectopic expression of RAV6 in Epi-rav6 plants. Bisulfite analysis revealed that cytosine methylation of four CG and two CNG loci within a continuous 96-bp region plays essential roles in regulating RAV6 expression; this region contains a conserved miniature inverted repeat transposable element transposon insertion in cultivated rice genomes. Overexpression of RAV6 in the wild type phenocopied the Epi-rav6 phenotype. The brassinosteroid (BR) receptor BR INSENSITIVE1 and BR biosynthetic genes EBISU DWARF, DWARF11, and BR-DEFICIENT DWARF1 were ectopically expressed in Epi-rav6 plants. Also, treatment with a BR biosynthesis inhibitor restored the leaf angle defects of Epi-rav6 plants. This indicates that RAV6 affects rice leaf angle by modulating BR homeostasis and demonstrates an essential regulatory role of epigenetic modification on a key gene controlling important agricultural traits. Thus, our work identifies a unique rice epiallele, which may represent a common phenomenon in complex crop genomes.
A convention for international trade (based on Islamic Sufi teachings)
Authors: Bidabad Bijan 
Published: September 2015

Purpose
– This paper aims to propose a procedure to remove international trade barriers globally. Trade is confronting various barriers in the present world, and this is due to the policies of governments to protect interests of their own citizens. Experience shows that trade barriers end up with incurring losses for both sides (traders) in practice, but a look at history of polemics on trade barriers removal in World Trade Organization (WTO) shows that countries are unable to overcome the obstacles they have created. Trade partners understand that removal of counter barriers is advantageous for both parties. In the meantime, being concerned of other party’s response impedes the benefits of free trade for all parties.

Design/methodology/approach
– This proposition is based upon Islamic Sufism teachings. The propounded principles and goals are in accordance with high understanding of social and economic subtleties of humankind’s life. The authors try to form and formalize Islamic Sufi teachings to establish a base for compiling new international convention that facilitates international trade in all aspects.

Findings
– To facilitate and promote international trade relations in short run, interested countries may accept a convention to remove all trade barriers among themselves all at once.

Research limitations/implications
– The proposed convention does not go against General Agreement on Tariff and Trade and WTO, but it is complementary to both.

Practical implications
– The proposed principles are actually shortcuts to what WTO may access in far futures.

Social implications
– Islamic Sufism teachings can lead us to solve current international problems.

Originality/value
– WTO has taken important steps to facilitate international trade. To reach the main goal of trade liberalization of WTO, a shortcut solution is proposed here.