bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drugs modulating stochastic gene expression affect the erythroid differentiation process
Authors: Guillemin Anissa , Duchesne Ronan , Crauste Fabien , Gonin-Giraud Sandrine , Gandrillon Olivier 
Published: July 2018

AbstractBackgroundTo understand how a metazoan cell makes the decision to differentiate, we assessed the role of stochastic gene expression (SGE) during the erythroid differentiation process. Our hypothesis is that stochastic gene expression has a role in single-cell decision-making. In agreement with this hypothesis, we and others recently showed that SGE significantly increased during differentiation. However, evidence for the causative role of SGE is still lacking. Such demonstration would require being able to experimentally manipulate SGE levels and analyze the resulting impact of these variations on cell differentiation.ResultWe identified three drugs that modulate SGE in primary erythroid progenitor cells. Artemisinin and Indomethacin simultaneously decreased SGE and reduced the amount of differentiated cells. Inversely, α-methylene-γ-butyrolactone-3 (MB-3) simultaneously increased the level of SGE and the amount of differentiated cells. We then used a dynamical modelling approach which confirmed that differentiation rates were indeed affected by the drug treatment.ConclusionUsing single-cell analysis and modeling tools, we provide experimental evidence that in a physiologically relevant cellular system, control of SGE can directly modify differentiation, supporting a causal link between the two.
Not one hormone or another: Aggression differentially affects progesterone and testosterone in a South American ovenbird
Authors: Adreani Nicolas M. , Goymann Wolfgang , Mentesana Lucia 
Published: July 2018

AbstractBehaviors such as territorial interactions among individuals can modulate vertebrate physiology and vice versa. Testosterone has been pointed out as a key hormone that can be rapidly affected by aggressive interactions. However, experimental evidence for such a link is mixed. In addition, behaviors can elicit changes in multiple hormones, which in turn have the potential to synergistically feedback to behavior. For example testosterone and progesterone can act interdependently in modulating male behavior. However, if aggression can affect progesterone levels in males remain unknown and – to the best of our knowledge – no one has yet tackled if and how aggressive behavior simultaneously affects testosterone and progesterone in free-living animals. We addressed these questions by performing simulated territorial intrusion experiments measuring both hormones and their ratio in male rufous horneros (Aves, Furnarius rufus) during the mating and parental care periods. Aggression affected testosterone and progesterone differentially depending on the period of testing: challenged birds had higher levels of progesterone during the mating period and lower levels of testosterone during parental care compared to controls. Challenged individuals had similar progesterone to testosterone ratios during both periods and these ratios were higher than those of control birds. In summary, territorial aggression triggered hormonal pathways differentially depending on the stage of the breeding cycle, but equally altered their ratio independent of it. Our results indicate that multiple related hormones could be playing a role rather than each hormone alone in response to social interactions.
Identification of salivary and plasma biomarkers for obesity in children by non-targeted metabolomic analysis
Authors: Goodson J. Max , Hardt Marcus , Hartman Mor-Li , Schulte Fabian , Tavares Mary , Mutawa Al-Sabiha , Ariga Jitendra , Soparkar Pramod , Behbehani Jawad , Behbehani Kazem , Razzaque Mohammed 
Published: July 2018

AbstractChemical compounds in the saliva most likely to be associated with obesity are identified in a metabolomic analysis of paired whole saliva and plasma samples from 68 children (10-year old) who have also been evaluated for their gingival redness.ResultsThrough metabolomic analysis119 compounds were found only in saliva, 210 only in plasma and 126 in both. The most common plasma metabolites were lipids. The most common saliva metabolites were peptides. Amino acids and their metabolites were common in both samples.Surrogate indicators were identified by computing correlations between saliva and plasma. 29 of the 126 found in both saliva and plasma had significant positive correlation and only 4 of those (urate, creatinine, pipecolate and hydroxyproline) were associated with obesity as potential surrogate biomarkers. The uremic toxin N1-Methyl-2-pyridone-5-carboxamide (2PY) was also elevated in the saliva of obese children. 21 biochemicals were elevated in both obesity and gingivitis suggesting that some biochemical pathways for gingivitis and obesity are shared.Of the metabolites found only in saliva, 35 were associated with obesity (p<0.01). The most significant was phosphate. Saliva had 53 dipeptides, seven of which were associated with obesity. Two volatile amines (putrescine and cadaverine) and their amino acid precursors (ornithine and lysine) were also associated with obesity.Of the metabolites found only in plasma, 64 were associated with obesity (p<0.01). Significant increases in branched-chain and aromatic amino acids, significant reductions in serotonin, serine, and glycine and increased androgen metabolism are changes observed in 10-year old obese children that have also been reported with adult patients having type II diabetes.ConclusionsSalivary urate may be a valuable measure of metabolic disease particularly in association with fructose consumption. Elevated salivary creatinine levels and presence of 2PY suggests a possible association of obesity with developing kidney disease in obese children. Though not a surrogate variable, salivary phosphate, (AUROC= 0.8) could also be an important indicator of obesity. Cadaverine, putrescine and dipeptides are also likely oral bacterial products that could help define the metabolic pathways responsible for obesity. The results of this study indicate that salivary metabolites can be important indicators of developing metabolic disease in children and provide a biochemical signature in the pathways that lead to obesity.
Survival and development of potato psyllid (Hemiptera: Triozidae) on Convolvulaceae: effects of a plant-fungus symbiosis (Periglandula)
Authors: Kaur N. , Cooper W.R. , Duringer J.M. , Badillo-Vargas I.E. , Esparza-Díaz G. , Rashed A. , Horton D.R. 
Published: July 2018

AbstractPlant species in the family Solanaceae are the usual hosts of potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Psylloidea: Triozidae). However, the psyllid has also been shown to develop on some species of Convolvulaceae (bindweeds and morning glories). Developmental success on Convolvulaceae is surprising given the rarity of psyllid species worldwide associated with this plant family. We assayed 14 species of Convolvulaceae across four genera (Convolvulus, Calystegia, Ipomoea, Turbina) to identify species that allow development of potato psyllid. Two populations of psyllids were assayed (Texas, Washington). The Texas population overlaps extensively with native Convolvulaceae, whereas Washington State is noticeably lacking in Convolvulaceae. Results of assays were overlain on a phylogenetic analysis of plant species to examine whether Convolvulaceae distantly related to the typical host (potato) were less likely to allow development than species of Convolvulaceae more closely related. Survival was independent of psyllid population and location of the plant species on our phylogenetic tree. We then examined whether presence of a fungal symbiont of Convolvulaceae (Periglandula spp.) affected psyllid survival. These fungi associate with Convolvulaceae and produce a class of mycotoxins (ergot alkaloids) that may confer protection against plant-feeding arthropods. Periglandula was found in 11 of our 14 species, including in two genera (Convolvulus, Calystegia) not previously known to host the symbiont. Of these 11 species, leaf tissues from five contained large quantities of two classes of ergot alkaloids (clavines, amides of lysergic acid) when evaluated by LC-MS/MS. All five species also harbored Periglandula. No ergot alkaloids were detected in species free of the fungal symbiont. Potato psyllid rapidly died on species found to harbor Periglandula and fungus-produced alkaloids, but survived on species in which the mutualism was absent. These results support the hypothesis that a plant-fungus symbiotic relationship affects the suitability of certain Convolvulaceae to potato psyllid.
Head-to-Head Comparison of Three Methods of Quantifying Competitive Fitness inC. elegans
Authors: Crombie Timothy A. , Saber Sayran , Saxena Ayush Shekhar , Egan Robyn , Baer Charles F. 
Published: July 2018

AbstractOrganismal fitness is relevant in many contexts in biology. The most meaningful experimental measure of fitness iscompetitivefitness, when two or more entities (e.g., genotypes) are allowed to compete directly. In theory, competitive fitness is simple to measure: an experimental population is initiated with the different types in known proportions and allowed to evolve under experimental conditions to a predefined endpoint. In practice, there are several obstacles to obtaining robust estimates of competitive fitness in multicellular organisms, the most pervasive of which is simply the time it takes to count many individuals of different types from many replicate populations. Methods by which counting can be automated in high throughput are desirable, but for automated methods to be useful, the bias and technical variance associated with the method must be (a) known, and (b) sufficiently small relative to other sources of bias and variance to make the effort worthwhile.The nematodeCaenorhabditis elegansis an important model organism, and the fitness effects of genotype and environmental conditions are often of interest. We report a comparison of three experimental methods of quantifying competitive fitness, in which wild-type strains are competed against GFP-marked competitors under standard laboratory conditions. Population samples were split into three replicates and counted (1) “by eye” from a saved image, (2) from the same image using CellProfiler image analysis software, and (3) with a large particle flow cytometer (a “worm sorter”). From 720 replicate samples, neither the frequency of wild-type worms nor the among-sample variance differed significantly between the three methods. CellProfiler and the worm sorter provideat leasta tenfold increase in sample handling speed with little (if any) bias or increase in variance.
25-Hydroxyl-cholesterol Binds and Enhance Anti-viral Effects of Zebrafish Monomeric C-reactive Proteins
Authors: Bello-Perez Melissa , Falco Alberto , Encinar Jose Antonio , Novoa Beatriz , Perez Luis , Coll Julio 
Published: July 2018

AbstractC-reactive proteins (CRP) are among the faster acute-phase inflammation-responses coded by one gene in humans (hcrp) and seven genes (crp1-7) in zebrafish (Danio rerio). In this study, preferential 25-hydroxycholesterol (25HOCh) binding to zebrafish CRP1-7 compared to other lipids were predicted by in silico docking and confirmed by solid-phase binding-assays. In addition, 25HOCh enhanced methyl-betacyclodextrin-sensitive (Cholesterol-dependent) CRP1-7 anti-viral effects in a fine-tunned isoform-dependent manner. In silico and structural studies suggested that the crosstalk between the anti-viral enhancements of both 25HOCh and CRP1-7 were dependent on protein monomers rather than oligomers but differred among isoforms. The presence of oxidized cholesterols in human atherosclerotic plaques amplifies the importance that similar interactions may have for vascular and/or neurodegenerative diseases during viral infections. In this context, the zebrafish model offers a genetic tool to further investigate how the expression and functions of different CRP isoforms and/or transcript variants may be controlled.
Maternal immunity and antibodies to dengue promote Zika virus-induced microcephaly in fetuses
Authors: Rathore Abhay P. S. , Saron Wilfried A. A. , Lim Ting , Jahan Nusrat , St John Ashley L. 
Published: July 2018

AbstractZika virus (ZIKV), a recently emerged flaviviral pathogen, has been linked to microcephaly in neonates1. Yet, it is not understood why some fetuses develop severe microcephaly due to maternal ZIKV infection while others do not. The risk for ZIKV-induced microcephaly is greatest during the first trimester of pregnancy in humans2,3, yet this alone cannot account for the varied presentation of microcephaly observed. Given the antigenic similarity between ZIKV and closely related dengue virus (DENV)4, combined with the substantial immunity to DENV in ZIKV target populations in recent outbreaks, we hypothesized that maternal antibodies against DENV could promote ZIKV-induced microcephaly. Here, using immune-competent mice, we show that maternal to fetal transmission of ZIKV occurs, leading to fetal infection and disproportionate microcephaly. DENV-specific antibodies in pregnant female mice enhance vertical transmission of infection and result in a severe microcephaly like-syndrome during ZIKV infection. Furthermore, fetal infection was promoted by the neonatal Fc receptor (FcRN). Our results identify a novel immune-mediated mechanism of vertical transmission of viral infection and raise caution since ZIKV epidemic regions are also endemic to DENV.
Analysis and Engineering of Substrate Shuttling by the Acyl Carrier Protein (ACP) in Fatty Acid Synthases (FASs)
Authors: Rossini Emanuele , Gajewski Jan , Klaus Maja , Hummer Gerhard , Grininger Martin 
Published: July 2018

ABSTRACTIn the large enzyme complexes of natural biosynthetic pathways, molecules are assembled like in a factory. Carrier domains shuttle substrates and intermediates as covalently attached cargo within the enzyme complex between active sites. The physical confinement of the reaction increases reaction rates and hinders pathway branching. Alternating interactions of substrate-loaded carrier domains with different catalytic domains modulate the chemical environment. In this study, we aim at assessing the impact of domain-domain interactions (DDIs) on the reaction progress of a multienzyme type I fatty acid synthase (FAS) in quantitative terms. We modulate DDIs by single interface mutations, and read out the impact on substrate shuttling by recording fatty acid (FA) chain length product spectra and FAS activities. Our data show that even single interface point mutations can severely affect FA synthesis. With molecular dynamics simulations and modeling, we relate the mutation effects to specific alterations in the molecular interaction networks and domain-domain binding energetics. Some of the presented mutations induce the synthesis of short-chain FAs. These compounds are important commodity products and potent precursors for microbial biofuel production.
Phylogenetic conflicts, combinability, and deep phylogenomics in plants
Authors: Smith Stephen A. , Walker-Hale Nathanael , Walker Joseph F. , Brown Joseph W. 
Published: July 2018

AbstractStudies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a dataset in order to resolve recalcitrant relationships and, importantly, identify what the dataset is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant dataset. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested conflicts limited the ability of data filtering methods to fully ameliorate conflicting signal amongst gene trees. These analyses confirmed that the underlying conflicting signal does not support broad concatenation of genes. Our approach provides a means of dissecting a specific dataset to address deep phylogenetic relationships while also identifying the inferential boundaries of the dataset.
Maizedefective kernel5is a bacterial tamB homolog required for chloroplast envelope biogenesis
Authors: Zhang Junya , Wu Shan , Boehlein Susan K. , McCarty Donald R. , Song Gaoyuan , Walley Justin W. , Myers Alan , Settles A. Mark 
Published: July 2018

ABSTRACTChloroplasts are of prokaryotic origin with a double membrane envelope that separates plastid metabolism from the cytosol. Envelope membrane proteins integrate the chloroplast with the cell, but the biogenesis of the envelope membrane remains elusive. We show that the maizedefective kernel5(dek5) locus is critical for plastid membrane biogenesis. Amyloplasts and chloroplasts are larger and reduced in number indek5with multiple ultrastructural defects. We show thatdek5encodes a protein homologous to riceSUBSTANDARD STARCH GRAIN4(SSG4) andE.colitamB. TamB functions in bacterial outer membrane biogenesis. The DEK5 protein is localized to the chloroplast envelope with a topology analogous to TamB. Increased levels of soluble sugars indek5developing endosperm and elevated osmotic pressure in mutant leaf cells suggest defective intracellular solute transport. Both proteomics and antibody-based analyses show thatdek5chloroplasts have reduced levels of chloroplast envelope transporters. Moreover,dek5chloroplasts reduce inorganic phosphate uptake with at least an 80% reduction relative to normal chloroplasts. These data suggest that DEK5 functions in plastid envelope biogenesis to enable metabolite transport.
Mouse REC114 is essential for meiotic DNA double-strand break formation and forms a complex with MEI4
Authors: Kumar Rajeev , Oliver Cecilia , Brun Christine , Juarez-Martinez Ariadna B. , Tarabay Yara , Kadlec Jan , de Massy Bernard 
Published: July 2018

AbstractProgrammed formation of DNA double strand breaks (DSBs) initiates the meiotic homologous recombination pathway. This pathway allows homologous chromosomes to find each other and the formation of crossing overs, the products of reciprocal exchanges, which are required for proper chromosome segregation at the first meiotic division. Meiotic DSBs are catalyzed by Spo11 that forms a complex with a second subunit, TopoVIBL, and mediates a DNA type II topoisomerase-like cleavage. Several other proteins are essential for meiotic DSB formation, including three evolutionarily conserved proteins first identified in Saccharomyces cerevisiae (Mer2, Mei4 and Rec114). These three S. cerevisiae proteins and their mouse orthologs (IHO1, MEI4 and REC114) co-localize on the axes of meiotic chromosomes, and mouse IHO1 and MEI4 are essential for meiotic DSB formation. Here, we show that mouse Rec114 is required for meiotic DSB formation. Moreover, MEI4 forms a complex with REC114 and IHO1 in mouse spermatocytes, consistent with cytological observations. We then demonstrated in vitro the formation of a stable complex between REC114 C-terminal domain and MEI4 N-terminal domain. We further determine the structure of REC114 N-terminal domain that revealed similarity with Pleckstrin Homology domains and its property to dimerize. These analyses provide direct insights into the architecture of these essential components of the meiotic DSB machinery.
qPCR assays for the detection of two western North American freshwater mussel species, Anodonta nuttalliana and Anodonta oregonensis, from environmental DNA
Authors: Rodgers Torrey W. , Mock Karen E. 
Published: July 2018

AbstractWe developed species-specific quantitative PCR assays for the detection of two freshwater mussel species native to the western North America, Anodonta nuttalliana and Anodonta oregonensis, from environmental DNA. These species have experienced dramatic declines over the last century, and are currently threatened in many portions of their range. Improved tools for detecting and monitoring these species are needed. Species-specificity and sensitivity of the assays was empirically tested in the lab, and both assays were also validated with field collected eDNA samples. We found that the assays we designed are species-specific, sensitive, and are effective for detecting Anodonta nuttalliana and Anodonta oregonensis from environmental DNA samples collected from streams and rivers. These assays will aid in the detection, monitoring, management, and conservation of these threatened species.
Live, visual, social, and mobile: media ecology in emergencies and ordinary times
Authors: Lev-On Azi , Uziel Vered 
Published: July 2018

Purpose
The purpose of this paper is to analyze contemporary uses and gratifications (U&G) of the media, focusing on the differences between emergency and ordinary times, and between media consumers in the border region and in the home front during the Israel-Gaza War (2014).

Design/methodology/approach
The study used a questionnaire containing 184 items. This significant number of items was necessary due to the large number of media channels and potential uses examined. Due to the length of the questionnaire, and the inclusion of individuals who are not habitual internet users, data were collected in the field rather than through a telephone survey or online. The list of media and uses was compiled based on a review of existing literature regarding functions of media in emergencies.

Findings
Television and news websites are dominant suppliers of national and local information, but mobile and social channels lead in terms of social uses, discussions, requests and provision of assistance. The same channels were almost always used during emergencies and ordinary times to satisfy a specific need. The leading channels – television, Facebook, WhatsApp and SMS – were used significantly more on the frontlines than on the home front. The findings demonstrate that people use diverse media, but channels that are live, visual, social and mobile are dominant.

Originality/value
Very few academic studies have compared media uses during ordinary times and emergencies, and those existing focus on the uses of a specific medium. The present study examines various U&G of traditional and new media during the war, compares uses during the war with uses during ordinary times, and compares the population in the border region with the population in the home front.