bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occurrence of Lymphedema in Wild-Caught Anurans
Authors: McCallum Malcolm L. 
Published: June 2018

AbstractLymphedema is a condition in which the lymph hearts fail to pump fluid from the lymph sacs of anurans and other amphibians. This causes the sacs to fill with fluid and provide the frog with balloon-like swellings or over-all appearance. The condition has previously been connected with various diseases including tadpole edema virus and chytrids. I observed lymphedema in six anuran species (Acris blanchadi*, Anaxyrus fowleri*, Hyla squirrela*, Pseudacris streckeri illinoensis*, Rana sylvatica, Rana sphenocephala*[species with * are species records for lymphedema]).
Disruption of the KH1 domain of Fmr1 leads to transcriptional alterations and attentional deficits in rats
Authors: Golden Carla E. M. , Breen Michael S. , Koro Lacin , Sonar Sankalp , Niblo Kristi , Browne Andrew , Di Marino Daniele , De Rubeis Silvia , Baxter Mark G. , Buxbaum Joseph D. , Harony-Nicolas Hala 
Published: June 2018

AbstractFragile X Syndrome (FXS) is a neurodevelopmental disorder caused by mutations in the FMR1 gene. FXS is a leading monogenic cause of autism spectrum disorder (ASD) and inherited intellectual disability (ID). In most cases, the mutation is an expansion of a microsatellite (CGG triplet), which leads to suppressed expression of the fragile X mental retardation protein (FMRP), an RNA-binding protein involved in multiple aspects of mRNA metabolism. Interestingly, we found that the previously published Fmr1 knockout rat model of FXS expresses a transcript with an in-frame deletion of a K-homology (KH) domain, KH1. KH domains are RNA-binding domains of FMR1 and several of the few, known point mutations associated with FXS are found within them. We observed that this deletion leads to medial prefrontal cortex (mPFC)-dependent attention deficits, similar to those observed in FXS, and to alterations in transcriptional profiles within the mPFC, which mapped to two weighted gene coexpression network analysis modules. We demonstrated that these modules are conserved in human frontal cortex, are enriched for known FMRP targets and for genes involved in neuronal and synaptic processes, and that one is enriched for genes that are implicated in ASD, ID, and schizophrenia. Hub genes in these conserved modules represent potential targets for FXS. These findings provide support for a prefrontal deficit in FXS, indicate that attentional testing might be a reliable cross-species tool for investigating the pathophysiology of FXS and a potential readout for pharmacotherapy testing, and identify dysregulated gene expression modules in a relevant brain region.Significance StatementThe significance of the current study lies in two key domains. First, this study demonstrates that deletion of the Fmrp-KH1 domain is sufficient to cause major mPFC-dependent attention deficits in both males and females, like those observed in both individuals with FXS and in knockout mouse models for FXS. Second, the study shows that deletion of the KH1 domain leads to alterations in the transcriptional profiles within the medial prefrontal cortex (mPFC), which are of potential translational value for subjects with FXS. These findings indicate that attentional testing might be a reliable cross-species tool for investigating the pathophysiology of FXS and a potential readout for pharmacotherapy testing and also highlight hub genes for follow up.
Investigating the long-term stability of protein immunogen(s) for whole recombinant yeast-based vaccines
Authors: Kumar Ravinder 
Published: June 2018

AbstractEven today vaccine(s) remains a mainstay in combating infectious diseases. Many yeast-based vaccines are currently in different phases of clinical trials. Despite the encouraging results of whole recombinant yeast (WRY) and yeast display (YD), the systematic study assessing the long-term stability of protein antigen(s) in yeast cells is still missing. Therefore, in the present study, I investigate the stability of heterologous protein antigen in the cellular environment ofS. cerevisiaethroughE. colisurface protein (major curlin or CsgA). Present biochemical data showed that the stationary phase yeast cells were able to keep the antigen stable for almost one year when stored at 2-8 °C and 23-25 °C. Further, iTRAQ based quantitative proteomics of yeast whole cell lysate showed that the level of heterologous fusion protein was low in cells stored at 23-25 °C compared to those at 2-8 °C. In the end, I also proposed a workable strategy to test integrity or completeness of heterologous protein in the yeast cell. I believe that the observations made in the present study will be really encouraging for those interested in the development of a whole recombinant yeast-based vaccine(s).
Contrasting effects of aging on the expression of transposons, the piRNA machinery and mitochondrial transcripts in theDrosophilaovary
Authors: Erwin Alexandra A. , Blumenstiel Justin P. 
Published: June 2018

ABSTRACTRedistribution of heterochromatin during aging has been linked to the de-repression of transposable elements and an overall loss of gene regulation in the soma. Whether or not epigenetic factors such as heterochromatin marks are perturbed in reproductive and germline tissues is of particular interest because some epigenetic factors are known to transmit across generations. Additionally, the relative contribution of factors intrinsic or extrinsic to the germ line have in reproductive decline remains unknown. Using mRNA sequencing data from late stage egg chambers inDrosophila melanogaster, we show that age-related expression changes occur in genes residing in heterochromatin, particularly on the largely heterochromatic 4thchromosome. In addition, we identify an increase in expression of the piRNA machinery. We further identify a striking age-related reduction in mitochondrial transcripts that we can attribute to the somatic tissues. Other than a modest increase in overall TE expression in the aging germline, we find no global TE de-repression in reproductive tissues. Rather, the observed effects of aging on TEs are primarily strain and family specific. These results indicate unique responses in somatic versus germline tissue with regards to epigenetic aging effects and suggest that the global loss of TE control observed in other studies may be specific to certain tissues, genetic backgrounds and TE family. This study also demonstrates that while age-related effects can be maternally transmitted, the germline is generally robust to age-related changes.
Nrf1D is the first candidate secretory transcription factor in the blood plasma, with its precursor existing as a unique redox-sensitive transmembrane CNC-bZIP protein in somatic tissues
Authors: Yuan Jianxin , Wang Hongxia , Li Shaojun , Xiang Yuancai , Hu Shaofan , Wang Meng , Qiu Lu , Zhang Yiguo 
Published: June 2018

ABSTRACTAmongst multiple distinct isoforms, Nrf1D is synthesized from translation of an alternatively-spliced transcript of Nrf1 mRNA, with a naturally-occurring deletion of its stop codon-flanking 1466 nucleotides. This molecular event leads to the reading frameshift mutation, which results in a constitutive substitution of the intact Nrf1’s C-terminal 72 amino acids (aa, covering the second half of the leucine zipper motif to C-terminal Neh3L domain) by an additional extended 80-aa stretch to generate a unique variant Nrf1D. The C-terminal extra 80-aa region of Nrf1D was identified to fold into a redox-sensitive transmembrane domain that enables it to be tightly integrated within the endoplasmic reticulum (ER) membranes. Notably, the salient feature of Nrf1D confers it to be distinguishable from prototypic Nrf1, such that Nrf1D is endowed with only a less ability than wild-type Nrf1 at mediating target gene expression. Further evidence has been presented revealing that both mRNA and protein levels of Nrf1D were detected to varying extents in somatic tissues. Surprisingly, we also found the existence of Nrf1D-derived isoforms in the blood plasma, implying that it is a candidate secretory transcription factor, although its precursor acts as an integral transmembrane-bound CNC-bZIP protein that entails dynamic topologies, before being unleashed from the ER to enter the blood plasma.
Lipidomic and biophysical homeostasis of mammalian membranes in response to dietary lipids is essential for cellular fitness
Authors: Levental Kandice R , Malmberg Eric , Symons Jessica , Fan Yang-Yi , Chapkin Robert S. , Ernst Robert , Levental Ilya 
Published: June 2018

ABSTRACTBiological membranes form the functional, dynamic interface that hosts a major fraction of all cellular bioactivity. Proper membrane physiology requires maintenance of a narrow range of physicochemical properties, which must be buffered from external perturbations. While homeostatic adaptation of membrane fluidity to temperature variation is a ubiquitous design feature of ectothermic organisms, such responsive membrane adaptation to external inputs has not been directly observed in mammals. Here, we report that challenging mammalian membrane homeostasis by dietary lipids leads to robust lipidomic remodeling to preserve membrane physical properties. Specifically, exogenous polyunsaturated fatty acids (PUFAs) are rapidly and extensively incorporated into membrane lipids, inducing a reduction in membrane packing. These effects are rapidly compensated both in culture and in vivo by lipidome-wide remodeling, most notably upregulation of saturated lipids and cholesterol. These lipidomic changes result in recovery of membrane packing and permeability. This lipidomic and biophysical compensation is mediated in part by lipid regulatory machinery, whose pharmacological or genetic abrogation results in cytotoxicity when membrane homeostasis is challenged by dietary lipids. These results reveal an essential mammalian mechanism for membrane homeostasis wherein lipidome remodeling in response to dietary lipid inputs preserves functional membrane phenotypes.
Gut Microbiota Diversity across Ethnicities in the United States
Authors: Brooks Andrew W. , Priya Sambhawa , Blekhman Ran , Bordenstein Seth R. 
Published: June 2018

AbstractComposed of hundreds of microbial species, the composition of the human gut microbiota can vary with chronic diseases underlying health disparities that disproportionally affect ethnic minorities. However, the influence of ethnicity on the gut microbiota remains largely unexplored and lacks reproducible generalizations across studies. By distilling associations between ethnicity and differences in two United States based 16S gut microbiota datasets including 1,673 individuals, we report 12 microbial genera and families that reproducibly vary by ethnicity. Interestingly, a majority of these microbial taxa, including the most heritable bacterial family, Christensenellaceae, overlap with genetically-associated taxa and form co-occurring clusters linked by similar fermentative and methanogenic metabolic processes. These results demonstrate recurrent associations between specific taxa in the gut microbiota and ethnicity, providing hypotheses for examining specific members of the gut microbiota as mediators of health disparities.
Isoform and protein region abnormalities of dysbindin and copper transporter proteins in postmortem schizophrenia substantia nigra
Authors: Schoonover Kirsten E. , Roberts Rosalinda C. 
Published: June 2018

AbstractObjectiveDysbindin is downregulated in several schizophrenia brain regions and modulates copper transport required for myelination and monoamine metabolism. We sought to determine dysbindin and copper transporter protein expression in schizophrenia subjects.MethodsWe studied the substantia nigra (which exhibits one of the highest copper contents of the human brain) using Western blot analysis. We characterized specific protein domains of copper transporters ATP7A, CTR1, ATP7B, and dysbindin isoforms 1A and 1B/C in postmortem substantia nigra in schizophrenia subjects (n=15) and matched controls (n=11). As a preliminary investigation, we examined medication status in medicated (n=11) versus unmedicated schizophrenia subjects (n=4).ResultsThe combined schizophrenia group exhibited increased levels of C-terminus, but not N-terminus, ATP7A. Schizophrenia subjects expressed less transmembrane CTR1 and dysbindin 1B/C than controls. When subdivided, the increased C-terminus ATP7A protein was present only in medicated subjects versus controls. Unmedicated subjects exhibited less N-terminus ATP7A protein than controls and medicated subjects, suggesting medication-induced rescue of the ATP7A N-terminus. Transmembrane CTR1 was decreased to a similar extent in both treatment groups versus controls, suggesting no medication effect.ConclusionsThese results provide the first evidence of disrupted copper transport into and within schizophrenia nigral cells that may be modulated by specific dysbindin isoforms and antipsychotic treatment.
PIKfyve/Fab1 is required for efficient V-ATPase and hydrolase delivery to phagosomes, phagosomal killing, and restriction ofLegionellainfection
Authors: Buckley Catherine M. , Heath Victoria L. , Guého Aurélie , Bosmani Cristina , Knobloch Paulina , Sikakana Phumzile , Personnic Nicolas , Dove Stephen K. , Michell Robert H. , Meier Roger , Hilbi Hubert , Soldati Thierry , Insall Robert H. , King Jason S. 
Published: June 2018

AbstractBy engulfing potentially harmful microbes, professional phagocytes are continually at risk from intracellular pathogens. To avoid becoming infected, the host must kill pathogens in the phagosome before they can escape or establish a survival niche. Here, we analyse the role of the phosphoinositide (PI) 5-kinase PIKfyve in phagosome maturation and killing, using the amoeba and model phagocyteDictyostelium discoideum.PIKfyve plays important but poorly understood roles in vesicular trafficking by catalysing formation of the lipids phosphatidylinositol (3,5)-bisphosphate (PI(3,5)2) and phosphatidylinositol-5-phosphate (PI(5)P). Here we show that its activity is essential during early phagosome maturation inDictyostelium. Disruption ofPIKfyveinhibited delivery of both the vacuolar V-ATPase and proteases, dramatically reducing the ability of cells to acidify newly formed phagosomes and digest their contents. Consequently,PIKfyve-cells were unable to generate an effective antimicrobial environment and efficiently kill captured bacteria. Moreover, we demonstrate that cells lackingPIKfyveare more susceptible to infection by the intracellular pathogenLegionella pneumophila. We conclude that PIKfyve-catalysed phosphoinositide production plays a crucial and general role in ensuring early phagosomal maturation, protecting host cells from diverse pathogenic microbes.ImportanceCells that capture or eat bacteria must swiftly kill them to prevent pathogens from surviving long enough to escape the bactericidal pathway and establish an infection. This is achieved by the rapid delivery of components that produce an antimicrobial environment in the phagosome, the compartment containing the captured microbe. This is essential both for the function of immune cells and for amoebae that feed on bacteria in their environment. Here we identify a central component of the pathway used by cells to deliver antimicrobial components to the phagosome and show that bacteria survive over three times as long within the host if this pathway is disabled. We show that this is of general importance for killing a wide range of pathogenic and non-pathogenic bacteria, and that it is physiologically important if cells are to avoid infection by the opportunistic human pathogenLegionella.
Win‐wins for biodiversity and ecosystem service conservation depend on the trophic levels of the species providing services
Authors: Xiao Hui , Dee Laura E. , Chadès Iadine , Peyrard Nathalie , Sabbadin Régis , Stringer Martin , McDonald‐Madden Eve 
Published: June 2018

Abstract

Confronted by significant impacts to ecosystems world‐wide, decision makers face the challenge of maintaining both biodiversity and the provision of ecosystem services (ES). However, the objectives of managing biodiversity and supplying ES may not always be in concert, resulting in the need for trade‐offs. Understanding these potential trade‐offs is crucial for identifying circumstances under which conservation strategies designed to maximise either biodiversity or ES will result in win‐win or win‐lose outcomes. One important factor that may influence these outcomes are species interactions and the structure of the networks in which they are embedded.

We combine optimisation and network theory to investigate the difference in species prioritisation and management outcomes when targeting biodiversity or ES, by considering trophic interactions between species. We analyse 360 simulated ecosystem networks with different ecosystem structures, including the trophic level of the species providing the ES, the number of ES considered, and the food web connectivity. We then illustrate the framework on a saltmarsh case study.

We find that trade‐offs between biodiversity and ES depend on the network structure of the ecosystem being managed. The trophic level of the species providing the ES is an important determinant of optimal species protection priorities and the biodiversity‐ES trade‐offs. A strategy targeting ES leads to similar levels of biodiversity conservation (a win‐win situation) only when basal species provide the services. In contrast, food web connectivity and the number of services considered have little impact on biodiversity‐ES trade‐offs.

Synthesis and applications. Our research provides the first optimisation model to examine trade‐offs between a biodiversity‐ or ecosystem service‐based approach for managing a network of interacting species that provide services. Importantly, results from considering species‐services interactions in ecosystem network dynamics can provide managers with quantitative insights to identify opportunities for win‐wins and or to avoid win‐loss outcomes, by focusing on the trophic level of the species providing services. Future research could build on our model to add multiple interaction types among species, ecosystem functions, and ecosystem services to analyse optimal ecosystem management for multiple conservation objectives.
A cost‐and‐time effective procedure to develop SNP markers for multiple species: A support for community genetics
Authors: Delord Chrystelle , Lassalle Gilles , Oger Adrien , Barloy Dominique , Coutellec Marie‐Agnes , Delcamp Adline , Evanno Guillaume , Genthon Clemence , Guichoux Erwan , Le Bail Pierre‐Yves , Le Quilliec Patricia , Longin Guillaume , Lorvelec Olivier , Massot Marie , Reveillac Elodie , Rinaldo Raphaelle , Roussel Jean‐Marc , Vigouroux Regis , Launey Sophie , Petit Eric J. 
Published: June 2018

Abstract

Multispecies population genetics is an emerging field that provides insight relevant to conservation biology and community ecology. However, to date, this approach is limited to species with available genetic resources. The use of thousands of single‐nucleotide polymorphism (SNP) markers developed from recent genotyping‐by‐sequencing (GBS) technologies is a roadmap for the study of nonmodel species, but remains cost prohibitive when several, distantly related species are involved.

We aimed to overcome this issue using a single HiSeq3000 run of restriction‐site associated DNA sequencing (RAD‐Seq) to retrieve SNP markers for 40 diverse species including plants, invertebrates, fish, and mammals. We developed a Python‐based pipeline to isolate c. 100–500 high‐quality SNP markers for each species that could be genotyped through classical PCR amplification methods. To assess the quality of these markers, we validated our approach on c. 160 of the characterized SNPs for each of 18 Neotropical fish species from the river Maroni (French Guiana, South America), using the MassARRAY iPLEX platform from Agena Bioscience (San Diego, CA, USA).

A run of the pipeline applying stringent filtering parameters enabled the successful design of between 130 and 3,492 SNP markers for 30 of the 40 study species. Relaxing pipeline parameters allows for an increase in the number of detected SNPs. Across the 18 species from French Guiana, an average of 85% of markers were successfully amplified, polymorphic, and scored in ≥90% of individuals (c. 200 individuals per species). The great majority (>98%) of these markers were at Hardy–Weinberg equilibrium in each sampling site from the river Maroni.

This SNP discovery was performed at the cost of c. $US110 for each of the 40 species. Genotyping was performed at the cost of c. $US6000 for each of the 18 fish species with an average of 200 individuals per species. This strategy was found cost‐and‐time efficient to develop hundreds of SNP markers for a large range of nonmodel species, which can be used to investigate ecological and evolutionary questions that do not require whole‐genome coverage.
Uncertainty in geographical estimates of performance and fitness
Authors: Woods H. Arthur , Kingsolver Joel G. , Fey Samuel B. , Vasseur David A. 
Published: June 2018

Abstract

Thermal performance curves (TPCs) have become key tools for predicting geographical distributions of performance by ectotherms. Such TPC‐based predictions, however, may be sensitive to errors arising from diverse sources.

We analysed potential errors that arise from common choices faced by biologists integrating TPCs with climate data by constructing case studies focusing on experimental sets of TPCs and simulating geographical patterns of mean performance. We first analysed differences in geographical patterns of performance derived from two pairs of commonly used TPCs. Mean performance differed most (up to 30%) in regions with relatively constant mean temperatures similar to those at which the TPCs diverged the most.

We also analysed the effects of thermal history by comparing geographical estimates derived from (a) a broad TPC based on short‐term measurements of insect larvae (Manduca sexta) with a history of exposure to thermal variation versus (b) a narrow TPC based on long‐term measurements of larvae held at constant temperatures. Estimated mean performance diverged by up to 40%, and differences were magnified in simulated future climates.

Finally, to quantify geographical error arising from statistical error in fitted TPCs, we propose and illustrate a bootstrapping technique for establishing 95% prediction intervals on mean performance at each location (pixel).

Collectively, our analyses indicate that error arising from several underappreciated sources can significantly affect the mean performance values derived from TPCs, and we suggest that the magnitudes of these errors should be estimated routinely in future studies.