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https://www.readbyqxmd.com/read/29454089/genome-wide-gene-expression-analysis-of-45-days-pregnant-fetal-cotyledons-vis-a-vis-non-pregnant-caruncles-in-buffalo-bubalus-bubalis
#1
Masoud Lotfan, Syed Azmal Ali, Munnalal Yadav, Suman Chuadhary, Manoj Kumar Jena, Sudarshan Kumar, Ashok Kumar Mohanty
The crosstalk between fetus and mother starts with the onset of placental attachment to the uterus. The cotyledons and caruncles are the two anatomically distinct structures that play a crucial role in this physiological communication. Using Agilent Gene Chip Genome microarray, we measured the expression profile of pregnancy cotyledons in comparison to caruncular reminiscence of the uteri in non-pregnant buffalo (Bubalus bubalis) for the detection of the early post-pregnancy rapid changes in cellular expression of mRNA transcripts...
February 14, 2018: Gene
https://www.readbyqxmd.com/read/29453715/the-influence-of-heavy-metals-polyaromatic-hydrocarbons-and-polychlorinated-biphenyls-pollution-on-the-development-of-antibiotic-resistance-in-soils
#2
Andrey Vladimirovich Gorovtsov, Ivan Sergeevich Sazykin, Marina Alexandrovna Sazykina
The minireview is devoted to the analysis of the influence of soil pollution with heavy metals, polyaromatic hydrocarbons (PAHs), and the polychlorinated biphenyls (PCBs) on the distribution of antibiotics resistance genes (ARGs) in soil microbiomes. It is shown that the best understanding of ARGs distribution process requires studying the influence of pollutants on this process in natural microbiocenoses. Heavy metals promote co-selection of genes determining resistance to them together with ARGs in the same mobile elements of a bacterial genome, but the majority of studies focus on agricultural soils enriched with ARGs originating from manure...
February 16, 2018: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29453266/the-gills-of-reef-fish-support-a-distinct-microbiome-influenced-by-host-specific-factors
#3
Zoe A Pratte, Marc Besson, Rebecca D Hollman, Frank J Stewart
Teleost fish represent the most diverse of the vertebrate groups and play important roles in food webs, as ecosystem engineers, and as vectors for microorganisms. However, the microbial ecology of fishes remains underexplored for most host taxa, and for certain niches on the fish body. This is particularly true for the gills, the key sites for respiration and waste exchange in fishes. Here, we provide a comprehensive analysis of the gill microbiome. We focus on ecologically diverse taxa from coral reefs around Moorea, sampling the gill and intestines of adults and juveniles representing 15 families...
February 16, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29453259/common-hydraulic-fracturing-fluid-additives-alter-the-structure-and-function-of-anaerobic-microbial-communities
#4
Adam C Mumford, Denise M Akob, J Grace Klinges, Isabelle M Cozzarelli
The development of unconventional oil and gas (UOG) resources results in production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. Release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain, and may serve as sentinels for changes in stream health. Iron reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, DBNPA and Bronopol...
February 16, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29452767/uptake-and-distribution-of-organo-iodine-in-deep-sea-corals
#5
Nancy G Prouty, E Brendan Roark, Leslye M Mohon, Ching-Chih Chang
Understanding iodine concentration, transport, and bioavailability is essential in evaluating iodine's impact to the environment and its effectiveness as an environmental biogeotracer. While iodine and its radionuclides have proven to be important tracers in geologic and biologic studies, little is known about transport of this element to the deep sea and subsequent uptake in deep-sea coral habitats. Results presented here on deep-sea black coral iodine speciation and iodine isotope variability provides key information on iodine behavior in natural and anthropogenic environments, and its geochemical pathway in the Gulf of Mexico...
February 13, 2018: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/29450709/biofilm-formation-and-potential-for-iron-cycling-in-serpentinization-influenced-groundwater-of-the-zambales-and-coast-range-ophiolites
#6
D'Arcy R Meyer-Dombard, Caitlin P Casar, Alexander G Simon, Dawn Cardace, Matthew O Schrenk, Carlo A Arcilla
Terrestrial serpentinizing systems harbor microbial subsurface life. Passive or active microbially mediated iron transformations at alkaline conditions in deep biosphere serpentinizing ecosystems are understudied. We explore these processes in the Zambales (Philippines) and Coast Range (CA, USA) ophiolites, and associated surface ecosystems by probing the relevance of samples acquired at the surface to in situ, subsurface ecosystems, and the nature of microbe-mineral associations in the subsurface. In this pilot study, we use microcosm experiments and batch culturing directed at iron redox transformations to confirm thermodynamically based predictions that iron transformations may be important in subsurface serpentinizing ecosystems...
February 15, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29449859/latitudinal-patterns-in-european-seagrass-carbon-reserves-influence-of-seasonal-fluctuations-versus-short-term-stress-and-disturbance-events
#7
Laura M Soissons, Eeke P Haanstra, Marieke M van Katwijk, Ragnhild Asmus, Isabelle Auby, Laurent Barillé, Fernando G Brun, Patricia G Cardoso, Nicolas Desroy, Jerome Fournier, Florian Ganthy, Joxe-Mikel Garmendia, Laurent Godet, Tiago F Grilo, Petra Kadel, Barbara Ondiviela, Gloria Peralta, Araceli Puente, Maria Recio, Loic Rigouin, Mireia Valle, Peter M J Herman, Tjeerd J Bouma
Seagrass meadows form highly productive and valuable ecosystems in the marine environment. Throughout the year, seagrass meadows are exposed to abiotic and biotic variations linked to (i) seasonal fluctuations, (ii) short-term stress events such as, e.g., local nutrient enrichment, and (iii) small-scale disturbances such as, e.g., biomass removal by grazing. We hypothesized that short-term stress events and small-scale disturbances may affect seagrass chance for survival in temperate latitudes. To test this hypothesis we focused on seagrass carbon reserves in the form of starch stored seasonally in rhizomes, as these have been defined as a good indicator for winter survival...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29449838/the-divergence-in-bacterial-components-associated-with-bactrocera-dorsalis-across-developmental-stages
#8
Xiaofeng Zhao, Xiaoyu Zhang, Zhenshi Chen, Zhen Wang, Yongyue Lu, Daifeng Cheng
Eco-evolutionary dynamics of microbiotas at the macroscale level are largely driven by ecological variables. The diet and living environment of the oriental fruit fly, Bactrocera dorsalis , diversify during development, providing a natural system to explore convergence, divergence, and repeatability in patterns of microbiota dynamics as a function of the host diet, phylogeny, and environment. Here, we characterized the microbiotas of 47 B. dorsalis individuals from three distinct populations by 16S rRNA amplicon sequencing...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29448546/microbially-induced-formation-of-fe-carbonates-by-metal-reducing-bacteria-enriched-from-a-co%C3%A2-repository-candidate-site
#9
Serku Kang, Yul Roh
The objectives of this research were to study the microbial diversity of metal-reducing bacteria enriched from sedimentary rock collected from a CO2 repository candidate site and to examine the effect that the bicarbonate concentration had on the iron reduction and biomineralization by the cultures. The enriched metal-reducing bacteria (i.e., JG-3) consisted mostly of Exiguobacterium sp. and Shewanella sp., and the microbial reduction of akaganeite (β-FeOOH), an Fe(III) oxyhydroxide, was examined over 7 days of bacterial cultivation at 30 °C under different concentrations of bicarbonate (0~210 mM)...
February 1, 2018: Journal of Nanoscience and Nanotechnology
https://www.readbyqxmd.com/read/29447476/sequencing-and-characterization-of-lncrnas-in-the-breast-muscle-of-gushi-and-arbor-acres-chicken
#10
Tuanhui Ren, Zhuanjian Li, Yu Zhou, Xuelian Liu, Ruili Han, Yongcai Wang, Fengbin Yan, Guirong Sun, Hong Li, Xiangtao Kang
Chicken muscle quality is one of the most important factors determining the economic value of poultry, and muscle development and growth are affected by genetics, environment, and nutrition. However, little is known about the molecular regulatory mechanisms of long non-coding RNAs (lncRNAs) in chicken skeletal muscle development. Our study aimed to better understand muscle development in chickens and thereby improve meat quality. In this study, Ribo-Zero RNA-Seq was used to investigate differences in the expression profiles of muscle development-related genes and associated pathways between Gushi (GS) and Arbor Acres (AA) chickens...
February 15, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29447391/comparative-analysis-of-epidermal-differentiation-genes-of-crocodilians-suggests-new-models-for-the-evolutionary-origin-of-avian-feather-proteins
#11
Karin Brigit Holthaus, Bettina Strasser, Julia Lachner, Supawadee Sukseree, Wolfgang Sipos, Anton Weissenbacher, Erwin Tschachler, Lorenzo Alibardi, Leopold Eckhart
The epidermis of amniotes forms a protective barrier against the environment and the differentiation program of keratinocytes, the main cell type in the epidermis, has undergone specific alterations in the course of adaptation of amniotes to a broad variety of environments and lifestyles. The epidermal differentiation complex (EDC) is a cluster of genes expressed at late stages of keratinocyte differentiation in both sauropsids and mammals. In the present study we identified and analyzed the crocodilian equivalent of the EDC...
February 12, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29447294/evidence-of-sex-bias-in-gene-expression-in-the-brain-transcriptome-of-two-populations-of-rainbow-trout-oncorhynchus-mykiss-with-divergent-life-histories
#12
Matthew C Hale, Garrett J McKinney, Frank P Thrower, Krista M Nichols
Sex-bias in gene expression is a mechanism that can generate phenotypic variance between the sexes, however, relatively little is known about how patterns of sex-bias vary during development, and how variable sex-bias is between different populations. To that end, we measured sex-bias in gene expression in the brain transcriptome of rainbow trout (Oncorhynchus mykiss) during the first two years of development. Our sampling included from the fry stage through to when O. mykiss either migrate to the ocean or remain resident and undergo sexual maturation...
2018: PloS One
https://www.readbyqxmd.com/read/29445901/geology-and-geochemistry-of-the-atacama-desert
#13
J Tapia, R González, B Townley, V Oliveros, F Álvarez, G Aguilar, A Menzies, M Calderón
The Atacama Desert, the driest of its kind on Earth, hosts a number of unique geological and geochemical features that make it unlike any other environment on the planet. Considering its location on the western border of South America, between 17 and 28 °S, its climate has been characterized as arid to hyperarid for at least the past 10 million years. Notably dry climatic conditions of the Atacama Desert have been related to uplift of the Andes and are believed to have played an important role in the development of the most distinctive features of this desert, including: (i) nitrates and iodine deposits in the Central Depression, (ii) secondary enrichment in porphyry copper deposits in the Precordillera, (iii) Li enrichment in salt flats of the Altiplano, and (iv) life in extreme habitats...
February 14, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29444173/transcriptome-variations-among-human-embryonic-stem-cell-lines-are-associated-with-their-differentiation-propensity
#14
Changbin Sun, Jiawen Zhang, Dongmin Zheng, Jian Wang, Huanming Yang, Xi Zhang
Human embryonic stem cells (hESCs) have the potential to form any cell type in the body, making them attractive cell sources in drug screening, regenerative medicine, disease and developmental processes modeling. However, not all hESC lines have the equal potency to generate desired cell types in vitro. Significant variations have been observed for the differentiation efficiency of various human ESC lines. The precise underpinning molecular mechanisms are still unclear. In this work, we compared transcriptome variations of four hESC lines H7, HUES1, HUES8 and HUES9...
2018: PloS One
https://www.readbyqxmd.com/read/29441565/metabolomics-and-transcriptomics-profiles-reveal-the-dysregulation-of-the-tricarboxylic-acid-cycle-and-related-mechanisms-in-prostate-cancer
#15
Yaping Shao, Guozhu Ye, Shancheng Ren, Hai-Long Piao, Xinjie Zhao, Xin Lu, Fubo Wang, Ma Wang, Jia Li, Peiyuan Yin, Tian Xia, Chuanliang Xu, Jane J Yu, Yinghao Sun, Guowang Xu
Genetic alterations drive metabolic reprogramming to meet increased biosynthetic precursor and energy demands for cancer cell proliferation and survival in unfavorable environments. A systematic study of gene-metabolite regulatory networks and metabolic dysregulation should reveal the molecular mechanisms underlying prostate cancer (PCa) pathogenesis. Herein, we performed gas chromatography-mass spectrometry (GC-MS)-based metabolomics and RNA-seq analyses in prostate tumors and matched adjacent normal tissues (ANTs) to elucidate the molecular alterations and potential underlying regulatory mechanisms in PCa...
February 14, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29440663/a-new-method-to-optimize-root-order-classification-based-on-the-diameter-interval-of-fine-root
#16
Ying Liu, Guoliang Wang, Kunxia Yu, Peng Li, Lie Xiao, Guobin Liu
Plant roots are a highly heterogeneous and hierarchical system. Although the root-order method is superior to the root diameter method for revealing differences in the morphology and physiology of fine roots, its complex partitioning limits its application. Whether root order can be determined by partitioning the main root based on its diameter remains uncertain. Four methods were employed for studying the morphological characteristics of seedling roots of two Pinus species in a natural and nitrogen-enriched environment...
February 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29439662/comparative-genome-analysis-of-52-fish-species-suggests-differential-associations-of-repetitive-elements-with-their-living-aquatic-environments
#17
Zihao Yuan, Shikai Liu, Tao Zhou, Changxu Tian, Lisui Bao, Rex Dunham, Zhanjiang Liu
BACKGROUND: Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. RESULTS: The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions...
February 13, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29435633/multi-layer-solid-phase-extraction-and-evaporation-enrichment-methods-for-polar-organic-chemicals-from-aqueous-matrices
#18
Niklas Köke, Daniel Zahn, Thomas P Knepper, Tobias Frömel
Analysis of polar organic chemicals in the aquatic environment is exacerbated by the lack of suitable and widely applicable enrichment methods. In this work, we assessed the suitability of a novel combination of well-known solid-phase extraction (SPE) materials in one cartridge as well as an evaporation method and for the enrichment of 26 polar model substances (predominantly log D < 0) covering a broad range of physico-chemical properties in three different aqueous matrices. The multi-layer solid-phase extraction (mlSPE) and evaporation method were investigated for the recovery and matrix effects of the model substances and analyzed with hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS)...
February 12, 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29434576/candidatus-nitrosocaldus-cavascurensis-an-ammonia-oxidizing-extremely-thermophilic-archaeon-with-a-highly-mobile-genome
#19
Sophie S Abby, Michael Melcher, Melina Kerou, Mart Krupovic, Michaela Stieglmeier, Claudia Rossel, Kevin Pfeifer, Christa Schleper
Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29433419/changes-in-tactile-function-during-intensive-bimanual-training-in-children-with-unilateral-spastic-cerebral-palsy
#20
Geoffroy Saussez, Marie Van Laethem, Yannick Bleyenheuft
Recently, an intensive bimanual intervention using sensory enriched materials resulted in improved tactile function in children with unilateral spastic cerebral palsy (USCP), raising the question of whether the observed tactile function improvement was due to the sensory enriched environment or the bimanual intervention per se. The present study investigates whether a bimanual intensive intervention improves tactile function. Nineteen children with USCP received 90 hours of bimanual training without enriched environment...
March 2018: Journal of Child Neurology
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