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https://www.readbyqxmd.com/read/29236189/manure-and-mineral-fertilization-change-enzyme-activity-and-bacterial-community-in-millet-rhizosphere-soils
#1
Lixia Xu, Min Yi, Huilan Yi, Erhu Guo, Aiying Zhang
Fertilization is a key agricultural practice for increasing millet yields and influencing soil properties, enzyme activities and rhizosphere bacterial communities. High throughput Illumina sequencing of the 16S rDNA was applied to compare the bacterial community structures and diversities among six different soil samples. The experiments involved the following: no fertilizer (CK), phosphate (P) and potassium (K) plus organic manure (M) (PKM), nitrogen (N) and K plus M (NKM), NPM, NPK and NPKM fertilization...
December 13, 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29234874/mmab-a-novel-candidate-gene-to-be-screened-in-the-molecular-diagnosis-of-mevalonate-kinase-deficiency
#2
Massimo Mezzavilla, Ronald Rodrigues Moura, Fulvio Celsi, Paola Maura Tricarico, Sergio Crovella
Mevalonate kinase deficiency (MKD) is an autosomal recessive inflammatory disease. Mutations in MVK gene are associated with MKD with modest genotype-phenotype correlation. In spite of recent guidelines indicating specific MVK mutations for the more severe form or the milder one, little is known about MVK variability within and between populations. The aim of this work is to provide supplementary information about MVK variability useful in the molecular diagnosis of MKD, as well as to unravel the presence of novel genes potentially involved as involved in the clinical heterogeneity of MKD phenotype...
December 12, 2017: Rheumatology International
https://www.readbyqxmd.com/read/29234312/parallelized-aerobic-single-carbon-source-enrichments-from-different-natural-environments-contain-divergent-microbial-communities
#3
Theodore M Flynn, Jason C Koval, Stephanie M Greenwald, Sarah M Owens, Kenneth M Kemner, Dionysios A Antonopoulos
Microbial communities that inhabit environments such as soil can contain thousands of distinct taxa, yet little is known about how this diversity is maintained in response to environmental perturbations such as changes in the availability of carbon. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29234140/altered-gut-microbiota-profiles-in-sows-and-neonatal-piglets-associated-with-porcine-epidemic-diarrhea-virus-infection
#4
Deping Song, Qi Peng, Yanjun Chen, Xinrong Zhou, Fanfan Zhang, Anqi Li, Dongyan Huang, Qiong Wu, Yu Ye, Houjun He, Leyi Wang, Yuxin Tang
Porcine epidemic diarrhea virus (PEDV) is a devastating cause of diarrhea in pigs worldwide. Most of studies have focused on molecular and pathogenic characterization of PEDV, whereas there were limited studies in understanding the role of gut microbiota (GM) in viral-associated diarrhea. Here, using the Illumina MiSeq platform, we examined and compared the impact of PEDV infection on the GM of sows and their piglets less than 10 days old. Our results showed that PEDV caused alternations in the structure and abundance of GM from levels of phylum to genus, and even species...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29232918/population-specific-associations-of-deleterious-rare-variants-in-coding-region-of-p2ry1-p2ry12-purinergic-receptor-genes-in-large-vessel-ischemic-stroke-patients
#5
Piotr K Janicki, Ceren Eyileten, Victor Ruiz-Velasco, Khaled Anwar Sedeek, Justyna Pordzik, Anna Czlonkowska, Iwona Kurkowska-Jastrzebska, Shigekazu Sugino, Yuka Imamura-Kawasawa, Dagmara Mirowska-Guzel, Marek Postula
The contribution of low-frequency and damaging genetic variants associated with platelet function to ischemic stroke (IS) susceptibility remains unknown. We employed a deep re-sequencing approach in Polish patients in order to investigate the contribution of rare variants (minor allele frequency, MAF < 1%) to the IS genetic susceptibility in this population. The genes selected for re-sequencing consisted of 26 genes coding for proteins associated with the surface membrane of platelets. Targeted pooled re-sequencing (Illumina HiSeq 2500) was performed on genomic DNA of 500 cases (patients with history of clinically proven diagnosis of large-vessel IS) and 500 controls...
December 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29231988/methylation-based-estimated-biological-age-and-cardiovascular-disease
#6
Lars Lind, Erik Ingelsson, Johan Sundström, Agneta Siegbahn, Erik Lampa
BACKGROUND: DNA methylation changes over life at specific sites in the genome, which can be used to estimate "biological age". The aim of this population-based longitudinal cohort study was to investigate the association between estimated biological age and incident cardiovascular disease (CVD). MATERIALS AND METHODS: Based on formulas published by Hannum et al and Horvath et al, "biological age" was calculated using data from the Illumina 450k Bead Methylation chip in 832 participants free from cardiovascular disease in the Prospective Study of the Vasculature in Uppsala Seniors (PIVUS) study (50% women, all aged 70 years at the examination)...
December 12, 2017: European Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29231925/expression-profiling-of-the-retina-of-pde6c-a-zebrafish-model-of-retinal-degeneration
#7
Liyun Zhang, Xinlian Zhang, Gaonan Zhang, Chi Pui Pang, Yuk Fai Leung, Mingzhi Zhang, Wenxuan Zhong
Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. The molecular basis of the retinal defect can potentially be determined by gene-expression profiling of the whole retina. In this study, we measured the gene-expression profile of retinas microdissected from a zebrafish pde6cw59 (pde6c) mutant. This retinal-degeneration model not only displays cone degeneration caused by a cone-specific mutation, but also other secondary cellular changes starting from 4 days postfertilization (dpf)...
December 12, 2017: Scientific Data
https://www.readbyqxmd.com/read/29231872/a-deeper-examination-of-thorellius-atrox-scorpion-venom-components-with-omic-techonologies
#8
Teresa Romero-Gutierrez, Esteban Peguero-Sanchez, Miguel A Cevallos, Cesar V F Batista, Ernesto Ortiz, Lourival D Possani
This communication reports a further examination of venom gland transcripts and venom composition of the Mexican scorpion Thorellius atrox using RNA-seq and tandem mass spectrometry. The RNA-seq, which was performed with the Illumina protocol, yielded more than 20,000 assembled transcripts. Following a database search and annotation strategy, 160 transcripts were identified, potentially coding for venom components. A novel sequence was identified that potentially codes for a peptide with similarity to spider ω-agatoxins, which act on voltage-gated calcium channels, not known before to exist in scorpion venoms...
December 12, 2017: Toxins
https://www.readbyqxmd.com/read/29230649/investigating-monsoon-and-post-monsoon-variabilities-of-bacterioplankton-communities-in-a-mangrove-ecosystem
#9
Anwesha Ghosh, Punyasloke Bhadury
In mangrove environments, bacterioplankton communities constitute an important component of aquatic biota and play a major role in ecosystem processes. Variability of bacterioplankton communities from Sundarbans mangrove, located in the Indian subcontinent in South Asia and sits on the apex of Bay of Bengal, was investigated over monsoon and post-monsoon seasons. The study was undertaken in two stations in Sundarbans using 16S rRNA clone library and Illumina MiSeq approaches with focus on the functionally important members that participate in coastal biogeochemical cycling...
December 11, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29230385/urinary-microbiome-and-psychological-factors-in-women-with-overactive-bladder
#10
Peng Wu, Yang Chen, Jie Zhao, Guihao Zhang, Jiawei Chen, Junpeng Wang, Huijian Zhang
Objectives: Emerging evidence indicates that alterations to the urinary microbiome are related to lower urinary tract symptoms. Overactive bladder (OAB) is a common disorder with complex etiologies and usually accompanied by psychological diseases. More information concerning the urinary microbiome and psychological factors in OAB is required. The aim of this study was to characterize the female urinary microbiome associated with OAB and investigate the relationships between urinary microbiome and psychological factors...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29230378/species-diversity-and-drivers-of-arbuscular-mycorrhizal-fungal-communities-in-a-semi-arid-mountain-in-china
#11
He Zhao, Xuanzhen Li, Zhiming Zhang, Yong Zhao, Jiantao Yang, Yiwei Zhu
Arbuscular mycorrhizal fungi (AMF) play an essential role in complex ecosystems. However, the species diversity and composition of AMF communities remain unclear in semi-arid mountains. Further, it is not well understood if the characteristics of AMF community assemblies differ for different habitat types, e.g., agricultural arable land, artificial forest land, natural grassland, and bush/wood land. Here, using the high-throughput technology by Illumina sequencing on the MiSeq platform, we explored the species diversity and composition of soil AMF communities among different habitat types in a semi-arid mountain (Taihang Mountain, Mid-western region of China)...
2017: PeerJ
https://www.readbyqxmd.com/read/29229636/topical-antibiotic-use-co-selects-for-the-carriage-of-mobile-genetic-elements-conferring-resistance-to-unrelated-antimicrobials-in-staphylococcus-aureus
#12
Glen P Carter, Mark B Schultz, Sarah L Baines, Anders Goncalves da Silva, Helen Heffernan, Audrey Tiong, Peter H Pham, Ian R Monk, Timothy P Stinear, Benjamin P Howden, Deborah A Williamson
Topical antibiotics such as mupirocin and fusidic acid are commonly used in the prevention and treatment of skin infections, particularly those caused by staphylococci. However, widespread use of these agents is associated with increased resistance to these agents, potentially limiting their efficacy. Of particular concern is the observation that resistance to topical antibiotics is often associated with multidrug resistance, suggesting that topical antibiotics may play a role in the emergence of multidrug-resistant (MDR) strains...
December 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29229569/the-hardy-rubber-tree-genome-provides-insights-into-the-evolution-of-polyisoprene-biosynthesis
#13
Ta-Na Wuyun, Lin Wang, Huimin Liu, Xuewen Wang, Liangsheng Zhang, Jeffrey L Bennetzen, Tiezhu Li, Lirong Yang, Panfeng Liu, Lanying Du, Lu Wang, Mengzhen Huang, Jun Qing, Lili Zhu, Wenquan Bao, Hongguo Li, Qingxin Du, Jingle Zhu, Hong Yang, Shuguang Yang, Hui Liu, Hui Yue, Jiang Hu, Guoliang Yu, Yu Tian, Fan Liang, Jingjing Hu, Depeng Wang, Ruiwen Gao, Dejun Li, Hongyan Du
Eucommia ulmoides is an economically important tree; however, the lack of its genome sequence restricts the theoretical and applied studies. Here we present a high-quality assembly of its ∼1.2 Gb genome (scaffold N50 = 1.88 Mb) with at least 26,723 predicted genes for E. ulmoides, the first sequenced genome of the order Garryales, which we obtained using an integrated strategy combining Illumina sequencing, Pacbio sequencing and Bionano mapping. As a sister taxon to lamiids and campanulids, the E. ulmoides underwent an ancient genome triplication shared by core eudicots but no further whole-genome duplication (WGD) in the last ∼125 million years...
December 8, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29229530/trichoderma-harzianum-mtcc-5179-impacts-the-population-and-functional-dynamics-of-microbial-community-in-the-rhizosphere-of-black-pepper-piper-nigrum-l
#14
Palaniyandi Umadevi, Muthuswamy Anandaraj, Vivek Srivastav, Sailas Benjamin
Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p=1...
November 29, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29228974/central-nervous-system-transcriptome-of-biomphalaria-alexandrina-an-intermediate-host-for-schistosomiasis
#15
Tamer A Mansour, Mohamed R Habib, Laura C Vicente Rodríguez, Anthony Hernández Vázquez, Julián Maldonado Alers, Alfredo Ghezzi, Roger P Croll, C Titus Brown, Mark W Miller
OBJECTIVE: Globally, more than 200 million people live at risk of the neglected tropical disease schistosomiasis (or snail fever). Larval schistosomes require the presence of specific snail species that act as intermediate hosts, supporting their multiplication and transformation into forms that can infect humans. This project was designed to generate a transcriptome from the central nervous system (CNS) of Biomphalaria alexandrina, the major intermediate host for Schistosoma mansoni in Egypt...
December 11, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29228314/demodifying-rna-for-transcriptomic-analyses-of-archival-formalin-fixed-paraffin-embedded-samples
#16
Leah C Wehmas, Charles E Wood, Remi Gagne, Andrew Williams, Carole Yauk, Mark M Gosink, Deidre Dalmas, Ruixin Hao, Raegan O'Lone, Susan Hester
Archival formalin-fixed paraffin-embedded (FFPE) tissue samples offer a vast but largely untapped resource for genomic research. The primary technical issues limiting use of FFPE samples are RNA yield and quality. In this study, we evaluated methods to demodify RNA highly fragmented and crosslinked by formalin fixation. Primary endpoints were RNA recovery, RNA-sequencing quality metrics, and transcriptional responses to a reference chemical (phenobarbital, PB). Frozen mouse liver samples from control and PB groups (n = 6/group) were divided and preserved for 3 months as follows: frozen (FR); 70% ethanol (OH); 10% buffered formalin for 18 hours followed by ethanol (18F); or 10% buffered formalin (3F)...
December 7, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29228270/influenza-a-virus-subtype-h9n2-infection-disrupts-the-composition-of-intestinal-microbiota-of-chickens
#17
Alexander Yitbarek, J Scott Weese, Tamiru Negash Alkie, John Parkinson, Shayan Sharif
The impact of low pathogenic influenza viruses such as subtype H9N2, which infect the respiratory and the gastrointestinal tracts of chickens, on microbial composition are not known. Twenty day-old specific pathogen free chickens were assigned to two treatment groups, control (Uninfected) and H9N2-infected (challenged via the oral-nasal route). Fecal genomic DNA was extracted, and the V3-V4 regions of the 16S rRNA gene was sequenced using the Illumina Miseq® platform. Sequences were curated using Mothur as described in the MiSeq SOP...
December 6, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29228248/comparison-of-the-intestinal-mucosal-microbiota-in-dogs-diagnosed-with-idiopathic-inflammatory-bowel-disease-and-dogs-with-food-responsive-diarrhea-before-and-after-treatment
#18
K Kalenyak, A Isaiah, R M Heilmann, J S Suchodolski, I A Burgener
We report the first study to evaluate the intestinal mucosal microbiota of dogs with inflammatory bowel disease (IBD) and dogs with food-responsive diarrhea (FRD) before and after treatment. It was hypothesized that differences in the microbial composition exist between both disease groups and within groups pre- vs. post-treatment. Duodenal and colonic biopsies were obtained endoscopically from 24 dogs (15 FRD, 9 IBD) before and after treatment. The intestinal microbiota was evaluated by Illumina sequencing of the bacterial 16S rRNA gene...
December 6, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29228055/transcriptional-profiling-of-sugarcane-leaves-and-roots-under-progressive-osmotic-stress-reveals-a-regulated-coordination-of-gene-expression-in-a-spatiotemporal-manner
#19
Alejandro Pereira-Santana, Edyciel J Alvarado-Robledo, Jesus A Zamora-Briseño, Jorge T Ayala-Sumuano, Victor M Gonzalez-Mendoza, Francisco Espadas-Gil, Luis D Alcaraz, Enrique Castaño, Miguel A Keb-Llanes, Felipe Sanchez-Teyer, Luis Carlos Rodriguez-Zapata
Sugarcane is one of the most important crops worldwide and is a key plant for the global production of sucrose. Sugarcane cultivation is severely affected by drought stress and it is considered as the major limiting factor for their productivity. In recent years, this plant has been subjected to intensive research focused on improving its resilience against water scarcity; particularly the molecular mechanisms in response to drought stress have become an underlying issue for its improvement. To better understand water stress and the molecular mechanisms we performed a de novo transcriptomic assembly of sugarcane (var...
2017: PloS One
https://www.readbyqxmd.com/read/29228005/rna-seq-reveals-transcriptome-changes-in-goats-following-myostatin-gene-knockout
#20
Lamei Wang, Bei Cai, Shiwei Zhou, Haijing Zhu, Lei Qu, Xiaolong Wang, Yulin Chen
Myostatin (MSTN) is a powerful negative regulator of skeletal muscle mass in mammalian species that is primarily expressed in skeletal muscles, and mutations of its encoding gene can result in the double-muscling trait. In this study, the CRISPR/Cas9 technique was used to edit MSTN in Shaanbei Cashmere goats and generate knockout animals. RNA sequencing was used to determine and compare the transcriptome profiles of the muscles from three wild-type (WT) goats, three fibroblast growth factor 5 (FGF5) knockout goats (FGF5+/- group) and three goats with disrupted expression of both the FGF5 and MSTN genes (FM+/- group)...
2017: PloS One
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