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https://www.readbyqxmd.com/read/28454035/occurrence-and-genetic-diversity-of-cryptosporidium-and-giardia-in-urban-wastewater-treatment-plants-in-north-eastern-spain
#1
Ana Ramo, Emilio Del Cacho, Caridad Sánchez-Acedo, Joaquín Quílez
This study was designed to investigate the presence and removal efficiency of Cryptosporidium and Giardia in wastewater treatment plants at the 20 most populated towns in Aragón (north-eastern Spain). Samples of influent and effluent wastewater and dewatered sewage sludge were collected seasonally from 23 plants and processed according to USEPA Method 1623. All samples from raw and treated wastewater tested positive for Giardia, at an average concentration of 3247±2039cysts/l and 50±28cysts/l, respectively...
April 25, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28453559/evaluation-of-the-reproducibility-of-amplicon-sequencing-with-illumina-miseq-platform
#2
Chongqing Wen, Liyou Wu, Yujia Qin, Joy D Van Nostrand, Daliang Ning, Bo Sun, Kai Xue, Feifei Liu, Ye Deng, Yuting Liang, Jizhong Zhou
Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33...
2017: PloS One
https://www.readbyqxmd.com/read/28453549/idiosyncratic-recognition-of-uug-uua-codons-by-modified-nucleoside-5-taurinomethyluridine-%C3%AF-m5u-present-at-wobble-position-in-anticodon-loop-of-trnaleu-a-molecular-modeling-approach
#3
Asmita S Kamble, Prayagraj M Fandilolu, Susmit B Sambhare, Kailas D Sonawane
Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the 'wobble' 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD) simulations of various anticodon stem loop (ASL) models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process...
2017: PloS One
https://www.readbyqxmd.com/read/28453515/reliable-reference-genes-for-normalization-of-gene-expression-data-in-tea-plants-camellia-sinensis-exposed-to-metal-stresses
#4
Ming-Le Wang, Qing-Hui Li, Hua-Hong Xin, Xuan Chen, Xu-Jun Zhu, Xing-Hui Li
Tea plants [Camellia sinensis (L.) O. Kuntze] are an important leaf-type crop that are widely used for the production of non-alcoholic beverages in the world. Exposure to excessive amounts of heavy metals adversely affects the quality and yield of tea leaves. To analyze the molecular responses of tea plants to heavy metals, a reliable quantification of gene expression is important and of major importance herein is the normalization of the measured expression levels for the target genes. Ideally, stably expressed reference genes should be evaluated in all experimental systems...
2017: PloS One
https://www.readbyqxmd.com/read/28449322/a-bacterium-with-close-genetic-identity-to-pseudomonas-mandelii-associated-with-spring-fish-kills-in-wild-bluegill-lepomis-macrochirus-rafinesque-and-pumpkinseed-sunfish-lepomis-gibbosus-linnaeus
#5
J Lovy, D Dicarlo-Emery, J M Hutcheson
Pseudomonas fluorescens are known bacterial pathogens in fish. The P. fluorescens group contains at least nine different bacterial species, although species from fish have rarely been differentiated. Two isolated fish kills affecting wild bluegills, Lepomis macrochirus Rafinesque, and pumpkinseed sunfish, Lepomis gibbosus (Linnaeus), occurred in the spring of 2015 during cool water temperatures (12.5°C-15.5°C). Disease signs included severe bacteraemia with rare gross external signs. Pure bacterial cultures isolated from kidneys of all affected fish were identified as P...
April 27, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28449118/polyphosphate-accumulating-bacterial-community-colonizing-the-calcium-bodies-of-terrestrial-isopod-crustaceans-titanethes-albus-and-hyloniscus-riparius
#6
Rok Kostanjšek, Vittori Miloš, Vesna Srot, Peter A van Aken, Štrus Jasna
Terrestrial isopods from the group Trichoniscidae accumulate calcium in specialized organs, known as the calcium bodies. These consist of two pairs of epithelial sacs located alongside the digestive system. These organs contain various forms of calcium and constantly present bacteria. To elucidate their origin and role, we analyzed the bacteria of the calcium bodies in the cave-dwelling isopod Titanethes albus and the epigean species Hyloniscus riparius, by microscopy, histochemistry, energy dispersive X-ray spectrometry, 16S rRNA analysis and in situ hybridization...
April 25, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28449106/microbiomeanalyst-a-web-based-tool-for-comprehensive-statistical-visual-and-meta-analysis-of-microbiome-data
#7
Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L King, Luis B Agellon, Jianguo Xia
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449079/small-non-coding-rna-and-cancer
#8
Giulia Romano, Dario Veneziano, Mario Acunzo, Carlo M Croce
The ENCODE project has reported that at least 80% of the human genome is biologically active, yet only a small part of human DNA encodes for protein. The massive amount of RNA transcribed but not translated into protein can be classified as housekeeping RNA (such as rRNA, tRNA) and regulatory RNA (such as miRNA, piRNA, lncRNA). Small non-coding RNAs, in particular, have been the focus of many studies in the last 20 years and their fundamental role in many human diseases is currently well established. Inter alia, their role in cancer development and progression, as well as in drug resistance, is being increasingly investigated...
April 26, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28449065/a-homozygous-missense-mutation-in-eral1-encoding-a-mitochondrial-rrna-chaperone-causes-perrault-syndrome
#9
Iliana A Chatzispyrou, Marielle Alders, Sergio Guerrero-Castillo, Ruben Zapata Perez, Martin A Haagmans, Laurent Mouchiroud, Janet Koster, Rob Ofman, Frank Baas, Hans R Waterham, Johannes N Spelbrink, Johan Auwerx, Marcel M Mannens, Riekelt H Houtkooper, Astrid S Plomp
Perrault syndrome (PS) is a rare recessive disorder characterized by ovarian dysgenesis and sensorineural deafness. It is clinically and genetically heterogeneous, and previously mutations have been described in different genes, mostly related to mitochondrial proteostasis. We diagnosed three unrelated females with PS and set out to identify the underlying genetic cause using exome sequencing. We excluded mutations in the known PS genes, but identified a single homozygous mutation in the ERAL1 gene (c.707A>T; p...
April 25, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28448941/geochemistry-and-microbial-diversity-of-cave-waters-in-the-gypsum-karst-aquifers-of-emilia-romagna-region-italy
#10
Ilenia M D'Angeli, Diana I Serrazanetti, Chiara Montanari, Lucia Vannini, Fausto Gardini, Jo De Waele
Fifty-seven control points of waters (sinking streams, rivers in caves, and resurgences) hosted in gypsum karst areas in Emilia Romagna region (N-Italy) were sampled in the framework of a Project LIFE+08NAT/IT/000369 "Gypsum" in the period 2010-2014. The microbiology and chemistry of these waters have been analyzed to evaluate the impact of human activities or natural factors, in the gypsum karst systems. Waters have been analyzed for major chemistry (Ca, Mg, Na, K, SO4, HCO3, Cl, NO3) and some minor constituents (F, Br, NH4 and PO4), measuring pH, electric conductivity (EC), total dissolved solids (TDS) and temperature (T) in situ...
April 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28448623/development-of-the-cutaneous-microbiome-in-the-preterm-infant-a-prospective-longitudinal-study
#11
Mohan Pammi, Jacqueline L O'Brien, Nadim J Ajami, Matthew C Wong, James Versalovic, Joseph F Petrosino
BACKGROUND: Neonatal sepsis in preterm infants is often due to organisms that colonize the skin including Staphylococcus spp. and Candida spp. Development and maturation of the skin microbiome in the neonatal period, especially in preterm infants, may be critical in preventing colonization with pathogens and subsequent progression to neonatal sepsis. Development of the skin microbiome in preterm infants or its determinants in the first 4 weeks of life has not been evaluated. METHODS: We evaluated the skin microbiome from three body sites, antecubital fossa, forehead and gluteal region, in a prospective cohort of 15 preterm (birth weight < 1500 g and < 32 weeks of gestation) and 15 term neonates...
2017: PloS One
https://www.readbyqxmd.com/read/28448583/characterization-of-the-fecal-microbiome-during-neonatal-and-early-pediatric-development-in-puppies
#12
Blake C Guard, Hanna Mila, Jörg M Steiner, Claire Mariani, Jan S Suchodolski, Sylvie Chastant-Maillard
Limited information is available describing the development of the neonatal fecal microbiome in dogs. Feces from puppies were collected at 2, 21, 42, and 56 days after birth. Feces were also collected from the puppies' mothers at a single time point within 24 hours after parturition. DNA was extracted from fecal samples and 454-pyrosequencing was used to profile 16S rRNA genes. Species richness continued to increase significantly from 2 days of age until 42 days of age in puppies. Furthermore, microbial communities clustered separately from each other at 2, 21, and 42 days of age...
2017: PloS One
https://www.readbyqxmd.com/read/28447395/land-scale-biogeography-of-arsenic-biotransformation-genes-in-estuarine-wetland
#13
Si-Yu Zhang, Jian-Qiang Su, Guo-Xin Sun, Yunfeng Yang, Yi Zhao, Junjun Ding, Yong-Shan Chen, Yu Shen, Guibing Zhu, Christopher Rensing, Yong-Guan Zhu
As an analog of phosphorus, arsenic (As) has a biogeochemical cycle coupled closely with other key elements on the Earth, such as iron, sulfate and phosphate. It has been documented that microbial genes associated with As biotransformation are widely present in As-rich environments. Nonetheless, their presence in natural environment with low As levels remains unclear. To address this issue, we investigated the abundance levels and diversities of aioA, arrA, arsC and arsM genes in estuarine sediments at low As levels across Southeastern China to uncover biogeographic patterns at a large spatial scale...
April 26, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28447044/molecular-and-phylogenetic-characterization-of-thelohanellus-boggoti-qadri-1962-cnidaria-myxosporea-bivalvulida-infecting-the-fin-of-indian-minor-carp-labeo-dero-hamilton-1822
#14
Harpreet Kaur, Aditya Gupta
A myxozoan parasite belonging to the genus Thelohanellus Kudo, 1933 (Cnidaria, Myxosporea, Bivalvulida) was isolated from the fins of Labeo dero inhabiting Ranjit Sagar Wetland, Punjab, India. The plasmodium was 0.5-0.7 mm in diameter each containing 80- 100 number of myxospores. Myxospores were egg shaped to ovoidal in valvular view having bluntly pointed anterior and broad rounded posterior end measuring 8.36x 4.77 µm. Polar capsule was single, broadly pyriform in shape, measuring 4.77x3.98 µm in size containing a polar filament coiled perpendicular to the longitudinal axis of myxospore body making 7-9 turns...
March 2017: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28446899/clonal-spread-of-16s-rrna-methyltransferase-producing-klebsiella-pneumoniae-st37-with-high-prevalence-of-esbls-from-companion-animals-in-china
#15
Jing Xia, Liang-Xing Fang, Ke Cheng, Guo-Hao Xu, Xi-Ran Wang, Xiao-Ping Liao, Ya-Hong Liu, Jian Sun
We screened 30 Klebsiella pneumoniae isolates from dogs and cats at a single animal hospital in Guangdong Province, China. Among them, 12 K. pneumoniae strains possessed high-level resistance to amikacin and gentamicin and these were screened for 16S rRNA methyltransferase (16S-RMTase) genes. And then the genes positive isolates were detected for ESBLs (extended spectrum β-lactamases) and analyzed by pulsed-field gel electrophoresis, multilocus sequence typing, PCR-based replicon typing and plasmid analysis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28445008/prevalence-of-complement-mediated-cell-lysis-like-gene-sicg-in-streptococcus-dysgalactiae-subsp-equisimilis-isolates-from-japan-2014-2016
#16
Takashi Takahashi, Tomohiro Fujita, Akiyoshi Shibayama, Yuzo Tsuyuki, Haruno Yoshida
BACKGROUND: Streptococcus dysgalactiae subsp. equisimilis (SDSE; a β-hemolytic streptococcus of human or animal origin) infections are emerging worldwide. We evaluated the clonal distribution of complement-mediated cell lysis-like gene (sicG) among SDSE isolates from three central prefectures of Japan. METHODS: Group G/C β-hemolytic streptococci were collected from three institutions from April 2014 to March 2016. Fifty-five strains (52 from humans and three from animals) were identified as SDSE on the basis of 16S rRNA sequencing data...
July 2017: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/28444508/study-protocol-on-the-role-of-intestinal-microbiota-in-colorectal-cancer-treatment-a-pathway-to-personalized-medicine-2-0
#17
R Aarnoutse, J M P G M de Vos-Geelen, J Penders, E G Boerma, F A R M Warmerdam, B Goorts, S W M Olde Damink, Z Soons, S S M Rensen, M L Smidt
PURPOSE: Investigate in patients with metastatic and/or irresectable colorectal cancer treated with systemic treatment with capecitabine or TAS-102 whether: 1. Intestinal microbiota composition can act as a predictor for response. 2. Intestinal microbiota composition changes during systemic treatment and its relation to chemotoxicity. BACKGROUND: Gut microbiota and host determinants evolve in symbiotic and dependent relationships resulting in a personal ecosystem...
April 25, 2017: International Journal of Colorectal Disease
https://www.readbyqxmd.com/read/28444190/biological-aging-and-the-human-gut-microbiota
#18
Vincent J Maffei, Sangkyu Kim, Eugene Blanchard, Meng Luo, S Michal Jazwinski, Christopher M Taylor, David A Welsh
The human gastrointestinal microbiota plays a key homeostatic role in normal functioning of physiologic processes commonly undermined by aging. We used a previously validated 34-item frailty index (FI34) to identify changes in gut microbiota community structure associated with biological age of community-dwelling adults. Stool 16S rRNA cDNA libraries from 85 subjects ranging in age (43-79) and FI34 score (0-0.365) were deep sequenced, denoised, and clustered using DADA2. Subject biological age but not chronological age correlated with a decrease in stool microbial diversity...
April 25, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28443847/the-impact-of-dietary-sn-2-palmitic-triacylglycerols-in-combination-with-docosahexaenoic-acid-or-arachidonic-acid-on-lipid-metabolism-and-host-faecal-microbiota-composition-in-sprague-dawley-rats
#19
Jianchun Wan, Songyou Hu, Jörg J Jacoby, Jie Liu, Yaqiong Zhang, Liangli Lucy Yu
Sn-2 palmitic acid triacylglycerols (sn2PA fat) and polyunsaturated fatty acids are thought to influence the metabolic status and intestinal bacterial population of the host. In this study, the impact of sn2PA fat in combination with DHA or ARA in the diet on lipid metabolism in the liver and faecal microbiota composition were investigated in rats fed diets containing sn2PA fat, 90% sn2PA fat + 10% DHA oil (wt%), or 90% sn2PA fat + 10% ARA oil (wt%). Tissue fatty acid composition was measured using gas chromatography (GC), whereas the faecal microbial composition was assessed using 16S rRNA high-throughput sequencing technology...
April 26, 2017: Food & Function
https://www.readbyqxmd.com/read/28443082/inbred-mouse-populations-exhibit-intergenerational-changes-in-intestinal-microbiota-composition-and-function-following-introduction-to-a-facility
#20
Jocelyn M Choo, Paul J Trim, Lex E X Leong, Guy C J Abell, Carly Brune, Nicole Jeffries, Steve Wesselingh, T N Dear, Marten F Snel, Geraint B Rogers
Inbred mice are used to investigate many aspects of human physiology, including susceptibility to disease and response to therapies. Despite increasing evidence that the composition and function of the murine intestinal microbiota can substantially influence a broad range of experimental outcomes, relatively little is known about microbiome dynamics within experimental mouse populations. We investigated changes in the intestinal microbiome between C57BL/6J mice spanning six generations (assessed at generations 1, 2, 3, and 6), following their introduction to a stringently controlled facility...
2017: Frontiers in Microbiology
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