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https://www.readbyqxmd.com/read/29768545/hcmv-ul97-phosphotransferase-gene-mutations-may-be-associated-with-antiviral-resistance-in-immunocompromised-patients-in-bel%C3%A3-m-pa-northern-brazil
#1
Dorotéa de Fátima Lobato da Silva, Jedson Ferreira Cardoso, Sandro Patroca da Silva, Leda Mani França Arruda, Renato Lopes Fernandes de Medeiros, Marluce Matos Moraes, Rita Catarina Medeiros Sousa
INTRODUCTION: Human cytomegalovirus is one of the causes of opportunist infections in immunocompromised patients, and is triggered by factors such as state of viral latency, weakened immune responses, and development of antiviral resistance to ganciclovir, the only drug offered by the public health system in Brazil to treat the infection. The goal of this study was to identify mutations that may be associated with antiviral resistance in immunocompromised patients. METHODS: Molecular analysis was performed in 82 blood samples and subjected to genomic DNA extraction by a silica-based method...
March 2018: Revista da Sociedade Brasileira de Medicina Tropical
https://www.readbyqxmd.com/read/29765558/the-fallopian-tube-microbiome-implications-for-reproductive-health
#2
Elise S Pelzer, Dana Willner, Melissa Buttini, Louise M Hafner, Christina Theodoropoulos, Flavia Huygens
Objective: There is a paucity of data characterizing the microbiota of the female upper genital tract, which controversially is described as a sterile site. We examine whether the fallopian tube harbours an endogenous microbial community. Design: This prospective study collected from women undergoing total hysterectomy or salpingectomy-oophorectomy. Setting: Private hospital gynaecology department. Patients: Fallopian tubes were collected from women diagnosed with benign disease or for prophylaxis...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29765364/rearing-water-treatment-induces-microbial-selection-influencing-the-microbiota-and-pathogen-associated-transcripts-of-cod-gadus-morhua-larvae
#3
Ragnhild I Vestrum, Kari J K Attramadal, Per Winge, Keshuai Li, Yngvar Olsen, Atle M Bones, Olav Vadstein, Ingrid Bakke
We have previously shown that K-selection and microbial stability in the rearing water increases survival and growth of Atlantic cod ( Gadus morhua ) larvae, and that recirculating aquaculture systems (RAS) are compatible with this. Here, we have assessed how water treatment influenced the larval microbiota and host responses at the gene expression level. Cod larvae were reared with two different rearing water systems: a RAS and a flow-through system (FTS). The water microbiota was examined using a 16S rDNA PCR/DGGE strategy...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29762666/discovery-and-validation-of-methylation-biomarkers-for-ulcerative-colitis-associated-neoplasia
#4
Andrew D Beggs, Jonathan James, Germaine Caldwell, Toby Prout, Mark P Dilworth, Phillipe Taniere, Tariq Iqbal, Dion G Morton, Glenn Matthews
Background and aims: Ulcerative colitis (UC) is associated with a higher background risk of dysplasia and/or neoplasia due to chronic inflammation. There exist few biomarkers for identification of patients with dysplasia, and targeted biopsies in this group of patients are inaccurate in reliably identifying dysplasia. We aimed to examine the epigenome of UC dysplasia and to identify and validate potential biomarkers. Methods: Colonic samples from patients with UC-associated dysplasia or neoplasia underwent epigenome-wide analysis on the Illumina 450K methylation array...
May 14, 2018: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/29760911/strong-associations-between-plant-genotypes-and-bacterial-communities-in-a-natural-salt-marsh
#5
Gregory P Zogg, Steven E Travis, Daniel A Brazeau
Although microbial communities have been shown to vary among plant genotypes in a number of experiments in terrestrial ecosystems, relatively little is known about this relationship under natural conditions and outside of select model systems. We reasoned that a salt marsh ecosystem, which is characterized by twice-daily flooding by tides, would serve as a particularly conservative test of the strength of plant-microbial associations, given the high degree of abiotic regulation of microbial community assembly resulting from alternating periods of inundation and exposure...
May 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29758902/organic-carbon-source-and-salinity-shape-sediment-bacterial-composition-in-two-china-marginal-seas-and-their-major-tributaries
#6
Kai Wang, Li Zou, Xinxin Lu, Xiaozhen Mou
Marginal sea sediments receive organic substrates of different origins, but whether and to what extent sediment microbial communities are reflective of the different sources of organic substrates remain unclear. To address these questions, sediment samples were collected in two connected China marginal seas, i.e., Bohai Sea and Yellow Sea, and their two major tributaries (Yellow River and Liao River). Sediment bacterial community composition (BCC) was examined using 16S rRNA gene pyrosequencing. In addition, physicochemical variables that describe environmental conditions and sediment features were measured...
August 15, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29756208/impact-of-loss-of-function-mutations-at-the-rnf43-locus-on-colorectal-cancer-development-and-progression
#7
Tsugio Eto, Keisuke Miyake, Katsuhiko Nosho, Masaki Ohmuraya, Yu Imamura, Kota Arima, Shinichi Kanno, Lingfeng Fu, Yuki Kiyozumi, Daisuke Izumi, Hidetaka Sugihara, Yukiharu Hiyoshi, Yuji Miyamoto, Hiroshi Sawayama, Masaaki Iwatsuki, Yoshifumi Baba, Naoya Yoshida, Toru Furukawa, Kimi Araki, Hideo Baba, Takatsugu Ishimoto
RNF43 mutations are frequently detected in colorectal cancer cells and lead to a loss of function of the ubiquitin E3 ligase. Here, we investigated the clinical significance of RNF43 mutations in a large Japanese cohort and the role of RNF43 at various stages of colorectal cancer development and progression. Mutation analysis of the RNF43 gene locus using pyrosequencing technology detected RNF43 hotspot mutations in 1 (0.88%) of 113 colorectal polyp cases and 30 (6.45%) of 465 colorectal cancer cases. Moreover, patients with colorectal cancer harboring mutated RNF43 experienced a higher recurrence rate than those harboring non-mutated RNF43...
May 13, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29755690/prognostic-value-of-line-1-methylation-level-in-321-patients-with-primary-liver-cancer-including-hepatocellular-carcinoma-and-intrahepatic-cholangiocarcinoma
#8
Tatsunori Miyata, Yo-Ichi Yamashita, Yoshifumi Baba, Kazuto Harada, Takanobu Yamao, Naoki Umezaki, Masayo Tsukamoto, Yuki Kitano, Kensuke Yamamura, Kota Arima, Shigeki Nakagawa, Hirohisa Okabe, Katsunori Imai, Daisuke Hashimoto, Akira Chikamoto, Mototsugu Shimokawa, Hideo Baba
Background: The methylation level of long interspersed nucleotide element-1 (LINE-1) is a good surrogate marker of the global DNA methylation level. The relationship between LINE-1 methylation level and prognosis in primary liver cancer (PLC) patients remains unclear. Results: LINE-1 methylation levels were significantly lower in HCC and cHCC-CC tissues, but not in ICC tissues, than those in noncancerous liver parenchyma (HCC: p < 0.0001; cHCC-CC: p < 0.001; and ICC: p = 0...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29755656/single-walled-and-multi-walled-carbon-nanotubes-induce-sequence-specific-epigenetic-alterations-in-16-hbe-cells
#9
Manosij Ghosh, Deniz Öner, Radu C Duca, Bram Bekaert, Jeroen A J Vanoirbeek, Lode Godderis, Peter H M Hoet
Recent studies have identified carbon nanotube (CNT)-induced epigenetic changes as one of the key players in patho-physiological response. In the present study, we investigated whether CNT exposure is associated with epigenetic changes in human bronchial epithelial cells (16 HBE), in vitro . We focused on global DNA methylation, methylation of LINE-1 elements and promoter sequence of twelve functionally important genes ( SKI, DNMT1, HDAC4 , NPAT, ATM, BCL2L11, MAP3K10, PIK3R2, MYO1C, TCF3, FGFR 1 and AGRN )...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29755446/different-diversity-and-distribution-of-archaeal-community-in-the-aqueous-and-oil-phases-of-production-fluid-from-high-temperature-petroleum-reservoirs
#10
Bo Liang, Kai Zhang, Li-Ying Wang, Jin-Feng Liu, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu
To get a better knowledge on how archaeal communities differ between the oil and aqueous phases and whether environmental factors promote substantial differences on microbial distributions among production wells, we analyzed archaeal communities in oil and aqueous phases from four high-temperature petroleum reservoirs (55-65°C) by using 16S rRNA gene based 454 pyrosequencing. Obvious dissimilarity of the archaeal composition between aqueous and oil phases in each independent production wells was observed, especially in production wells with higher water cut, and diversity in the oil phase was much higher than that in the corresponding aqueous phase...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29752127/implementation-of-next-generation-sequencing-technology-for-somatic-mutation-detection-in-routine-laboratory-practice
#11
Tindaro Giardina, Cleo Robinson, Fabienne Grieu-Iacopetta, Michael Millward, Barry Iacopetta, Dominic Spagnolo, Benhur Amanuel
The introduction of next generation sequencing (NGS) in the routine diagnostic setting is still in the development phase and has been limited by its complexity. Targeted NGS offers an attractive alternative to performing multiple single target assays and is very useful in meeting the increasing clinical demand for testing of multiple genetic aberrations in cancer specimens. To this end, we carried out a blinded validation study on 113 tumours in a diagnostic laboratory and compared mutation results from targeted NGS with those from Sanger sequencing, pyrosequencing, competitive allele specific TaqMan polymerase chain reaction (CAST PCR) and Cobas assays...
May 8, 2018: Pathology
https://www.readbyqxmd.com/read/29748401/genome-sequence-of-bacillus-cereus-strain-tg1-6-a-plant-beneficial-rhizobacterium-that-is-highly-salt-tolerant
#12
Juan Ignacio Vílchez, Qiming Tang, Richa Kaushal, Shenglan Chen, Renyi Liu, Huiming Zhang
The complete genome sequence of Bacillus cereus strain TG1-6, which is a highly salt-tolerant rhizobacterium that enhances plant tolerance to drought stress, is reported here. The sequencing process was performed based on a combination of pyrosequencing and single-molecule sequencing. The complete genome is estimated to be approximately 5.42 Mb, containing a total of 5,610 predicted protein-coding DNA sequences (CDSs).
May 10, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29746519/diversity-and-potential-activity-patterns-of-planktonic-eukaryotic-microbes-in-a-mesoeutrophic-coastal-area-eastern-english-channel
#13
Sara Rachik, Urania Christaki, Luen Luen Li, Savvas Genitsaris, Elsa Breton, Sébastien Monchy
The diversity of planktonic eukaryotic microbes was studied at a coastal station of the eastern English Channel (EEC) from March 2011 to July 2015 (77 samples) using high throughput sequencing (454-pyrosequencing and Illumina) of the V2-V3 hypervariable region of the 18S SSU rDNA gene. Similar estimations of OTU relative abundance and taxonomic distribution for the dominant higher taxonomic groups (contributing >1% of the total number of OTUs) were observed with the two methods (Kolmogorov-Smirnov p-value = 0...
2018: PloS One
https://www.readbyqxmd.com/read/29744782/comparative-study-on-the-gut-microbiotas-of-four-economically-important-asian-carp-species
#14
Xinghao Li, Yuhe Yu, Chang Li, Qingyun Yan
Gut microbiota of four economically important Asian carp species (silver carp, Hypophthalmichthys molitrix; bighead carp, Hypophthalmichthys nobilis; grass carp, Ctenopharyngodon idella; common carp, Cyprinus carpio) were compared using 16S rRNA gene pyrosequencing. Analysis of more than 590,000 quality-filtered sequences obtained from the foregut, midgut and hindgut of these four carp species revealed high microbial diversity among the samples. The foregut samples of grass carp exhibited more than 1,600 operational taxonomy units (OTUs) and the highest alpha-diversity index, followed by the silver carp foregut and midgut...
May 7, 2018: Science China. Life Sciences
https://www.readbyqxmd.com/read/29743058/abnormal-pitx1-gene-methylation-in-adolescent-idiopathic-scoliosis-a-pilot-study
#15
Benlong Shi, Liang Xu, Saihu Mao, Leilei Xu, Zhen Liu, Xu Sun, Zezhang Zhu, Yong Qiu
BACKGROUND: The gene of pituitary homeobox 1 (PITX1) has been reported to be down-regulated in adolescent idiopathic scoliosis (AIS), of which the cause has not been well addressed. The abnormal DNA methylation was recently assumed to be an important mechanism for the down-regulated genes expression. However, the association between PITX1 promoter methylation and the etiology of AIS was not clear. METHODS: The peripheral blood samples of 50 AIS patients and 50 healthy controls were collected and the genomic DNA was extracted...
May 9, 2018: BMC Musculoskeletal Disorders
https://www.readbyqxmd.com/read/29742980/bacterial-community-analysis-in-three-types-of-the-fermented-seafood-jeotgal-produced-in-south-korea
#16
Eun-Ji Song, Eun-Sook Lee, So-Lim Park, Hak-Jong Choi, Seong Woon Roh, Young-Do Nam
Jeotgal is a traditional Korean seafood fermented by indigenous microbes. The bacterial community in five myeolchi-jeot (Engraulis japonica), five meongge-jeot (Halocynthia roretzi), and six saeu-jeot (Acetes japonicas) produced in South Korea was analyzed by barcoded pyrosequencing targeting the V1/V2 hyper-variable regions of the 16S rRNA gene. All samples were dominated by the phyla Firmicutes, which represented 67.7% (SD = 27.2%) of the population. Tetragenococcus halophilus and Tetragenococcus muriaticus were the predominant species in myeolchi-jeot...
May 9, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29739114/mutations-in-core-gene-region-of-hepatitis-b-virus-in-patients-with-chronic-hepatitis-b
#17
Sevgi Ciftci, Fahriye Keskin, Neslihan Abaci, Filiz Akyuz, Aris Cakiris, Selim Badur, Sabahattin Kaymakoglu, Duran Ustek
BACKGROUND: The HBV core protein plays a major role in host immune response. Mutations occurring in the HBV core gene may cause alterations in the major epitopes being effective in the host immune response. Until now, the persistent effects of core gene mutations on HBV infections have not been fully understood. The aim of this study is to analyze the core gene mutations for epitopes in the T lymphocytes [T helper (Th) and cytotoxic (CTL)] and B cell and C terminal region in patients with chronic hepatitis using ultra-deep pyrosequencing (UDPS) method...
March 1, 2018: Clinical Laboratory
https://www.readbyqxmd.com/read/29735783/antiproliferative-effects-of-epigenetic-modifier-drugs-through-e-cadherin-up-regulation-in-liver-cancer-cell-lines
#18
Diego Uribe, Andres Cardona, Davide Degli Esposti, Marie-Pierre Cros, Cyrille Cuenin, Zdenko Herceg, Mauricio Camargo, Fabian M Cortés-Mancera
INTRODUCTION: Epigenetic alterations play an essential role in cancer onset and progression, thus studies of drugs targeting the epigenetic machinery are a principal concern for cancer treatment. Here, we evaluated the potential of the combination of the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5aza-dC) and the pan-deacetylase inhibitor Trichostatin A (TSA), at low cytotoxic concentrations, to modulate the canonical Wnt/β-catenin pathway in liver cancer cells. MATERIAL AND METHODS: Pyrosequencing was used for DNA methylation analyses of LINE-1 sequences and the Wnt/β-catenin pathway antagonist DKK3, SFRP1, WIF1 and CDH1...
April 9, 2018: Annals of Hepatology
https://www.readbyqxmd.com/read/29734589/population-and-community-structure-shifts-of-ammonia-oxidizers-after-four-year-successive-biochar-application-to-agricultural-acidic-and-alkaline-soils
#19
Lili He, Yucui Bi, Jin Zhao, Cameron M Pittelkow, Xu Zhao, Shenqiang Wang, Guangxi Xing
Long-term studies that advance our mechanistic understanding of biochar (BC)‑nitrogen (N) interactions in agricultural soils are lacking. In this study, soil potential nitrification rates (PNR), the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities following 4-year of BC application were investigated using the shaken-slurry procedure and molecular sequencing techniques for an acidic Oxisol (QU) and an alkaline Cambisol (YU). Soils were obtained from an outdoor soil column experiment with straw-BC application rates of 0 (BC0), 2...
April 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29732726/functional-characterisation-of-the-osteoarthritis-genetic-risk-residing-at-aldh1a2-identifies-rs12915901-as-a-key-target-variant
#20
Colin Shepherd, Dongxing Zhu, Andrew J Skelton, Jennifer Combe, Harrison Threadgold, Linyi Zhu, Tonia L Vincent, Paul Stuart, Louise N Reynard, John Loughlin
OBJECTIVE: To identify the functional single nucleotide polymorphisms (SNPs) and mechanisms conferring increased hand osteoarthritis (OA) risk at the ALDH1A2 locus, which is a retinoic acid (RA) regulatory gene. METHODS: Tissues from 247 knee, hip or hand OA patients who had undergone joint surgery were included. RNA-sequencing was used to investigate differential expression of ALDH1A2 and other RA signalling pathway genes in cartilage. ALDH1A2 expression in multiple joint tissues was quantified by qPCR...
May 6, 2018: Arthritis & Rheumatology
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