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https://www.readbyqxmd.com/read/28079802/promoter-methylation-of-yes-associated-protein-yap1-gene-in-polycystic-ovary-syndrome
#1
Li-Le Jiang, Juan-Ke Xie, Jin-Quan Cui, Duo Wei, Bao-Li Yin, Ya-Nan Zhang, Yuan-Hui Chen, Xiao Han, Qian Wang, Cui-Lian Zhang
BACKGROUND: DNA methylation modification has been proved to influence the phenotype of polycystic ovary syndrome (PCOS). Genome-wide association studies (GWAS) demonstrate that yes-associated protein (YAP1) genetic sites are associated with PCOS. The study aims to detect the methylation status of YAP1 promoter in ovary granulosa cells (GCs) of PCOS patients and explore novel therapeutic targets for PCOS. METHODS: Randomized controlled trial was applied and a total of 72 women were included in the study, including 36 cases of PCOS patients and 36 cases of health controls...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28076823/guazuma-ulmifolia-bark-synthesized-ag-au-and-ag-au-alloy-nanoparticles-photocatalytic-potential-dna-protein-interactions-anticancer-activity-and-toxicity-against-14-species-of-microbial-pathogens
#2
Viswanathan Karthika, Ayyakannu Arumugam, Kasi Gopinath, Periyannan Kaleeswarran, Marimuthu Govindarajan, Naiyf S Alharbi, Shine Kadaikunnan, Jamal M Khaled, Giovanni Benelli
In the present study, we focused on a quick and green method to fabricate Ag, Au and Ag/Au alloy nanoparticles (NPs) using the bark extract of Guazuma ulmifolia L. Green synthesized metal NPs were characterized using different techniques, including UV-Vis spectroscopy, FT-IR, XRD, AFM and HR-TEM analyses. The production of Ag, Au and Ag/Au alloy NPs was observed monitoring color change from colorless to brown, followed by pink and dark brown, as confirmed by UV-Vis spectroscopy characteristic peaks at 436, 522 and 510nm, respectively...
January 4, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28074246/draft-genome-of-scalindua-rubra-obtained-from-the-interface-above-the-discovery-deep-brine-in-the-red-sea-sheds-light-on-potential-salt-adaptation-strategies-in-anammox-bacteria
#3
Daan R Speth, Ilias Lagkouvardos, Yong Wang, Pei-Yuan Qian, Bas E Dutilh, Mike S M Jetten
Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua...
January 10, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28070089/development-of-a-one-run-real-time-pcr-detection-system-for-pathogens-associated-with-bovine-respiratory-disease-complex
#4
Mai Kishimoto, Shinobu Tsuchiaka, Sayed Samim Rahpaya, Ayako Hasebe, Keiko Otsu, Satoshi Sugimura, Suguru Kobayashi, Natsumi Komatsu, Makoto Nagai, Tsutomu Omatsu, Yuki Naoi, Kaori Sano, Sachiko Okazaki-Terashima, Mami Oba, Yukie Katayama, Reiichiro Sato, Tetsuo Asai, Tetsuya Mizutani
Bovine respiratory disease complex (BRDC) is frequently found in cattle worldwide. The etiology of BRDC is complicated by infections with multiple pathogens, making identification of the causal pathogen difficult. Here, we developed a detection system by applying TaqMan real-time PCR (Dembo respiratory-PCR) to screen a broad range of microbes associated with BRDC in a single run. We selected 16 bovine respiratory pathogens (bovine viral diarrhea virus, bovine coronavirus, bovine parainfluenza virus 3, bovine respiratory syncytial virus, influenza D virus, bovine rhinitis A virus, bovine rhinitis B virus, bovine herpesvirus 1, bovine adenovirus 3, bovine adenovirus 7, Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, Trueperella pyogenes, Mycoplasma bovis and Ureaplasma diversum) as detection targets and designed novel specific primer-probe sets for nine of them...
January 8, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28060812/a-novel-human-t-lymphotropic-virus-type-1c-molecular-variant-in-an-indigenous-individual-from-new-caledonia-melanesia
#5
Olivier Cassar, Françoise Charavay, Frédéric Touzain, Patricia Jeannin, Jean-Paul Grangeon, Sylvie Laumond, Eliane Chungue, Paul M V Martin, Antoine Gessain
BACKGROUND: Human T-Lymphotropic Virus type 1 (HTLV-1) is endemic among people of Melanesian descent in Papua New Guinea, Solomon Islands and Vanuatu, and in Indigenous populations from Central Australia. Molecular studies revealed that these Australo-Melanesian strains constitute the highly divergent HTLV-1c subtype. New Caledonia is a French overseas territory located in the Southwest Pacific Ocean. HTLV-1 situation is poorly documented in New Caledonia and the molecular epidemiology of HTLV-1 infection remains unknown...
January 6, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28042859/a-novel-role-of-silibinin-as-a-putative-epigenetic-modulator-in-human-prostate-carcinoma
#6
Ioannis Anestopoulos, Aristeidis P Sfakianos, Rodrigo Franco, Katerina Chlichlia, Mihalis I Panayiotidis, David J Kroll, Aglaia Pappa
Silibinin, extracted from milk thistle (Silybum marianum L.), has exhibited considerable preclinical activity against prostate carcinoma. Its antitumor and chemopreventive activities have been associated with diverse effects on cell cycle, apoptosis, and receptor-dependent mitogenic signaling pathways. Here we hypothesized that silibinin's pleiotropic effects may reflect its interference with epigenetic mechanisms in human prostate cancer cells. More specifically, we have demonstrated that silibinin reduces gene expression levels of the Polycomb Repressive Complex 2 (PRC2) members Enhancer of Zeste Homolog 2 (EZH2), Suppressor of Zeste Homolog 12 (SUZ12), and Embryonic Ectoderm Development (EED) in DU145 and PC3 human prostate cancer cells, as evidenced by Real Time Polymerase Chain Reaction (RT-PCR)...
December 31, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28040777/genome-report-identification-and-validation-of-antigenic-proteins-from-pajaroellobacter-abortibovis-using-de-novo-genome-sequence-assembly-and-reverse-vaccinology
#7
Bryan T Welly, Michael R Miller, Jeffrey L Stott, Myra T Blanchard, Alma D Islas-Trejo, Sean M O Rourke, Amy E Young, Juan F Medrano, Alison L Van Eenennaam
Epizootic bovine abortion (EBA), or "foothill abortion", is the leading cause of beef cattle abortion in California and has also been reported in Nevada and Oregon. In the 1970's, the soft-shelled tick Ornithodoros coriaceus, or "pajaroello tick", was confirmed as the disease-transmitting vector. In 2005, a novel Deltaproteobacterium was discovered as the etiologic agent of EBA (aoEBA), recently named Pajaroellobacter abortibovis This organism cannot be grown in culture using traditional microbiological techniques; it can only be grown in experimentally-infected severe combined immunodeficient (SCID) mice...
December 30, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28039632/development-of-a-pcr-free-dna-based-assay-for-the-specific-detection-of-vibrio-species-in-environmental-samples-by-targeting-the-16s-rrna
#8
E Da-Silva, L Barthelmebs, J Baudart
A novel PCR-free DNA-based assay was developed for the detection of Vibrio spp. A sandwich hybridization format using an immobilized capture probe and a labeled signal probe was selected and combined with chemiluminescent method for the detection of the RNA target. In a first step, probes were validated using positive controls (PCs). A linearity was observed between 0.1 and 2.5 nM of PC, and detection limit was determined as 0.1 nM. In a second step, specificity was checked by using RNA extracted from a panel of 31 environmental bacterial strains...
December 30, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28030571/multidisciplinary-identification-of-the-controversial-freedom-fighter-j%C3%A3-rg-jenatsch-assassinated-1639-in-chur-switzerland
#9
Martin Haeusler, Cordula Haas, Sandra Lösch, Negahnaz Moghaddam, Igor M Villa, Susan Walsh, Manfred Kayser, Roger Seiler, Frank Ruehli, Manuel Janosa, Christina Papageorgopoulou
Jörg Jenatsch, a leading freedom fighter during the Thirty Year's War in Graubünden, Switzerland, was assassinated on carnival 1639. Jenatsch's controversial biography and the unclear circumstances of his death inspired the formation of various legends, novels and films. In 1959, a skeleton discovered in the cathedral of Chur with remains of wealthy baroque clothing was tentatively attributed to Jenatsch. Here, we reassess the skeleton based on a new exhumation. Our multidisciplinary analysis and the head injuries are consistent with reports of the eyewitnesses of the crime, demonstrating that Jenatsch was killed from behind with a semi-sharp implement, supposedly an axe, as well as by a blow with a broad-surfaced object...
2016: PloS One
https://www.readbyqxmd.com/read/28028549/ssunique-detecting-sequence-novelty-in-microbiome-surveys
#10
Michael D J Lynch, Josh D Neufeld
High-throughput sequencing of small-subunit (SSU) rRNA genes has revolutionized understanding of microbial communities and facilitated investigations into ecological dynamics at unprecedented scales. Such extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain a substantial proportion of unclassified sequences, many representing organisms with novel taxonomy (taxonomic "blind spots") and potentially unique ecology. Indeed, these novel taxonomic lineages are associated with so-called microbial "dark matter," which is the genomic potential of these lineages...
November 2016: MSystems
https://www.readbyqxmd.com/read/28025389/direct-multiplex-pcr-dmpcr-for-the-identification-of-six-phlebotomine-sand-fly-species-diptera-psychodidae-including-major-leishmania-vectors-of-the-mediterranean
#11
Ioannis A Giantsis, Alexandra Chaskopoulou, Marie Claude Bon
Sand flies (Diptera: Psychodidae, subfamily Phlebotominae) are hematophagous insects that are known to transmit several anthroponotic and zoonotic diseases. Reliable identification of sand flies at species level is crucial for their surveillance, the detection and spread of their pathogens, and the implementation of targeted pest control strategies. Here, we designed a novel, time-saving, cost-effective and easy-to-apply molecular methodology, which avoids sequencing, for the identification of the following six Eastern Mediterranean sand fly species: Phebotomus perfiliewi Parrot, Phebotomus simici Theodor, Phebotomus tobbi Adler and Theodor, Phebotomus papatasi Scopoli, Sergentomyia dentata Sinton, and Sergentomyia minuta Theodor...
December 26, 2016: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28006685/in-vitro-selection-of-dna-aptamers-targeting-%C3%AE-lactoglobulin-and-their-integration-in-graphene-based-biosensor-for-the-detection-of-milk-allergen
#12
Shimaa Eissa, Mohammed Zourob
Food allergy has increased rapidly in recent years affecting millions of people worldwide. With the increased consumption of packed food nowadays, a sensitive, accurate and rapid screening method for potential food allergens has become an urgent need in order to protect the sensitive consumers from life-threatening reactions. The current detection methods for food allergens are mostly based on immunoassays which are costly and times-consuming. In this work, we developed an aptamer/graphene-based electrochemical biosensor for on-step, sensitive and low cost detection of β-lactoglobulin (β-LG) milk protein, one of the most common food allergens specially in infants...
December 10, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28005056/new-crispr-cas-systems-from-uncultivated-microbes
#13
David Burstein, Lucas B Harrington, Steven C Strutt, Alexander J Probst, Karthik Anantharaman, Brian C Thomas, Jennifer A Doudna, Jillian F Banfield
CRISPR-Cas systems provide microbes with adaptive immunity by employing short sequences, termed spacers, that guide Cas proteins to cleave foreign DNA(1,2). Class 2 CRISPR-Cas systems are streamlined versions in which a single Cas protein bound to RNA recognizes and cleaves targeted sequences(3,4). The programmable nature of these minimal systems has enabled their repurposing as a versatile technology that is broadly revolutionizing biological and clinical research(5). However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving untapped the vast majority of enzymes from organisms that have not been cultured...
December 22, 2016: Nature
https://www.readbyqxmd.com/read/27997742/reconstructing-the-plant-mitochondrial-genome-for-marker-discovery-a-case-study-using-pinus
#14
Kevin Donnelly, Joan Cottrell, Richard A Ennos, Giovanni Guiseppe Vendramin, Stuart A'Hara, Sarah King, Annika Perry, Witold Wachowiak, Stephen Cavers
Whole-genome-shotgun (WGS) sequencing of total genomic DNA was used to recover ~1 Mbp of novel mitochondrial (mtDNA) sequence from Pinus sylvestris (L.) and three members of the closely-related Pinus mugo species complex. DNA was extracted from megagametophyte tissue from six mother trees from locations across Europe and 100 bp paired-end sequencing was performed on the Illumina HiSeq platform. Candidate mtDNA sequences were identified by their size and coverage characteristics, and by comparison with published plant mitochondrial genomes...
December 20, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27992820/gja1-gene-variations-in-sudden-unexplained-nocturnal-death-syndrome-in-the-chinese-han-population
#15
Qiuping Wu, Yeda Wu, Liyong Zhang, Jinxiang Zheng, Shuangbo Tang, Jianding Cheng
Sudden unexplained nocturnal death syndrome (SUNDS) is a conundrum to both forensic pathologists and physicians, more than 80% of which the molecular pathogenesis remains unclear. Reported studies on both clinical and genetic phenotypes suggest SUNDS is related to congenital and acquired arrhythmias. Recent researches have linked the mutations of gene gap junction alpha 1 (GJA1) with arrhythmogenic cardiac disorders. In the present study, we investigate the potential correlation between GJA1 gene variations and the occurrence of SUNDS...
December 9, 2016: Forensic Science International
https://www.readbyqxmd.com/read/27989988/novel-mutations-and-structural-deletions-in-tubb8-expanding-mutational-and-phenotypic-spectrum-of-patients-with-arrest-in-oocyte-maturation-fertilization-or-early-embryonic-development
#16
Biaobang Chen, Bin Li, Da Li, Zheng Yan, Xiaoyan Mao, Yao Xu, Jian Mu, Qiaoli Li, Li Jin, Lin He, Yanping Kuang, Qing Sang, Lei Wang
STUDY QUESTION: Are there any new type of mutations and novel phenotypes in patients with arrest in oocyte maturation, fertilization or early embryonic development having tubulin beta eight class VIII (TUBB8) mutations? SUMMARY ANSWER: We identified new types of mutations in TUBB8 associated with maturation, fertilization and developmental arrest. WHAT IS KNOWN ALREADY: We previously found heterozygous mutations and a homozygous frameshift/internal seven amino acid deletion in TUBB8 that are responsible for oocyte maturation arrest...
December 17, 2016: Human Reproduction
https://www.readbyqxmd.com/read/27984801/isolation-of-pcr-ready-human-dna-using-copper-nanoparticles-from-skeletal-remains
#17
Anand Lodha, Niha Ansari, Shahil Shah, M V Rao, Shobhana K Menon
Present study represents a novel approach of PCR ready-human DNA extraction method from skeletal remains using copper nanoparticles (CuNPs) for personnel identification. To achieve rapid, cost effective, sensitive and non-hazardous method for DNA extraction we utilized CuNPs synthesized using microwave. The applicability of this approach was first tested in blood samples and afterwards, this system was extended to skeletal remains' samples also. This method yields good quality DNA that are ready for PCR reactions from small quantities of blood and skeletal remains...
December 8, 2016: Forensic Science International
https://www.readbyqxmd.com/read/27983475/calorithrix-insularis-gen-nov-sp-nov-a-novel-representative-of-the-phylum-calditrichaeota
#18
Elena I Kompantseva, Ilya V Kublanov, Anna A Perevalova, Nikolay A Chernyh, Stepan V Toshchakov, Yuriy V Litti, Alexey N Antipov, Elizaveta A Bonch-Osmolovskaya, Margarita L Miroshnichenko
A moderately thermophilic, anaerobic bacterium designated as strain KRT was isolated from a shallow water submarine hydrothermal vent (Kunashir Island, Southern Kurils, Russia). Cells of the strain KRT were thin (0.2-0.3 µm), flexible, motile, Gram-negative rods of variable length. Optimal growth conditions: pH 6.6, 55°C, 1-3% (w/v) NaCl. Strain KRT was able to ferment a wide range of proteinaceous substrates, pyruvate, mono-, di- and polysaccharides. The best growth occurred with proteinaceous compounds...
December 16, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27980708/bioinformatics-strategies-for-taxonomy-independent-binning-and-visualization-of-sequences-in-shotgun-metagenomics
#19
REVIEW
Karel Sedlar, Kristyna Kupkova, Ivo Provaznik
One of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome shotgun sequencing, which allows much more detailed analysis of the metagenomic data, including reconstruction of novel microbial genomes and to gain knowledge about genetic potential and metabolic capacities of whole environments...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27980100/synthetic-spike-in-standards-for-high-throughput-16s-rrna-gene-amplicon-sequencing
#20
Dieter M Tourlousse, Satowa Yoshiike, Akiko Ohashi, Satoko Matsukura, Naohiro Noda, Yuji Sekiguchi
High-throughput sequencing of 16S rRNA gene amplicons (16S-seq) has become a widely deployed method for profiling complex microbial communities but technical pitfalls related to data reliability and quantification remain to be fully addressed. In this work, we have developed and implemented a set of synthetic 16S rRNA genes to serve as universal spike-in standards for 16S-seq experiments. The spike-ins represent full-length 16S rRNA genes containing artificial variable regions with negligible identity to known nucleotide sequences, permitting unambiguous identification of spike-in sequences in 16S-seq read data from any microbiome sample...
December 15, 2016: Nucleic Acids Research
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