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https://www.readbyqxmd.com/read/28453906/oral-treponeme-major-surface-protein-sequence-diversity-and-distributions-within-periodontal-niches
#1
Meng You, Yuki Chan, Donnabella C Lacap-Bugler, Yong-Biao Huo, Wenling Gao, W Keung Leung, Rory M Watt
Treponema denticola and other species (phylotypes) of oral spirochetes are widely-considered to play important etiological roles in periodontitis and other oral infections. The major surface protein (Msp) of T. denticola is directly implicated in several pathological mechanisms. Here, we have analyzed msp sequence diversity across 68 strains of oral phylogroup 1 and 2 treponemes; including reference strains of T. denticola, Treponema putidum, Treponema medium, 'Treponema vincentii', and 'Treponema sinensis'...
April 28, 2017: Molecular Oral Microbiology
https://www.readbyqxmd.com/read/28453672/primerize-2d-automated-primer-design-for-rna-multidimensional-chemical-mapping
#2
Siqi Tian, Rhiju Das
Summary: Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453633/role-of-dna-gyrase-and-topoisomerase-iv-mutations-in-fluoroquinolone-resistance-of-capnocytophaga-spp-clinical-isolates-and-laboratory-mutants
#3
Elodie Ehrmann, Anne Jolivet-Gougeon, Martine Bonnaure-Mallet, Thierry Fosse
Objectives: Capnocytophaga spp. are often reported to cause bacteraemia and extra-oral infections and are characterized by their significant contribution to resistance to β-lactam and macrolide-lincosamide-streptogramin antibiotics in the human oral microbiota. The implication of mutations in the quinolone resistance-determining region (QRDR) of DNA gyrase A and B ( gyrA and gyrB ) and topoisomerase IV ( parC and parE ) of fluoroquinolone (FQ)-resistant Capnocytophaga spp., hitherto unknown, was explored in this study...
April 26, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28453368/establishment-of-expanded-and-streamlined-pipeline-of-pitch-knock-in-a-web-based-design-tool-for-mmej-mediated-gene-knock-in-pitch-designer-and-the-variations-of-pitch-pitch-tg-and-pitch-kiko
#4
Kazuki Nakamae, Yuki Nishimura, Mitsumasa Takenaga, Shota Nakade, Naoaki Sakamoto, Hiroshi Ide, Tetsushi Sakuma, Takashi Yamamoto
The emerging genome editing technology has enabled the creation of gene knock-in cells easily, efficiently, and rapidly, which has dramatically accelerated research in the field of mammalian functional genomics, including in humans. We recently developed a microhomology-mediated end-joining-based gene knock-in method, termed the PITCh system, and presented various examples of its application. Since the PITCh system only requires very short microhomologies (up to 40 bp) and single-guide RNA target sites on the donor vector, the targeting construct can be rapidly prepared compared with the conventional targeting vector for homologous recombination-based knock-in...
April 28, 2017: Bioengineered
https://www.readbyqxmd.com/read/28453251/influence-of-manure-application-on-the-environmental-resistome-under-finnish-agricultural-practice-with-restricted-antibiotic-use
#5
Johanna Muurinen, Robert D Stedtfeld, Antti Karkman, Katariina Pärnänen, James M Tiedje, Marko P J Virta
The co-occurrence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in farm environments can potentially foster the development of antibiotic resistant pathogens. We studied the resistome of Finnish dairy and swine farms where use of antibiotics is limited to treating bacterial infections and manure is only applied April to September. The resistome of manure, soil and tile drainage water from ditch was investigated from the beginning of the growing season until forage harvest. The relative ARG and MGE abundance was measured using a qPCR array with 363 primer pairs...
April 28, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28449521/cancer-of-the-esophagus-and-esophagogastric-junction-an-8-th-edition-staging-primer
#6
EDITORIAL
Claire L Donohoe, Alexander W Phillips
No abstract text is available yet for this article.
March 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28449423/the-detection-of-messenger-rna-for-carcinoembryonic-antigen-and-cytokeratin-20-in-peritoneal-washing-fluid-in-patients-with-advanced-gastric-cancer
#7
Yeon Ji Kim, Woo Chul Chung, Sooa Choi, Yun Duk Jung, Jaejun Lee, Seung Yun Chae, Kyong Hwa Jun, Hyung Min Chin
Background/Aims: Peritoneal micrometastasis is known to play an important role in the recurrence of gastric cancer. However, its effects remain equivocal. Herein, we examine the messenger RNA (mRNA) as tumor markers, carcinoembryonic antigen (CEA), and cytokeratin 20 (CK20), in peritoneal washing fluid. Moreover, we evaluate whether these results could predict the recurrence of gastric cancer following curative resection. Methods: We prospectively enrolled 132 patients with gastric cancers, who had received an operation, between January 2010 and January 2013...
April 25, 2017: Korean Journal of Gastroenterology, Taehan Sohwagi Hakhoe Chi
https://www.readbyqxmd.com/read/28449123/capturing-a-mammalian-dna-polymerase-extending-from-an-oxidized-nucleotide
#8
Amy M Whitaker, Mallory R Smith, Matthew A Schaich, Bret D Freudenthal
The oxidized nucleotide, 8-oxo-7,8-dihydro-2΄-deoxyguanosine (8-oxoG), is one of the most abundant DNA lesions. 8-oxoG plays a major role in tumorigenesis and human disease. Biological consequences of 8-oxoG are mediated in part by its insertion into the genome, making it essential to understand how DNA polymerases handle 8-oxoG. Insertion of 8-oxoG is mutagenic when opposite adenine but not when opposite cytosine. However, either result leads to DNA damage at the primer terminus (3΄-end) during the succeeding insertion event...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28447046/genetic-diversity-analysis-of-morchella-sp-by-rapd
#9
Muhammad Irfan, Shuang Yang, Luo Yuxin, Jia-Xing Sun
This study investigated the genetic diversity of morchella species using randomly amplified polymorphic DNA markers. Morchella species are an important group of edible mushrooms belonging to the family Helveliaceae with medicinal and economical significance. In this study we have developed an efficient method of genomic DNA isolation which was amplified by eight RAPD primers to test the polymorphism in three species of morchella. Out of all eight primers tested in current study, one of them (B8) resulted 100% polymorphism among the three studied species...
March 2017: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28445093/dynamics-of-cytokine-like-activity-in-the-hyperplasic-ovary-of-ex-fissiparous-planarians
#10
Abdel Halim Harrath, Abdelhabib Semlali, Lamjed Mansour, Waleed Aldahmash, Suliman Y Al Omar, Mohamed S Al Anazi, Jens R Nyengaard, Saleh Alwasel
The origin of infertility in the hyperplasic ovary of ex-fissiparous planarians remains poorly understood. In a previous study we demonstrated that a complex process of early autophagy, followed by apoptotic processes, occurs in the hyperplasic ovary of the freshwater planarian Dugesia arabica. The present study aimed to investigate whether the mRNA expression levels of selected mRNA-like genes are altered in the hyperplasic ovary of the ex-fissiparous freshwater planarian D. arabica compared to the normal ovary...
February 2017: Biological Bulletin
https://www.readbyqxmd.com/read/28444604/effect-of-%C3%AE-irradiation-on-fumonisin-producing-fusarium-associated-with-animal-and-poultry-feed-mixtures
#11
B V Deepthi, A P Gnanaprakash, M Y Sreenivasa
Contamination of animal and poultry feeds by Fusarium and the mycotoxin Fumonisin B1 is frequent in the feed supply chain. The present study evaluated the prevalence of fumonisin B1 producing Fusarium among irradiated and non-irradiated animal and poultry feed mixtures. Further, the efficiency of γ-rays (2.5, 5.0, 7.5, and 10.0 kGy) to minimize Fusarium growth and biosynthesis of fumonisin B1 in artificially inoculated feed was evaluated. A total of 108 feed samples were collected in which 45.37% of feed mixtures were contaminated with Fusarium species...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28444592/molecular-characterization-of-phytoplasma-of-16sri-b-group-association-with-acalypha%C3%A2-indica-in-india
#12
Ajay K Tiwari, M S Khan, Pradeep Kumar, Akhilesh Tiwari
The typical phytoplasma symptoms of little leaf, yellowing, chlorosis, witches' broom, and stunting growth were observed on Acalypha indica plants during the field survey conducted at Lucknow and surrounding districts in year 2015-2016. To confirm the association and possibility of phytoplasma etiology, PCR assays were performed using universal primer pairs (P1/P6) and nested primer pairs (R16F2n/R2) in a total of five diseased samples along with control. A ~1.2 Kb amplicon was observed in nested PCR assay in diseased sample; however, no band was observed in control sample...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28444538/occurrence-and-genetic-diversity-analysis-of-apple-stem-pitting-virus-isolated-from-apples-in-china
#13
Guo-Jun Hu, Ya-Feng Dong, Zun-Ping Zhang, Xu-Dong Fan, Fang Ren, Zhengnan Li
Two primer pairs were used to detect apple stem pitting virus (ASPV) using a reverse transcription (RT)-PCR test. 82 out of the 141 randomly collected samples, from ten orchards in five provinces and regions of China, tested positive. In the positive samples forty-five (55%) were infected by ASPV and two other viruses. The full coat protein (CP) and the triple gene block (TGB) gene 1, 2 and 3 of partial ASPV isolates were subsequently cloned. The nucleotide and amino acid identities of 39 CP sequence variants from 31 Chinese apple samples were compared with that of previously reported ASPV isolates and were 67...
April 25, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28444018/effect-of-nanotechnology-in-self-etch-bonding-systems-on-the-shear-bond-strength-of-stainless-steel-orthodontic-brackets
#14
Shaza M Hammad, Noha El-Wassefy, Ahmed Maher, Shafik M Fawakerji
OBJECTIVE: To evaluate the effect of silica dioxide (SiO2) nanofillers in different bonding systems on shear bond strength (SBS) and mode of failure of orthodontic brackets at two experimental times. METHODS: Ninety-six intact premolars were divided into four groups: A) Conventional acid-etch and primer Transbond XT; B) Transbond Plus self-etch primer; and two self-etch bonding systems reinforced with silica dioxide nanofiller at different concentrations: C) Futurabond DC at 1%; D) Optibond All-in-One at 7%...
February 2017: Dental Press Journal of Orthodontics
https://www.readbyqxmd.com/read/28443834/influence-of-different-pretreatments-on-the-microtensile-bond-strength-to-eroded-dentin
#15
Shengjile Deari, Florian J Wegehaupt, Tobias T Tauböck, Thomas Attin
PURPOSE: To evaluate the influence of different pretreatments on the microtensile bond strength (μTBS) of an etchand- rinse adhesive to eroded dentin. MATERIALS AND METHODS: Thirty-six human teeth were ground down to their dentin layer and randomly divided into six groups (G1-G6; n = 6), G1 being the control group. Only in the test groups (G2-G6) were samples subjected to erosion using citric acid (pH 2.6) 10 x 2 min per day for five days. Between the erosive attacks, samples were stored in artificial saliva...
April 25, 2017: Journal of Adhesive Dentistry
https://www.readbyqxmd.com/read/28443226/a-novel-pcr-assay-for-detecting-brucella-abortus-and-brucella-melitensis
#16
Saeed Alamian, Majid Esmaelizad, Taghi Zahraei, Afshar Etemadi, Mohsen Mohammadi, Davoud Afshar, Soheila Ghaderi
OBJECTIVES: Brucellosis is a major zoonotic disease that poses a significant public health threat worldwide. The classical bacteriological detection process used to identify Brucella spp. is difficult and time-consuming. This study aimed to develop a novel molecular assay for detecting brucellosis. METHODS: All complete sequences of chromosome 1 with 2.1-Mbp lengths were compared among all available Brucella sequences. A unique repeat sequence (URS) locus on chromosome 1 could differentiate Brucella abortus from Brucella melitensis...
February 2017: Osong Public Health and Research Perspectives
https://www.readbyqxmd.com/read/28442912/tumor-necrosis-factor-%C3%AE-and-%C3%AE-genetic-polymorphisms-as-a-risk-factor-in-saudi-patients-with-schizophrenia
#17
Saeed Kadasah, Misbahul Arfin, Sadaf Rizvi, Mohammed Al-Asmari, Abdulrahman Al-Asmari
BACKGROUND: Schizophrenia is one of the most common devastating psychiatric disorders that negatively affects the quality of life and psychosocial functions. Its etiology involves the interplay of complex polygenic influences and environmental risk factors. Inflammatory markers are well-known etiological factors for psychiatric disorders, including schizophrenia. OBJECTIVE: The aim of this study was to investigate the association of proinflammatory cytokine genes, tumor necrosis factor (TNF)-α (-308G/A) and TNF-β (+252A/G) polymorphisms with schizophrenia susceptibility...
2017: Neuropsychiatric Disease and Treatment
https://www.readbyqxmd.com/read/28442328/simple-quick-and-cost-efficient-a-universal-rt-pcr-and-sequencing-strategy-for-genomic-characterisation-of-foot-and-mouth-disease-viruses
#18
V Dill, M Beer, B Hoffmann
Foot-and-mouth disease (FMD) is a major contributor to poverty and food insecurity in Africa and Asia, and it is one of the biggest threats to agriculture in highly developed countries. As FMD is extremely contagious, strategies for its prevention, early detection, and the immediate characterization of outbreak strains are of great importance. The generation of whole-genome sequences enables phylogenetic characterization, the epidemiological tracing of virus transmission pathways and is supportive in disease control strategies...
April 22, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28441611/genotoxic-effect-of-pb-and-cd-on-in%C3%A2-vitro-cultures-of-sphagnum-palustre-an-evaluation-by-issr-markers
#19
Maria Cristina Sorrentino, Fiore Capozzi, Simonetta Giordano, Valeria Spagnuolo
In the present work, the genotoxic effect of cadmium and lead supplied in a laboratory trial, was investigated for the first time in the moss Sphagnum palustre, by ISSR molecular markers. A total of 169 reproducible bands were obtained with 12 primers, ten of which gave polymorphisms (i.e., appearance/disappearance of bands), indicating a clear genotoxic effect induced by the metals. Both metals induced a decrease of the genome template stability in a dose dependent manner. At concentration >10(-5) Cd also induced a general toxic effect in S...
April 17, 2017: Chemosphere
https://www.readbyqxmd.com/read/28441604/digital-quantitative-analysis-of-microrna-in-single-cell-based-on-ligation-depended-polymerase-colony-polony
#20
Hui Wang, Honghong Wang, Xinrui Duan, Chenghui Liu, Zhengping Li
The ability to dissect cell-to-cell variations of microRNA (miRNA) expression with single-cell resolution has become a powerful tool to investigate the regulatory function of miRNAs in biological processes and the pathogenesis of miRNA-related diseases. Herein, we have developed a novel scheme for digital detection of miRNA in single cell by using the ligation-depended DNA polymerase colony (polony). Firstly, two simply designed target-specific DNA probes were ligated by using individual miRNA as the template...
April 7, 2017: Biosensors & Bioelectronics
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