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https://www.readbyqxmd.com/read/27933517/a-novel-mutation-in-the-fibrinogen-a%C3%AE-chain-gly13arg-fibrinogen-nanning-causes-congenital-dysfibrinogenemia-associated-with-defective-peptide-a-release
#1
Jie Yan, Meiling Luo, Peng Cheng, Lin Liao, Xuelian Deng, Donghong Deng, Faquan Lin
Dysfibrinogenemia is characterized by blood coagulation dysfunction induced by an abnormal molecular structure of fibrinogen. Here, we describe a new case. A 32-year-old female was suspected of having dysfibrinogenemia during routine laboratory screening, based on her decreased functional fibrinogen level, normal fibrinogen antigen level, and prolonged thrombin time. We extracted DNA and performed polymerase chain reaction and DNA sequencing to identify genetic mutation. Fibrin polymerization, the kinetics of the fibrinopeptide release, scanning electron microscopy, mass spectrometric analysis, fibrin cross-linking, sodium dodecyl sulfate polyacrylamide gel electrophoresis and western blot were conducted...
December 8, 2016: International Journal of Hematology
https://www.readbyqxmd.com/read/27932456/physico-chemical-fingerprinting-of-rna-genes
#2
Ankita Singh, Akhilesh Mishra, Ali Khosravi, Garima Khandelwal, B Jayaram
We advance here a novel concept for characterizing different classes of RNA genes on the basis of physico-chemical properties of DNA sequences. As knowledge-based approaches could yield unsatisfactory outcomes due to limitations of training on available experimental data sets, alternative approaches that utilize properties intrinsic to DNA are needed to supplement training based methods and to eventually provide molecular insights into genome organization. Based on a comprehensive series of molecular dynamics simulations of Ascona B-DNA consortium, we extracted hydrogen bonding, stacking and solvation energies of all combinations of DNA sequences at the dinucleotide level and calculated these properties for different types of RNA genes...
December 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27930669/development-of-rna-fish-assay-for-detection-of-oncogenic-fgfr3-tacc3-fusion-genes-in-ffpe-samples
#3
Masahiro Kurobe, Takahiro Kojima, Kouichi Nishimura, Shuya Kandori, Takashi Kawahara, Takayuki Yoshino, Satoshi Ueno, Yuichi Iizumi, Koji Mitsuzuka, Yoichi Arai, Hiroshi Tsuruta, Tomonori Habuchi, Takashi Kobayashi, Yoshiyuki Matsui, Osamu Ogawa, Mikio Sugimoto, Yoshiyuki Kakehi, Yoshiyuki Nagumo, Masakazu Tsutsumi, Takehiro Oikawa, Koji Kikuchi, Hiroyuki Nishiyama
INTRODUCTION AND OBJECTIVES: Oncogenic FGFR3-TACC3 fusions and FGFR3 mutations are target candidates for small molecule inhibitors in bladder cancer (BC). Because FGFR3 and TACC3 genes are located very closely on chromosome 4p16.3, detection of the fusion by DNA-FISH (fluorescent in situ hybridization) is not a feasible option. In this study, we developed a novel RNA-FISH assay using branched DNA probe to detect FGFR3-TACC3 fusions in formaldehyde-fixed paraffin-embedded (FFPE) human BC samples...
2016: PloS One
https://www.readbyqxmd.com/read/27917431/a-novel-miniaturized-biofilter-based-on-silicon-micropillars-for-nucleic-acid-extraction
#4
Salvatore Petralia, Emanuele Luigi Sciuto, Sabrina Conoci
New miniaturised microfluidic biofilter (BF) devices based on silicon micropillars have been developed and tested regarding their ability to extract HBV (Hepatitis B Virus) bacterial DNA from biological sample solutions. The device is composed of a silicon microchannel in which the pillars are distributed at the bottom surface. The extracted DNA solutions were analysed by real time PCR amplification and the biofilter performance was evaluated. The results obtained show that the DNA binding to the biofilters and the elution efficiency strictly depend on the pillars' geometrical dimensions and increase proportionally with the surface/volume ratio...
December 5, 2016: Analyst
https://www.readbyqxmd.com/read/27914352/searching-for-novel-modes-of-toxic-actions-of-oil-spill-using-e-%C3%A2-coli-live-cell-array-reporter-system-a-hebei-spirit-oil-spill-study
#5
Dawoon Jung, Miao Guan, Sangwoo Lee, Cheolmin Kim, Hyesoo Shin, Seongjin Hong, Un Hyuk Yim, Won Joon Shim, John P Giesy, Jong Seong Khim, Xiaowei Zhang, Kyungho Choi
Oil is a complex mixture of numerous compounds. Therefore, oil spills near shore can cause various adverse effects on coastal ecosystems. However, most toxicological assessments conducted on oil spill sites have focused on limited modes of toxic actions. In the present study, we utilized the Escherichia coli (E. coli) live cell array system (LCA) to identify novel modes of toxicities of the oil spill-affected sediments. For this purpose, sediment samples were collected from an area heavily polluted by Hebei Spirit oil spill (HSOS) incident of 2007...
November 30, 2016: Chemosphere
https://www.readbyqxmd.com/read/27912317/production-of-bacillus-amyloliquefaciens-og-and-its-metabolites-in-renewable-media-valorisation-for-biodiesel-production-and-p-xylene-decontamination
#6
Augusto Etchegaray, François Coutte, Gabrielle Chataigné, Max Béchet, Ramon H Z Dos Santos, Valérie Leclère, Philippe Jacques
Biosurfactants are important in many areas; however, costs impede large-scale production. This work aimed to develop a global sustainable strategy for the production of biosurfactants by a novel strain of Bacillus amyloliquefaciens. Initially, Bacillus sp. strain 0G was renamed B. amyloliquefaciens subsp. plantarum (syn. Bacillus velezensis) after analysis of the gyrA and gyrB DNA sequences. Growth in modified Landy's medium produced 3 main recoverable metabolites: surfactin, fengycin, and acetoin, which promote plant growth...
September 2, 2016: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/27909844/design-and-fabrication-a-gold-nanoparticle-dna-based-nanobiosensor-for-detection-of-microrna-involved-in-alzheimer-s-disease
#7
Shokoufeh Delkhahi, Mahdi Rahaie, Fereshteh Rahimi
MicroRNAs are small RNAs which regulate gene expression by translational repression or degradation of messenger RNAs. Regards to important role of these biomolecules in human disease progress, to produce sensitive, simple and cost-effective assays for microRNAs are in urgent demand. miR-137 in Alzheimer's patients has demonstrated its potential as non-invasive biomarkers in blood for Alzheimer's disease diagnosis and prognosis. This paper describes a novel, sensitive and specific microRNA assay based on Colorimetric detection of gold nanoparticles and hybridization chain reaction amplification (HCR)...
December 1, 2016: Journal of Fluorescence
https://www.readbyqxmd.com/read/27906621/isolation-of-a-novel-protein-p12-from-adult-drosophila-melanogaster-that-inhibits-deoxyribonucleoside-and-protein-kinase-activities-and-activates-3-5-exonuclease-activity
#8
Louise Slot Christiansen, Gabriella van Zanten, Dvora Berenstein, Marianne Lauridsen, Søren Kjærulff, Leif Søndergaard, Birgitte Munch-Petersen
We have previously found that Drosophila melanogaster only has one deoxyribonucleoside kinase, Dm-dNK, however, capable to phosphorylate all four natural deoxyribonucleosides. Dm-dNK was originally isolated from an embryonic cell line. We wanted to study the expression of Dm-dNK during development from embryonic cells to adult flies and found declining Dm-dNK activity during development and no activity in adult flies. Surprisingly, the extract from adult flies exhibited a strong inhibitory effect on deoxyribonucloside kinase activity...
December 2016: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/27902335/defluviitalea-raffinosedens-sp-nov-a-novel-thermophilic-anaerobic-saccharolytic-bacterium-isolated-from-an-anaerobic-batch-digester-treating-animal-manure-and-rice-straw
#9
Shichun Ma, Yan Huang, Cong Wang, Hui Fan, Lirong Dai, Zheng Zhou, Xing Liu, Yu Deng
A thermophilic, anaerobic, fermentative bacterium, strain A6T, was obtained from an anaerobic batch digester treating animal manure and rice straw. The strain was Gram-positive, slightly curved rods with a size of 0.6-1 μm × 2.5-8.2 μm, non-motile, and produced terminal spores. The temperature, pH, and NaCl concentration ranges for growth were 40°C-60°C, 6.5-8.0, and 0-15.0 g/L, with optimum growth noted at 50°C-55°C, pH 7.5, and in the absence of NaCl, respectively. Yeast extract was required for growth...
November 14, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902294/actinocrinis-puniceicyclus-gen-nov-sp-nov-a-novel-actinobacterium-isolated-from-an-acidic-spring-in-kootenay-national-park-canada
#10
Joong-Jae Kim, Colbran E Marjerrison, Sabrina L Cornish Shartau, Allyson L Brady, Christine E Sharp, W Irene C Rijpstra, Jaap S Sinninghe Damsté, Peter Schumann, Stephen E Grasby, Peter F Dunfield
An aerobic, mildly acidophilic actinobacterium was isolated from the Ochre Beds bog in Kootenay National Park, Canada. Cells of isolate OB1T were Gram-positive, non-motile, pink-to purple-pigmented filaments. The pH range for growth was 3.5 - 6.5 (optimum 5.5), and the temperature range was 13-37 oC. The major cellular fatty acids were 16:0 iso (28.5 %), 15:0 iso (14.6 %) and 15:0 anteiso (14.3 %), and the major polar lipid was phosphohexose. The major quinone was menaquinone-11 (MK-11) and the peptidoglycan type was A1γ...
November 16, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902281/acidicapsa-acidisoli-sp-nov-from-the-acidic-soil-of-a-deciduous-forest
#11
Heizo Matsuo, Chisaki Kudo, Juan Li, Akio Tonouchi
A bacterial strain designated strain SK-11T was isolated from the acidic soil of a deciduous forest in the Shirakami Mountains in Japan. Cells of strain SK-11T were aerobic, non-motile, Gram-stain-negative rods, 0.7-1.0 µm in width and 1.0-1.4 µm in length. The pH range for growth was between 4.0 and 5.5, with an optimum at 5.0. The temperature range for growth was between 10°C and 35°C, with an optimum at around 25-30°C. Strain SK-11T utilized various carbohydrates as growth substrates as well as yeast extract and protein hydrolysates...
November 23, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902239/mucilaginibacter-psychrotolerans-sp-nov-isolated-from-the-riganqiao-peatlands-on-the-tibetan-plateau
#12
Yongcui Deng, Liang Shen, Baiqin Xu, Yongqin Liu, Zhengquan Gu, Hongcan Liu, Yuguang Zhou
A Gram-stain-negative, rod-shaped without flagella, pink colored, cold-tolerate bacteria strain NH7-4T was isolated from Riganqiao peatlands on the Tibetan Plateau. The novel isolate was classified into the genus Mucilaginibacter. 16S rRNA gene sequence of the novel isolate shares a pairwise similarity ranging from 96.69% to 93.41% with the type strains of the genus Mucilaginibacter. Growth of strain NH7-4T occurred between 0 and 30 °C and at pH 5.0-9.0, with optimum at 20 °C and pH about 7.0. The major isoprenoid quinone is MK-7...
October 11, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27901321/copy-number-variants-in-a-population-based-investigation-of-klippel-trenaunay-syndrome
#13
Aggeliki Dimopoulos, Robert J Sicko, Denise M Kay, Shannon L Rigler, Ruzong Fan, Paul A Romitti, Marilyn L Browne, Charlotte M Druschel, Michele Caggana, Lawrence C Brody, James L Mills
Klippel-Trenaunay syndrome (KTS) is a rare congenital vascular disorder that is thought to occur sporadically; however, reports of familial occurrence suggest a genetic component. We examined KTS cases to identify novel, potentially causal copy number variants (CNVs). We identified 17 KTS cases from all live-births occurring in New York (1998-2010). Extracted DNA was genotyped using Illumina microarrays and CNVs were called using PennCNV software. CNVs selected for follow-up had ≥10 single nucleotide polymorphisms (SNPs) and minimal overlap with in-house controls or controls from the Database of Genomic Variants...
November 30, 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#14
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J Colin Murrell, Josh D Neufeld, Marc G Dumont
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of (13)C, (18)O, or (15)N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27899992/beside-p53-and-pten-identification-of-molecular-alterations-of-the-ras-mapk-and-pi3k-akt-signaling-pathways-in-high-grade-serous-ovarian-carcinomas-to-determine-potential-novel-therapeutic-targets
#15
Shuhui Chen, Elisa Cavazza, Catherine Barlier, Julia Salleron, Pierre Filhine-Tresarrieu, Céline Gavoilles, Jean-Louis Merlin, Alexandre Harlé
Despite great histological and molecular heterogeneity, the clinical management of high-grade ovarian carcinomas remains unspecialized. As a major subgroup, high-grade serous ovarian carcinomas (HGSOCs) require novel therapies. In addition to utilizing conventional histological prognostic markers and performing oncogenetic investigations, the molecular diagnostic method of next generation sequencing (NGS) was performed to identify 'druggable' targets that could provide access to innovative therapy. The present study was performed in 45 HGSOC patients (mean age, 59...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899719/a-novel-hypothesis-for-histone-to-protamine-transition-in-bos-taurus-spermatozoa
#16
Gerly Sillaste, Lauris Kaplinski, Riho Meier, Ülle Jaakma, Elo Eriste, Andres Salumets
DNA compaction with protamines in sperm is essential for successful fertilization. However, a portion of sperm chromatin remains less tightly packed with histones, which genomic location and function remain unclear. We extracted and sequenced histone-associated DNA from sperm of nine ejaculates from three bulls. We found that the fraction of retained histones varied between samples but the variance was similar between samples from the same and different individuals. The most conserved regions showed similar abundance across all samples, while in other regions their presence correlated with the size of histone fraction...
November 29, 2016: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/27891625/validation-of-the-multiplex-ligation-dependent-probe-amplification-assay-and-its-application-on-the-distribution-study-of-the-major-alleles-of-17-blood-group-systems-in-chinese-donors-from-guangzhou
#17
Yanli Ji, Jizhi Wen, Barbera Veldhuisen, Lonneke Haer-Wigman, Zhen Wang, Martin Lodén-van Straaten, Ling Wei, Guangping Luo, Yongshui Fu, C Ellen van der Schoot
BACKGROUND: Genotyping platforms for common red blood cell (RBC) antigens have been successfully applied in Caucasian and black populations but not in Chinese populations. In this study, a genotyping assay based on multiplex ligation-dependent probe amplification (MLPA) technology was applied in a Chinese population to validate the MLPA probes. Subsequently, the comprehensive distribution of 17 blood group systems also was obtained. STUDY DESIGN AND METHODS: DNA samples from 200 Chinese donors were extracted and genotyped using the blood-MLPA assay...
November 27, 2016: Transfusion
https://www.readbyqxmd.com/read/27885492/polymorphism-of-growth-hormone-receptor-ghr-gene-in-nilagiri-sheep
#18
Amiya Ranjan Sahu, V Jeichitra, R Rajendran, A Raja
The allelic variation in the regulatory sequence of growth hormone receptor (GHR) gene influences the growth traits of sheep. A study was carried out to find out the polymorphisms associated with exon 10 of GHR gene and its association with growth traits of Nilagiri sheep. The blood samples were collected from Nilagiri sheep (n = 103) reared at Sheep Breeding Research Station, Sandynallah, Tamil Nadu, India. DNA was isolated using the phenol-chloroform extraction procedure and eight samples having amplified product of part of exon 10 (895 bp) sequenced...
November 24, 2016: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/27882080/a-novel-krt5-mutation-associated-with-generalized-severe-epidermolysis-bullosa-simplex-in-a-2-year-old-chinese-boy
#19
Jia Zhang, Ming Yan, Jianying Liang, Ming Li, Zhirong Yao
Mutations in keratin 5 (KRT5) or KRT14 genes are responsible for the most severe form of epidermolysis bullosa simplex (EBS), which is EBS generalized severe (EBS-gen sev). To date, only four pathogenic mutations (p.Arg165Ser and p.Lys199Asn in KRT5; p.Arg125Cys and p.Arg125His in KRT14) have been reported to be responsible for EBS-gen sev in the Chinese population. In the present study, a 2-year-old Chinese boy was clinically suspected to suffer from EBS, and thus Sanger sequencing was performed in the extracted genomic DNA samples from the patient, his parents and 100 healthy controls...
November 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/27875355/novel-mutations-in-epcam-cause-congenital-tufting-enteropathy
#20
Wenjuan Tang, Taosheng Huang, Zhongyao Xu, Ying Huang
BACKGROUND AND AIMS: Congenital tufting enteropathy (CTE) is a rare autosomal recessive form of intractable diarrhea of infancy. Patients develop chronic diarrhea within days after birth, leading to severe malabsorption and significant mortality. CTE is characterized by subtotal villous atrophy with crypt hyperplasia. Typical features include abnormal villi in the intestinal epithelium and disorganization of surface enterocytes with focal crowding, resembling tufts. The pathogenesis of CTE remains poorly understood...
November 21, 2016: Journal of Clinical Gastroenterology
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