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DNA Sequencing

Yuanyuan Zhou, Xia Zheng, Jiaojiao Lu, Wei Chen, Xu Li, Le Zhao
BACKGROUND/AIMS: The Warburg effect is one of the main energy metabolism features supporting cancer cell growth. 20(S)-Rg3 exerts anti-tumor effect on ovarian cancer partly by inhibiting the Warburg effect. microRNAs are important regulators of the Warburg effect. However, the microRNA regulatory network mediating the anti-Warburg effect of 20(S)-Rg3 was largely unknown. METHODS: microRNA deep sequencing was performed to identify the 20(S)-Rg3-influenced microRNAs in SKOV3 ovarian cancer cells...
March 16, 2018: Cellular Physiology and Biochemistry
Eric Seiti Yamanaka, Luis A Tortajada-Genaro, Nuria Pastor, Ángel Maquieira
The genotyping of a single-nucleotide polymorphism (SNP) is addressed through methods based on loop-mediated isothermal amplification (LAMP) combined with user-friendly optical read-outs to cover the current demand for point-of-care DNA biomarker detection. The modification of primer design and reaction composition improved the assay selectivity yielding allele-specific results and reducing false-positive frequency. Furthermore, the reduced cost, ease of use and effectiveness of colorimetric detection (solution and hybridisation chip formats) were availed for the image capture by a smartphone, reching high sensitivity...
March 8, 2018: Biosensors & Bioelectronics
Akim Felipe Santos Nobre, Danilo de Souza Almeida, Louise Canto Ferreira, Deimy Lima Ferreira, Edivaldo Costa Sousa Júnior, Maria de Nazaré do Socorro de Almeida Viana, Ingrid Christiane Silva, Bruna Teles Pinheiro, Stephen Francis Ferrari, Alexandre da Costa Linhares, Edna Aoba Ishikawa, Rita Catarina Medeiros Sousa, Maísa Silva de Sousa
The Human T-cell Lymphotropic Virus (HTLV-1) is a Deltaretrovírus that was first isolated in the 1970s, and associated with Adult T-cell Leucemia-Lymphoma (ATLL), and subsequently to Tropical Spastic Paraparesis-Myelopathy (TSP/HAM). The genetic diversity of the virus varies among geographic regions, although its mutation rate is very low (approximately 1% per thousand years) in comparison with other viruses. The present study determined the genetic diversity of HTLV-1 in the metropolitan region of Belém, in northern Brazil...
2018: PloS One
Balaram Mohapatra, Pinaki Sar, Sufia Khannam Kazy, Mrinal Kumar Maiti, Tulasi Satyanarayana
Reductive transformation of toxic arsenic (As) species by As reducing bacteria (AsRB) is a key process in As-biogeochemical-cycling within the subsurface aquifer environment. In this study, we have characterized a Gram-stain-negative, non-spore-forming, rod-shaped As reducing bacterium designated KAs 5-3T, isolated from highly As-contaminated groundwater of India. Strain KAs 5-3T displayed high 16S rRNA gene sequence similarity to the members of the genus Pseudoxanthomonas, with P. mexicana AMX 26BT (99.25% similarity), P...
2018: PloS One
Xiaofen Zhang, Guoyun Wang, Bin Chen, Heshan Du, Fenglan Zhang, Haiying Zhang, Qian Wang, Sansheng Geng
First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.), but the genetic mechanisms that control FFN are still poorly understood. In the present study, we developed 249 F2 plants derived from an intraspecific cross between the inbred pepper lines Z4 and Z5. Thirty plants with the highest FFN and 30 plants with the lowest FFN were chosen and their DNAs were pooled according to phenotype to construct two bulked DNA pools. Specific-locus amplified fragment sequencing (SLAF-seq) was combined with bulked segregant analysis (BSA) to identify candidate regions related to FFN...
2018: PloS One
Quanwei Zhang, Qi Wang, Jishang Gong, Jiaxing Du, Yong Zhang, Xingxu Zhao
Insulin-like growth factor 2 (IGF2) recapitulates many of the activities of insulin and promotes differentiation of myoblasts and osteoblasts, which likely contribute to genetic variations of growth potential. However, little is known about the functions and signaling properties of IGF2 variants in yaks. The over-expression vector and knockdown sequence of yak IGF2 were transfected into yak fibroblasts, and the effects were detected by a series of assays. IGF2 expression in yak muscle tissues was significantly lower than that of other tissues...
March 20, 2018: Genes
Magdalena Dryglewska, Bogdan Kolarz, Maria Majdan
Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disease that results in uncontrolled immune system activation and overproduction of autoantibodies. The pathogenesis of the disease is complex and not fully understood, nevertheless, genetic and environmental factors play an important role. So far, about 30 genes have been identified to be involved in the SLE pathomechanism. However, not all genetically predisposed individuals develop the disease. This phenomenon can be associated with epigenetic changes that occur under the influence of environmental factors...
2018: Wiadomości Lekarskie: Organ Polskiego Towarzystwa Lekarskiego
Simeon U Springer, Chung-Hsin Chen, Maria Del Carmen Rodriguez Pena, Lu Li, Christopher Douville, Yuxuan Wang, Joshua David Cohen, Diana Taheri, Natalie Silliman, Joy Schaefer, Janine Ptak, Lisa Dobbyn, Maria Papoli, Isaac Kinde, Bahman Afsari, Aline C Tregnago, Stephania M Bezerra, Christopher VandenBussche, Kazutoshi Fujita, Dilek Ertoy, Isabela W Cunha, Lijia Yu, Trinity J Bivalacqua, Arthur P Grollman, Luis A Diaz, Rachel Karchin, Ludmila Danilova, Chao-Yuan Huang, Chia-Tung Shun, Robert J Turesky, Byeong Hwa Yun, Thomas A Rosenquist, Yeong-Shiau Pu, Ralph H Hruban, Cristian Tomasetti, Nickolas Papadopoulos, Ken W Kinzler, Bert Vogelstein, Kathleen G Dickman, George J Netto
Current non-invasive approaches for detection of urothelial cancers are suboptimal. We developed a test to detect urothelial neoplasms using DNA recovered from cells shed into urine. UroSEEK incorporates massive parallel sequencing assays for mutations in 11 genes and copy number changes on 39 chromosome arms. In 570 patients at risk for bladder cancer (BC), UroSEEK was positive in 83% of those who developed BC. Combined with cytology, UroSEEK detected 95% of patients who developed BC. Of 56 patients with upper tract urothelial cancer, 75% tested positive by UroSEEK, including 79% of those with non-invasive tumors...
March 20, 2018: ELife
Brenda K Schroeder, William L Schneider, Douglas G Luster, Aaron Sechler, Timothy D Murray
Aplanobacter agropyri was first described in 1915 by O'Gara and later transferred to the genus Corynebacterium by Burkholder in 1948 but it was not included in the Approved Lists of Bacterial Names in 1980 and, consequently, is not recognized as a validly published species. In the 1980s, bacteria resembling Corynebacterium agropyri were isolated from plant samples stored at the Washington State Mycological Herbarium and from a diseased wheatgrass plant collected in Cardwell, Montana, USA. In the framework of this study, eight additional isolates were recovered from the same herbarium plant samples in 2011...
March 20, 2018: International Journal of Systematic and Evolutionary Microbiology
Kerri M Malone, Kévin Rue-Albrecht, David A Magee, Kevin Conlon, Olga T Schubert, Nicolas C Nalpas, John A Browne, Alicia Smyth, Eamonn Gormley, Ruedi Aebersold, David E MacHugh, Stephen V Gordon
Members of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity yet distinct host tropism. Notably, while Mycobacterium bovis is highly virulent and pathogenic for cattle, the human pathogen M. tuberculosis is attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strains M...
March 20, 2018: Microbial Genomics
Yuli Wei, Jiasong Fang, Yunping Xu, Weiqiang Zhao, Junwei Cao
A novel heterotrophic, Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain NBT06-6T , was isolated from the deep seawater in the New Britain Trench and characterized phylogenetically and phenotypically. Optimal bacterial growth occurred at 35 °C (range 22-41 °C), at pH 6 (4-8) and with 4 % (w/v) NaCl (0-10 %). The strain grew at hydrostatic pressures of 0.1-100 MPa (optimum, 0.1 MPa) at 35 °C. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain NBT06-6T belonged to the genus Corynebacterium, with the highest sequence similarity (97...
March 20, 2018: International Journal of Systematic and Evolutionary Microbiology
G López, C Díaz-Cárdenas, J David Alzate, L N Gonzalez, N Shapiro, T Woyke, N C Kyrpides, S Restrepo, S Baena
Three morphologically similar thermo-acidophilic strains, USBA-GBX-501, USBA-GBX-502 and USBA-GBX-503T , were isolated from acidic thermal springs at the National Natural Park Los Nevados (Colombia). All isolates were spore-forming, Gram-stain-positive and motile, growing aerobically at 25-55 °C (optimum ~45 °C) and at pH 1.5-4.5 (optimum pH ~3.0). Phylogenetic analysis of the 16S rRNA gene sequences of these isolates showed an almost identical sequence (99.0 % similarity) and they formed a robust cluster with the closest relative Alicyclobacillus tolerans DSM 16297T with a sequence similarity of 99...
March 20, 2018: International Journal of Systematic and Evolutionary Microbiology
Shweta D Dabhi, Basant Roondhe, Prafulla K Jha
Understanding the interactions between biomolecules and boron nitride nanostructures is key for their use in nanobiotechnology and medical engineering. In this study, we investigated the adsorption of nucleobases adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) over armchair and zigzag boron nitride nanoribbons (BNNR) using density functional theory to define the applicability of BNNR for the sensing of nucleobases and DNA sequencing. To appropriately account for dispersion, the van der Waals forces (DFT-D2)-type method developed by Grimme was also included in the calculations...
March 20, 2018: Physical Chemistry Chemical Physics: PCCP
Shinya Fujie, Hiroyuki Matsubayashi, Hirotoshi Ishiwatari, Hiromasa Hazama, Takaaki Ito, Keiko Sasaki, Hiroyuki Ono
A 70-year-old man was referred to our hospital with exacerbation of diabetes. His blood tests showed elevated levels of serum IgG4 and HbA1c. Computed tomography of the pancreatic body demonstrated a weakly enhanced mass, 2 cm in size, with indistinct borders. Magnetic resonance cholangiopancreatography revealed a narrowing of the main pancreatic duct (MPD) at the pancreatic body, a markedly dilated upstream duct, and a slightly dilated downstream duct. Endoscopic ultrasonography demonstrated an iso-hypoechoic heterogeneous mass, protruding and spreading in the pancreatic duct...
March 2018: Journal of Gastrointestinal and Liver Diseases: JGLD
Nigani Willie, Rajeev K Mehlotra, Rosalind E Howes, Tovonahary A Rakotomanga, Stephanie Ramboarina, Arsène C Ratsimbasoa, Peter A Zimmerman
Plasmodium falciparum histidine-rich protein 2 (PfHRP2) forms the basis of many current malaria rapid diagnostic tests (RDTs). However, the parasites lacking part or all of the pfhrp2 gene do not express the PfHRP2 protein and are, therefore, not identifiable by PfHRP2-detecting RDTs. We evaluated the performance of the SD Bioline Malaria Ag P.f/Pan RDT together with pfhrp2 variation in Madagascar. Genomic DNA isolated from 260 patient blood samples were polymerase chain reaction (PCR)-amplified for the parasite 18S rRNA and pfhrp2 genes...
March 19, 2018: American Journal of Tropical Medicine and Hygiene
Jamie R Wood
Ancient samples present a number of technical challenges for DNA barcoding, including damaged DNA with low endogenous copy number and short fragment lengths. Nevertheless, techniques are available to overcome these issues, and DNA barcoding has now been used to successfully recover parasite DNA from a wide variety of ancient substrates, including coprolites, cesspit sediment, mummified tissues, burial sediments and permafrost soils. The study of parasite DNA from ancient samples can provide a number of unique scientific insights, for example: (1) into the parasite communities and health of prehistoric human populations; (2) the ability to reconstruct the natural parasite faunas of rare or extinct host species, which has implications for conservation management and de-extinction; and (3) the ability to view in 'real-time' processes that may operate over century- or millenial-timescales, such as how parasites responded to past climate change events or how they co-evolved alongside their hosts...
March 20, 2018: Parasitology
Taeman Han, Seung-Hyun Kim, Hyung Joo Yoon, In Gyun Park, Haechul Park
We reassessed species diversity and genetic structure in Korean bumble bees using DNA barcode analyses of 484 cytochrome c oxidase subunit I (COI) sequences from 24 morphospecies. Based on COI, all of the Korean species formed distinct clades in the phylogenetic trees, except for Bombus (Megabombus) koreanus in the maximum likelihood tree. Five species exhibited low interspecific genetic distances (range: 1.2-2.7%), indicating that they are recently diverged species. COI data could not be used to identify bumble bees at the subspecies level...
March 20, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Beata Peplonska, Mariusz Berdynski, Monika Mandecka, Anna Barczak, Magdalena Kuzma-Kozakiewicz, Maria Barcikowska, Cezary Zekanowski
Activation of the TREM2 receptor on microglia stimulates phagocytosis and decreases the microglial proinflammatory response. Mutations in exon 2 of the TREM2 gene have been reported to be associated with various neurodegenerative diseases characterized by chronic inflammation. The aim of our study was to evaluate exon 2 of TREM2 gene variants as a putative genetic risk factor for Alzheimer's disease (AD), frontotemporal dementia (FTD), and amyotrophic lateral sclerosis (ALS) in the Polish population. The results were interpreted using previously published data, especially highlighting differences in the prevalence of the variants among Caucasian subpopulations across different geographic regions...
March 20, 2018: Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration
Irena Urbanovska, Magdalena Houdova Megova, Zachary Dwight, Ondrej Kalita, Magdalena Uvirova, Jarmila Simova, Lucie Tuckova, Petr Buzrla, Tomas Palecek, Marian Hajduch, Jana Dvorackova, Jiri Drabek
Mutations in IDH1/2 genes are a marker of good prognosis for glioma patients, associated with low grade gliomas and secondary glioblastomas. Immunohistochemistry and Sanger sequencing are current standards for IDH1/2 genotyping while many other methods exist. The aim of this study was to validate Competitive amplification of differentially melting amplicons (CADMA) PCR for IDH genotyping by comparison with SNaPshot assay and two immunohistochemical methods. In our study, 87 glioma patients (46 from Olomouc and 41 from Ostrava) were analyzed...
March 19, 2018: Pathology Oncology Research: POR
Chunyao Zhou, Yongheng Wang, Xing Liu, Yuchao Liang, Ziwen Fan, Tao Jiang, Yinyan Wang, Lei Wang
BACKGROUND: The newly proposed putamen classification system shows good prognostic value in patients with insular LGGs, yet no study towards the molecular profiles of putamen involved LGGs has been proposed. METHODS: Clinical information and imaging data of patients diagnosed with insular low-grade gliomas were collected retrospectively. Genetic information of the 34 tumors was assessed using RNA-sequencing. Gene set enrichment analysis was further performed to identify the genes showing differential expression between putamen-involved tumors and putamen non-involved tumors...
March 19, 2018: Journal of Neuro-oncology
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