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DNA Sequencing

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https://www.readbyqxmd.com/read/29352323/identification-of-a-molecular-marker-tightly-linked-to-bacterial-wilt-resistance-in-tomato-by-genome-wide-snp-analysis
#1
Boyoung Kim, In Sun Hwang, Hyung Jin Lee, Je Min Lee, Eunyoung Seo, Doil Choi, Chang-Sik Oh
Genotyping of disease resistance to bacterial wilt in tomato by a genome-wide SNP analysis Bacterial wilt caused by Ralstonia pseudosolanacearum is one of the destructive diseases in tomato. The previous studies have identified Bwr-6 (chromosome 6) and Bwr-12 (chromosome 12) loci as the major quantitative trait loci (QTLs) contributing to resistance against bacterial wilt in tomato cultivar 'Hawaii7996'. However, the genetic identities of two QTLs have not been uncovered yet. In this study, using whole-genome resequencing, we analyzed genome-wide single-nucleotide polymorphisms (SNPs) that can distinguish a resistant group, including seven tomato varieties resistant to bacterial wilt, from a susceptible group, including two susceptible to the same disease...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29352281/differential-dna-methylation-and-transcription-profiles-in-date-palm-roots-exposed-to-salinity
#2
Ibtisam Al-Harrasi, Rashid Al-Yahyai, Mahmoud W Yaish
As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation...
2018: PloS One
https://www.readbyqxmd.com/read/29352198/orid-structure-controls-repd-initiation-during-rolling-circle-replication
#3
Algirdas Toleikis, Martin R Webb, Justin E Molloy
Bacterial antibiotic resistance is often carried by circular DNA plasmids that are copied separately from the genomic DNA and can be passed to other bacteria, spreading the resistance. The chloramphenicol-resistance plasmid pC221 from Staphylococcus aureus is duplicated by a process called asymmetric rolling circle replication. It is not fully understood how the replication process is regulated but its initiation requires a plasmid-encoded protein called RepD that nicks one strand of the parent plasmid at the double-stranded origin of replication (oriD)...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352182/chloroplast-genomic-resources-for-phylogeny-and-dna-barcoding-a-case-study-on-fritillaria
#4
Yu Bi, Ming-Fang Zhang, Jing Xue, Ran Dong, Yun-Peng Du, Xiu-Hai Zhang
The genus Fritillaria comprises approximately 130 perennial herbaceous species. In the Pharmacopoeia of the People's Republic of China, the bulbs of 11 Fritillaria species are used in Chinese herbal medicines. However, the traditional methods of morphological classification cannot accurately identify closely related species of Fritillaria. Previous studies have attempted to identify these species with universal molecular markers, but insufficient phylogenetic signal was available. In this study, the complete chloroplast genomes of eight Fritillaria species were compared...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352181/samhd1-is-recurrently-mutated-in-t-cell-prolymphocytic-leukemia
#5
Patricia Johansson, Ludger Klein-Hitpass, Axel Choidas, Peter Habenberger, Bijan Mahboubi, Baek Kim, Anke Bergmann, René Scholtysik, Martina Brauser, Anna Lollies, Reiner Siebert, Thorsten Zenz, Ulrich Dührsen, Ralf Küppers, Jan Dürig
T-cell prolymphocytic leukemia (T-PLL) is an aggressive malignancy with a median survival of the patients of less than two years. Besides characteristic chromosomal translocations, frequent mutations affect the ATM gene, JAK/STAT pathway members, and epigenetic regulators. We here performed a targeted mutation analysis for 40 genes selected from a RNA sequencing of 10 T-PLL in a collection of 28 T-PLL, and an exome analysis of five further cases. Nonsynonymous mutations were identified in 30 of the 40 genes, 18 being recurrently mutated...
January 19, 2018: Blood Cancer Journal
https://www.readbyqxmd.com/read/29352178/compositional-bias-in-na%C3%A3-ve-and-chemically-modified-phage-displayed-libraries-uncovered-by-paired-end-deep-sequencing
#6
Bifang He, Katrina F Tjhung, Nicholas J Bennett, Ying Chou, Andrea Rau, Jian Huang, Ratmir Derda
Understanding the composition of a genetically-encoded (GE) library is instrumental to the success of ligand discovery. In this manuscript, we investigate the bias in GE-libraries of linear, macrocyclic and chemically post-translationally modified (cPTM) tetrapeptides displayed on the M13KE platform, which are produced via trinucleotide cassette synthesis (19 codons) and NNK-randomized codon. Differential enrichment of synthetic DNA {S}, ligated vector {L} (extension and ligation of synthetic DNA into the vector), naïve libraries {N} (transformation of the ligated vector into the bacteria followed by expression of the library for 4...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352077/whole-genome-sequencing-of-suppressor-dna-mixtures-identifies-pathways-that-compensate-for-chromosome-segregation-defects-in-schizosaccharomyces-pombe
#7
Xingya Xu, Li Wang, Mitsuhiro Yanagida
Suppressor screening is a powerful method to identify genes that when mutated, rescue the temperature sensitivity of the original mutation. Previously, however, identification of suppressor mutations has been technically difficult. Due to the small genome size of Schizosaccharomyces pombe, we developed a spontaneous suppressor screening technique, followed by a cost-effective sequencing method. Genomic DNAs of 10 revertants which survived at the restrictive temperature of the original temperature sensitive (ts) mutant were mixed together as one sample before constructing a library for sequencing...
January 19, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29351919/high-yield-of-pathogenic-germline-mutations-causative-or-likely-causative-of-the-cancer-phenotype-in-selected-children-with-cancer
#8
Illja Diets, Esmé Waanders, Marjolijn J L Ligtenberg, Diede van Bladel, Eveline J Kamping, Peter M Hoogerbrugge, Saskia Hopman, Maran J W Olderode-Berends, Erica H Gerkes, David Koolen, Carlo Marcelis, Gijs We Santen, Martine van Belzen, Dylan Mordaunt, Lesley McGregor, Elizabeth Thompson, Antonis Kattamis, Agata Pastorczak, Wojciech Mlynarski, Denisa Ilencikova, Anneke Vulto-van Silfhout, Thatjana Gardeitchik, E S J M de Bont, Jan Loeffen, Anja Wagner, Arjen R Mensenkamp, Roland P Kuiper, Nicoline Hoogerbrugge, Marjolijn Jongmans
PURPOSE: In many children with cancer and characteristics suggestive of a genetic predisposition syndrome, the genetic cause is still unknown. We studied the yield of pathogenic mutations by applying whole exome sequencing on a selected cohort of children with cancer. EXPERIMENTAL DESIGN: To identify mutations in known and novel cancer predisposing genes, we performed trio-based whole exome sequencing on germline DNA of 40 selected children and their parents. These children were diagnosed with cancer and had at least one of the following features: (1) intellectual disability and/or congenital anomalies, (2) multiple malignancies, (3) family history of cancer or (4) an adult type of cancer...
January 19, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29351917/a-novel-method-for-rapid-molecular-subgrouping-of-medulloblastoma
#9
Soledad Gómez, Alícia Garrido-Garcia, Laura Garcia-Gerique, Isadora Lemos, Mariona Suñol, Carmen de Torres, Marta Kulis, Sara Perez-Jaume, Angel M Carcaboso, Betty Luu, Mark W Kieran, Nada Jabado, Alexey Kozlenkov, Stella Dracheva, Vijay Ramaswamy, Volker Hovestadt, Pascal Johann, David T W Jones, Stefan M Pfister, Andrés Morales La Madrid, Ofelia Cruz, Michael D Taylor, Jose I Martín-Subero, Jaume Mora, Cinzia Lavarino
PURPOSE: The classification of medulloblastoma into WNT, SHH, Group 3 and Group 4 subgroups has become of critical importance for patient risk-stratification and subgroup-tailored clinical trials. Here, we aimed to develop a simplified, clinically applicable classification approach that can be implemented in the majority of centers treating patients with medulloblastoma. EXPERIMENTAL DESIGN: We analyzed 1,577 samples comprising previously published DNA methylation microarray data (913 medulloblastomas, 457 non-medulloblastoma tumors, 85 normal tissues), and 122 frozen and formalin-fixed paraffin-embedded medulloblastoma samples...
January 19, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29351869/allosteric-kissing-complex-based-electrochemical-biosensor-for-sensitive-regenerative-and-versatile-detection-of-proteins
#10
Mingsha Zhao, Shanshan Zhang, Zhiqiang Chen, Changzhi Zhao, Li Wang, Shufeng Liu
Herein, an allosteric kissing complex-based electrochemical biosensor was ingeniously proposed for the simple, sensitive, regenerative and versatile detection of proteins. Two hairpins (Hp1 and Hp2) were designed and the Hp1 was immobilized on the electrode surface, which could form a kissing complex with Hp2 through the apical loop-loop or kissing interaction of the RNA-RNA base sequences. The Hp2 possesses the appended single-stranded tails on each end, which hybridize with the recognition element-conjugated DNA strands to construct a protein responsive switch of Hp2 scaffold...
January 9, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29351848/a-distinct-class-of-genome-rearrangements-driven-by-heterologous-recombination
#11
Ana María León-Ortiz, Stephanie Panier, Grzegorz Sarek, Jean-Baptiste Vannier, Harshil Patel, Peter J Campbell, Simon J Boulton
Erroneous DNA repair by heterologous recombination (Ht-REC) is a potential threat to genome stability, but evidence supporting its prevalence is lacking. Here we demonstrate that recombination is possible between heterologous sequences and that it is a source of chromosomal alterations in mitotic and meiotic cells. Mechanistically, we find that the RTEL1 and HIM-6/BLM helicases and the BRCA1 homolog BRC-1 counteract Ht-REC in Caenorhabditis elegans, whereas mismatch repair does not. Instead, MSH-2/6 drives Ht-REC events in rtel-1 and brc-1 mutants and excessive crossovers in rtel-1 mutant meioses...
January 18, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29351780/fancm-and-recql-genetic-variants-and-breast-cancer-susceptibility-relevance-to-south-poland-and-west-ukraine
#12
Tú Nguyen-Dumont, Aleksander Myszka, Pawel Karpinski, Maria M Sasiadek, Hayane Akopyan, Fleur Hammet, Helen Tsimiklis, Daniel J Park, Bernard J Pope, Ryszard Slezak, Nataliya Kitsera, Aleksandra Siekierzynska, Melissa C Southey
BACKGROUND: FANCM and RECQL have recently been reported as breast cancer susceptibility genes and it has been suggested that they should be included on gene panel tests for breast cancer predisposition. However, the clinical value of testing for mutations in RECQL and FANCM remains to be determined. In this study, we have characterised the spectrum of FANCM and RECQL mutations in women affected with breast or ovarian cancer from South-West Poland and West Ukraine. METHODS: We applied Hi-Plex, an amplicon-based enrichment method for targeted massively parallel sequencing, to screen the coding exons and proximal intron-exon junctions of FANCM and RECQL in germline DNA from unrelated women affected with breast cancer (n = 338) and ovarian cancer (n = 89) from Poland (n = 304) and Ukraine (n = 123)...
January 19, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29351565/sumo-targeting-of-a-stress-tolerant-ulp1-sumo-protease
#13
Jennifer Peek, Catherine Harvey, Dreux Gray, Danny Rosenberg, Likhitha Kolla, Reuben Levy-Myers, Rui Yin, Jonathan L McMurry, Oliver Kerscher
SUMO proteases of the SENP/Ulp family are master regulators of both sumoylation and desumoylation and regulate SUMO homeostasis in eukaryotic cells. SUMO conjugates rapidly increase in response to cellular stress, including nutrient starvation, hypoxia, osmotic stress, DNA damage, heat shock, and other proteotoxic stressors. Nevertheless, little is known about the regulation and targeting of SUMO proteases during stress. To this end we have undertaken a detailed comparison of the SUMO-binding activity of the budding yeast protein Ulp1 (ScUlp1) and its ortholog in the thermotolerant yeast Kluyveromyces marxianus, KmUlp1...
2018: PloS One
https://www.readbyqxmd.com/read/29351298/construction-of-an-infectious-horsepox-virus-vaccine-from-chemically-synthesized-dna-fragments
#14
Ryan S Noyce, Seth Lederman, David H Evans
Edward Jenner and his contemporaries believed that his variolae vaccinae originated in horses and molecular analyses show that modern vaccinia virus (VACV) strains share common ancestry with horsepox virus (HPXV). Given concerns relating to the toxicity of modern VACV vaccines, we asked whether an HPXV-based vaccine might provide a superior alternative. Since HPXV may be extinct and the only specimen of HPXV that has been identified is unavailable for investigation, we explored whether HPXV could be obtained by large-scale gene synthesis...
2018: PloS One
https://www.readbyqxmd.com/read/29351066/contamination-of-swimming-pools-and-hot-tubs-biofilms-with-acanthamoeba
#15
Behroz Mahdavi Poor, Abdolhossein Dalimi, Fatemeh Ghafarifar, Fariba Khoshzaban, Jalal Abdolalizadeh
The members of Acanthamoeba genus are ubiquitous amoeba which could be a pathogenic parasite. The amoeba is resistant to the common chlorine concentration that used for disinfecting the swimming pool water. Therefore, the pools can be suitable environments for the survival and multiplication of the amoeba. In this cross sectional study, 10 indoor recreational water centers from different regions of Tabriz city were selected and sampling was done from fixed and floating biofilms of the swimming pools and hot tubs...
March 26, 2018: Acta Parasitologica
https://www.readbyqxmd.com/read/29350524/development-of-a-multiplexed-microsphere-pcr-for-rapid-culture-free-detection-and-gram-typing-of-bacteria-in-human-blood-samples
#16
Fang Liang, Daniel J Browne, Megan J Gray, Kate H Gartlan, David D Smith, Ross Barnard, Geoff R Hill, Simon Robert Corrie, Kate Markey
Blood stream infection is a significant clinical problem, particularly in vulnerable patient groups such as those undergoing chemotherapy and bone marrow transplantation. Clinical diagnostics for suspected blood stream infection remain centered around blood culture (highly variable timing, hours to days), and empiric use of broad-spectrum antibiotics is often employed for patients presenting with febrile neutropenia. Gram-typing provides the first opportunity to target therapy (e.g. combinations containing vancomycin or teicoplanin for Gram-positives; piperacillin-tazobactam or a carbapenem for Gram-negatives), however current approaches require blood culture...
January 19, 2018: ACS Infectious Diseases
https://www.readbyqxmd.com/read/29350440/abrupt-burial-imparts-persistent-changes-to-the-bacterial-diversity-of-turbidite-associated-sediment-profiles
#17
B K Harrison, A Myrbo, B E Flood, J V Bailey
The emplacement of subaqueous gravity-driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical and biological signatures of turbidite deposition, the response of bacteria and archaea within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and those attached to allochthonous material must respond to substantially altered environmental conditions and selective pressures...
January 19, 2018: Geobiology
https://www.readbyqxmd.com/read/29350394/genetic-variants-in-the-polish-population-of-patients-with-pulmonary-arterial-hypertension-sequencing-of-bmpr2-alk1-and-eng-genes
#18
Barbara Uznańska-Loch, Kamil Wikło, Dominika Kulczycka-Wojdala, Bożena Szymańska, Łukasz Chrzanowski, Karina Wierzbowska-Drabik, Ewa Trzos, Jarosław Damian Kasprzak, Małgorzata Kurpesa
BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with a very serious prognosis. It seems that mutations in genes related to the transforming growth factor-beta signaling pathway are often related to the development of the disease. There was no study in Polish population that would cover this problem. AIM: To screen for genetic mutations in Polish cohort of patients with pulmonary hypertension, especially with idiopathic PAH, treated in a single hospital in Poland...
January 19, 2018: Kardiologia Polska
https://www.readbyqxmd.com/read/29350329/detection-of-human-papillomavirus-dna-in-tumors-from-rwandese-breast-cancer-patients
#19
REVIEW
Thierry Habyarimana, Mohammed Attaleb, Jean Baptiste Mazarati, Youssef Bakri, Mohammed El Mzibri
BACKGROUND: During the last decades, a great interest was given to viral etiology of breast cancer. Indeed, due to recent technical improvements and some encouraging new results, it has been a resurgence of interest in the possibility that a substantial proportion of human breast cancers may be caused by viral infections. High-risk genotypes of human papillomavirus (HPV) have been found in breast cancer cases. In the present study, we aimed to assess the presence of HPV DNA in breast cancer cases from Rwanda and to evaluate the association between HPV infection and clinico-pathological features...
January 19, 2018: Breast Cancer: the Journal of the Japanese Breast Cancer Society
https://www.readbyqxmd.com/read/29350245/chitinophaga-caseinilytica-sp-nov-a-casein-hydrolysing-bacterium-isolated-from-forest-soil
#20
Ram Hari Dahal, Jaisoo Kim
A novel casein hydrolysing bacterium designated strain S-52T was isolated from Kyonggi University forest soil. Cells were strictly aerobic, Gram stain-negative, oxidase- and catalase- positive, non-motile, non-spore-forming, rod-shaped, and golden-yellow-pigmented. Strain S-52T hydrolysed casein. It was able to grow at 20-37 °C (optimum 25-32 °C), pH 6.5-11.0 (optimum 7-9.5), and at 3% (w/v) NaCl concentration. Strain exhibits flexirubin-type pigments. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain S-52T formed a lineage within the genus Chitinophaga that was distinct from other species of the genus...
January 19, 2018: Archives of Microbiology
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