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DNA Sequencing

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https://www.readbyqxmd.com/read/29793141/new-contributions-to-gruberia-lanceolata-gruber-1884-kahl-1932-based-on-analyses-of-multiple-populations-and-genes-ciliophora-heterotrichea-gruberiidae
#1
Xiangrui Chen, Shahed Uddin Ahmed Shazib, Ji Hye Kim, Min Seok Kim, Mann Kyoon Shin
Gruberia Kahl, 1932 is a species-poor genus comprising only seven named species. Most of these species have not been reinvestigated since the original reports. In the present work, we investigated the taxonomy and phylogeny of Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of morphology and multiple gene sequences from four South Korean populations. This species is mainly characterized by a well-developed peristome region, segmented paroral membrane, and moniliform macronucleus. Some morphological features were not stable among the four populations investigated, such as body shape and size, cell color, and the ratio of oral length to body length...
May 9, 2018: European Journal of Protistology
https://www.readbyqxmd.com/read/29792944/enrichment-of-low-density-symbiont-dna-from-minute-insects
#2
Corinne M Stouthamer, Suzanne Kelly, Martha S Hunter
Symbioses between bacteria and insects are often associated with changes in important biological traits that can significantly affect host fitness. To a large extent, studies of these interactions have been based on physiological changes or induced phenotypes in the host, and the genetic mechanisms by which symbionts interact with their hosts have only recently become better understood. Learning about symbionts has been challenging in part due to difficulties such as obtaining enough high quality genomic material for high throughput sequencing technology, especially for symbionts present in low titers, and in small or difficult to rear non-model hosts...
May 21, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29792930/functional-genomics-for-the-oleaginous-yeast-yarrowia-lipolytica
#3
Kurt Patterson, James Yu, Jenny Landberg, Ivan Chang, Farbod Shavarebi, Virginia Bilanchone, Suzanne Sandmeyer
Oleaginous yeasts are valuable systems for biosustainable production of hydrocarbon-based chemicals. Yarrowia lipolytica is one of the best characterized of these yeast with respect to genome annotation and flux analysis of metabolic processes. Nonetheless, progress is hampered by a dearth of genome-wide tools enabling functional genomics. In order to remedy this deficiency, we developed a library of Y. lipolytica insertion mutants via transposon mutagenesis. The Hermes DNA transposon was expressed to achieve saturation mutagenesis of the genome...
May 21, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29792884/pharmacological-inhibition-of-dna-methylation-attenuates-pressure-overload-induced-cardiac-hypertrophy-in-rats
#4
Justus Stenzig, Yvonne Schneeberger, Alexandra Löser, Barbara S Peters, Andreas Schaefer, Rong-Rong Zhao, Shi Ling Ng, Grit Höppner, Birgit Geertz, Marc N Hirt, Wilson Tan, Eleanor Wong, Hermann Reichenspurner, Roger S-Y Foo, Thomas Eschenhagen
BACKGROUND: Heart failure is associated with altered gene expression and DNA methylation. De novo DNA methylation is associated with gene silencing, but its role in cardiac pathology remains incompletely understood. We hypothesized that inhibition of DNA methyltransferases (DNMT) might prevent the deregulation of gene expression and the deterioration of cardiac function under pressure overload (PO). To test this hypothesis, we evaluated a DNMT inhibitor in PO in rats and analysed DNA methylation in cardiomyocytes...
May 21, 2018: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/29792700/the-energy-landscapes-of-mini-dumbbell-dna-octanucleotides
#5
James S Klimavicz, Konstantin Röder, David J Wales
Single-stranded DNA structures play a significant role in biological systems, in particular during replication, translation and DNA repair. Tracts of simple repetitive DNA (srDNA) are associated with slipped-strand mispairing (SSMs), that can lead to genetic diseases. Recent NMR studies of TTTA and CCTG repeats have shown that these sequences form mini-dumbbells (MDBs), leading to frameshift mutations. Here we explore the energy landscapes of (CCTG)2 and (TTTA)2 , which are currently the smallest known molecules to form MDBs...
May 24, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29792694/biomimetic-artificial-epigenetic-code-for-targeted-acetylation-of-histones
#6
Junichi Taniguchi, Yihong Feng, Ganesh N Pandian, Fumitaka Hashiya, Takuya Hidaka, Kaori Hashiya, Soyoung Park, Toshikazu Bando, Shinji Ito, Hiroshi Sugiyama
While the central role of locus-specific acetylation of histone proteins in eukaryotic gene expression is well established, the availability of designer tools to regulate acetylation at particular nucleosome sites remains limited. Here, we develop a unique strategy to introduce acetylation by constructing a bifunctional molecule designated Bi-PIP. Bi-PIP has a P300/CBP-selective bromodomain inhibitor (Bi) as a P300/CBP recruiter and a pyrrole-imidazole polyamide (PIP) as a sequence-selective DNA binder. Biochemical assays verified that Bi-PIPs recruit P300 to the nucleosomes having their target DNA sequences and extensively accelerate acetylation...
May 24, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29792590/altererythrobacter-flavus-sp-nov-isolated-from-mangrove-sediment
#7
Hui Ma, Hao Ren, Lingfeng Huang, Yuanrong Luo
A Gram-negative, aerobic, non-motile, rod-shaped bacterium, designated MS1-4T , was isolated from mangrove sediment of the Jiulong River Estuary, Fujian Province, China. The isolate formed yellow colonies on ZB 2216E agar. Optimal growth was observed at pH 6.0, at 34 °C and in the presence of 4 % (w/v) NaCl. Strain MS1-4T shared highest 16S rRNA gene sequence similarity of 97.7 % with Altererythrobacter mangrovi C9-11T , followed by Altererythrobacter ishigakiensis JPCCMB0017T (97.2 %). Phylogenetic analysis indicated that strain MS1-4T formed a clade with A...
May 24, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29792566/clues-to-an-evolutionary-mystery-the-genes-for-t-toxin-enabler-of-the-devastating-1970-southern-corn-leaf-blight-epidemic-are-present-in-ancestral-species-suggesting-an-ancient-origin
#8
Bradford J Condon, Candace E Elliott, Jonathan Gonzalez, Sung-Hwan Yun, Yasunori Akagi, Tyr Wiesner-Hanks, Motoichiro Kodama, Gillian Turgeon
The Southern Corn Leaf Blight epidemic of 1970 devastated fields of T-cytoplasm corn planted in monoculture throughout the eastern US. The epidemic was driven by race T, a previously unseen race of Cochliobolus heterostrophus. A second fungus, Phyllosticta zeae-maydis, with the same biological specificity, appeared coincidentally. Race T produces T-toxin, while P. zeae-maydis produces PM-toxin, both host selective polyketide toxins necessary for supervirulence. Present abundance of genome sequences offers an opportunity to tackle the evolutionary origins of T- and PM- toxin biosynthetic genes, previously thought unique to these species...
May 24, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29792237/according-to-mitochondrial-dna-evidence-parascaris-equorum-and-parascaris-univalens-may-represent-the-same-species
#9
J F Gao, X X Zhang, X X Wang, Q Li, Y Li, W W Xu, Y Gao, C R Wang
Parascarosis is caused mainly by parasitic infections with Parascaris equorum and Parascaris univalens, the most common ascarid nematodes, in the small intestine of equines. Parascarosis often causes severe illness and even death in foals and yearlings. In this study, we obtained the complete sequence of the P. equorum mitochondrial (mt) genome and compared its organization and structure with that of P. equorum Japan isolate (nearly complete), and the complete mtDNA sequences of P. univalens Switzerland and USA isolates...
May 24, 2018: Journal of Helminthology
https://www.readbyqxmd.com/read/29792227/integrated-time-course-omics-analysis-distinguishes-immediate-therapeutic-response-from-acquired-resistance
#10
Genevieve Stein-O'Brien, Luciane T Kagohara, Sijia Li, Manjusha Thakar, Ruchira Ranaweera, Hiroyuki Ozawa, Haixia Cheng, Michael Considine, Sandra Schmitz, Alexander V Favorov, Ludmila V Danilova, Joseph A Califano, Evgeny Izumchenko, Daria A Gaykalova, Christine H Chung, Elana J Fertig
BACKGROUND: Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients' treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors...
May 23, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29792182/boostme-accurately-predicts-dna-methylation-values-in-whole-genome-bisulfite-sequencing-of-multiple-human-tissues
#11
Luli S Zou, Michael R Erdos, D Leland Taylor, Peter S Chines, Arushi Varshney, Stephen C J Parker, Francis S Collins, John P Didion
BACKGROUND: Bisulfite sequencing is widely employed to study the role of DNA methylation in disease; however, the data suffer from biases due to coverage depth variability. Imputation of methylation values at low-coverage sites may mitigate these biases while also identifying important genomic features associated with predictive power. RESULTS: Here we describe BoostMe, a method for imputing low-quality DNA methylation estimates within whole-genome bisulfite sequencing (WGBS) data...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792109/computational-functional-genomics-based-approaches-in-analgesic-drug-discovery-and-repurposing
#12
Catharina Lippmann, Dario Kringel, Alfred Ultsch, Jörn Lötsch
Persistent pain is a major healthcare problem affecting a fifth of adults worldwide with still limited treatment options. The search for new analgesics increasingly includes the novel research area of functional genomics, which combines data derived from various processes related to DNA sequence, gene expression or protein function and uses advanced methods of data mining and knowledge discovery with the goal of understanding the relationship between the genome and the phenotype. Its use in drug discovery and repurposing for analgesic indications has so far been performed using knowledge discovery in gene function and drug target-related databases; next-generation sequencing; and functional proteomics-based approaches...
May 24, 2018: Pharmacogenomics
https://www.readbyqxmd.com/read/29791837/phosphorylation-state-of-zfp24-controls-oligodendrocyte-differentiation
#13
Benayahu Elbaz, Joshua D Aaker, Sara Isaac, Anna Kolarzyk, Pedro Brugarolas, Amir Eden, Brian Popko
Zinc finger protein ZFP24, formerly known as ZFP191, is essential for oligodendrocyte maturation and CNS myelination. Nevertheless, the mechanism by which ZFP24 controls these processes is unknown. We demonstrate that ZFP24 binds to a consensus DNA sequence in proximity to genes important for oligodendrocyte differentiation and CNS myelination, and we show that this binding enhances target gene expression. We also demonstrate that ZFP24 DNA binding is controlled by phosphorylation. Phosphorylated ZFP24, which does not bind DNA, is the predominant form in oligodendrocyte progenitor cells...
May 22, 2018: Cell Reports
https://www.readbyqxmd.com/read/29791787/dna-barcoding-of-microgastrine-parasitoid-wasps-hymenoptera-braconidae-using-high-throughput-methods-more-than-doubles-the-number-of-species-known-for-australia
#14
Erinn P Fagan-Jeffries, Steven J B Cooper, Terry Bertozzi, Tessa M Bradford, Andrew D Austin
The Microgastrinae are a hugely diverse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents, and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Northern Hemisphere, the Australian fauna has received little attention. In total, 100 species have been described from or have been introduced into Australia, but the real species diversity for the region is clearly much larger than this...
May 23, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29791785/expressed-exome-capture-sequencing-eecseq-a-method-for-cost-effective-exome-sequencing-for-all-organisms
#15
Jonathan B Puritz, Katie E Lotterhos
Exome capture is an effective tool for surveying the genome for loci under selection. However, traditional methods require annotated genomic resources. Here, we present a method for creating cDNA probes from expressed mRNA, which are then used to enrich and capture genomic DNA for exon regions. This approach, called "EecSeq", eliminates the need for costly probe design and synthesis. We tested EecSeq in the eastern oyster, Crassostrea virginica, using a controlled exposure experiment. Four adult oysters were heat shocked at 36° C for 1 hour along with four control oysters kept at 14° C...
May 23, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29791719/molecular-and-morphological-diversity-of-trebouxia-microalgae-in-sphaerothallioid-circinaria-spp-lichens
#16
Arántzazu Molins, Patricia Moya, Francisco J García-Breijo, José Reig-Armiñana, Eva Barreno
Three vagrant (Circinaria hispida, Circinaria gyrosa, Circinaria sp. 'paramerae') and one crustose (semi-vagrant, Circinaria sp.'oromediterranea') lichens growing in very continental areas in the Iberian Peninsula were selected to study the phycobiont diversity. Mycobiont identification was checked using nrITS DNA barcoding: Circinaria sp.'oromediterranea' and Circinaria sp. 'paramerae' formed a new clade. Phycobiont diversity was analyzed in 50 thalli of Circinaria spp. using nrITS DNA and LSU rDNA, with microalgae coexistence being found in all the species analyzed by Sanger sequencing...
May 23, 2018: Journal of Phycology
https://www.readbyqxmd.com/read/29791459/species-identification-and-connectivity-of-marine-amphipods-in-canada-s-three-oceans
#17
Astrid Tempestini, Søren Rysgaard, France Dufresne
Monitoring the distribution of marine biodiversity is a crucial step to better assess the impacts of global changes. Arctic marine fauna is dominated by amphipods in terms of abundance and biomass. These peracarids are an important marine order of crustaceans but the number of species found in the different Canadian oceans is currently unknown. Furthermore, most species are difficult to identify due to poor taxonomic descriptions and morphological convergence. The aim of this study was to assess the species diversity of marine amphipods in the three Canadian oceans using DNA barcoding...
2018: PloS One
https://www.readbyqxmd.com/read/29791457/a-feasibility-study-of-colorectal-cancer-diagnosis-via-circulating-tumor-dna-derived-cnv-detection
#18
Bhuvan Molparia, Glenn Oliveira, Jennifer L Wagner, Emily G Spencer, Ali Torkamani
Circulating tumor DNA (ctDNA) has shown great promise as a biomarker for early detection of cancer. However, due to the low abundance of ctDNA, especially at early stages, it is hard to detect at high accuracies while keeping sequencing costs low. Here we present a pilot stage study to detect large scale somatic copy numbers variations (CNVs), which contribute more molecules to ctDNA signal compared to point mutations, via cell free DNA sequencing. We show that it is possible to detect somatic CNVs in early stage colorectal cancer (CRC) patients and subsequently discriminate them from normal patients...
2018: PloS One
https://www.readbyqxmd.com/read/29791411/optical-nondestructive-dynamic-measurements-of-wafer-scale-encapsulated-nanofluidic-channels
#19
Vladimir Liberman, Melissa Smith, Isaac Weaver, Mordechai Rothschild
Nanofluidic channels are of great interest for DNA sequencing, chromatography, and drug delivery. However, metrology of embedded or sealed nanochannels and measurement of their fill-state have remained extremely challenging. Existing techniques have been restricted to optical microscopy, which suffers from insufficient resolution, or scanning electron microscopy, which cannot measure sealed or embedded channels without cleaving the sample. Here, we demonstrate a novel method for accurately extracting nanochannel cross-sectional dimensions and monitoring fluid filling, utilizing spectroscopic ellipsometric scatterometry, combined with rigorous electromagnetic simulations...
May 20, 2018: Applied Optics
https://www.readbyqxmd.com/read/29791287/brca1-2-mutations-and-bevacizumab-in-the-neoadjuvant-treatment-of-breast-cancer-response-and-prognosis-results-in-patients-with-triple-negative-breast-cancer-from-the-geparquinto-study
#20
Peter A Fasching, Sibylle Loibl, Chunling Hu, Steven N Hart, Hermela Shimelis, Raymond Moore, Christian Schem, Hans Tesch, Michael Untch, Jörn Hilfrich, Mahdi Rezai, Bernd Gerber, Serban Dan Costa, Jens-Uwe Blohmer, Tanja Fehm, Jens Huober, Cornelia Liedtke, Richard M Weinshilboum, Liewei Wang, James N Ingle, Volkmar Müller, Valentina Nekljudova, Karsten E Weber, Brigitte Rack, Matthias Rübner, Gunter von Minckwitz, Fergus J Couch
Purpose BRCA1/2 mutations are frequent in patients with triple-negative breast cancer (TNBC). These patients are often treated with primary systemic chemotherapy. The aim of this study was to analyze the effects of BRCA1/2 mutations on pathologic complete response (pCR) and disease-free survival (DFS) in a cohort of patients with TNBC treated with anthracycline and taxane-containing chemotherapy, with or without bevacizumab. Patients and Methods Germline DNA was sequenced to identify mutations in BRCA1 and BRCA2 in 493 patients with TNBC from the GeparQuinto study...
May 23, 2018: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
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