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https://www.readbyqxmd.com/read/29454054/genomic-perspectives-of-spider-silk-genes-through-target-capture-sequencing-conservation-of-stabilization-mechanisms-and-homology-based-structural-models-of-spidroin-terminal-regions
#1
Matthew A Collin, Thomas H Clarke, Nadia A Ayoub, Cheryl Y Hayashi
A powerful system for studying protein aggregation, particularly rapid self-assembly, is spider silk. Spider silks are proteinaceous and silk proteins are synthesized and stored within silk glands as liquid dope. As needed, liquid dope is near-instantaneously transformed into solid fibers or viscous adhesives. The dominant constituents of silks are spidroins (spider fibroins) and their terminal domains are vital for the tight control of silk self-assembly. To better understand spidroin termini, we used target capture and deep sequencing to identify spidroin gene sequences from six species representing the araneoid families of Araneidae, Nephilidae, and Theridiidae...
February 14, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29453361/heterogeneity-and-mutation-in-kras-and-associated-oncogenes-evaluating-the-potential-for-the-evolution-of-resistance-to-targeting-of-kras-g12c
#2
Vincent L Cannataro, Stephen G Gaffney, Carly Stender, Zi-Ming Zhao, Mark Philips, Andrew E Greenstein, Jeffrey P Townsend
Activating mutations in RAS genes are associated with approximately 20% of all human cancers. New targeted therapies show preclinical promise in inhibiting the KRAS G12C variant. However, concerns exist regarding the effectiveness of such therapies in vivo given the possibilities of existing intratumor heterogeneity or de novo mutation leading to treatment resistance. We performed deep sequencing of 27 KRAS G12-positive lung tumors to determine the prevalence of other oncogenic mutations within KRAS or within commonly mutated downstream genes that could confer resistance at the time of treatment...
February 16, 2018: Oncogene
https://www.readbyqxmd.com/read/29449542/long-non-coding-rnas-in-ischemic-stroke
#3
REVIEW
Mei-Hua Bao, Vivian Szeto, Burton B Yang, Shu-Zhen Zhu, Hong-Shuo Sun, Zhong-Ping Feng
Stroke is one of the leading causes of mortality and disability worldwide. Uncovering the cellular and molecular pathophysiological processes in stroke have been a top priority. Long non-coding (lnc) RNAs play critical roles in different kinds of diseases. In recent years, a bulk of aberrantly expressed lncRNAs have been screened out in ischemic stroke patients or ischemia insulted animals using new technologies such as RNA-seq, deep sequencing, and microarrays. Nine specific lncRNAs, antisense non-coding RNA in the INK4 locus (ANRIL), metastasis-associate lung adenocarcinoma transcript 1 (MALAT1), N1LR, maternally expressed gene 3 (MEG3), H19, CaMK2D-associated transcript 1 (C2dat1), Fos downstream transcript (FosDT), small nucleolar RNA host gene 14 (SNHG14), and taurine-upregulated gene 1 (TUG1), were found increased in cerebral ischemic animals and/or oxygen-glucose deprived (OGD) cells...
February 15, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29449433/highly-similar-genomic-landscapes-in-monoclonal-b-cell-lymphocytosis-and-ultra-stable-chronic-lymphocytic-leukemia-with-low-frequency-of-driver-mutations
#4
Andreas Agathangelidis, Viktor Ljungström, Lydia Scarfò, Claudia Fazi, Maria Gounari, Tatjana Pandzic, Lesley-Ann Sutton, Kostas Stamatopoulos, Giovanni Tonon, Richard Rosenquist, Paolo Ghia
Despite the recent discovery of recurrent driver mutations in chronic lymphocytic leukemia, the genetic factors involved in disease onset remain largely unknown. To address this issue, we performed whole-genome sequencing in 11 individuals with monoclonal B-cell lymphocytosis, both of the low-count and high-count subtypes, and 5 patients with ultra-stable chronic lymphocytic leukemia (>10 years without progression from initial diagnosis). All three entities were indistiguishable at the genomic level exhibiting low genomic complexity and similar types of somatic mutations...
February 15, 2018: Haematologica
https://www.readbyqxmd.com/read/29449400/complete-genome-sequence-of-rice-hoja-blanca-tenuivirus-isolated-from-a-susceptible-rice-cultivar-in-colombia
#5
Jenyfer Jimenez, Monica Carvajal-Yepes, Ana Maria Leiva, Maribel Cruz, Luz Elena Romero, Carmen A Bolaños, Ivan Lozano, Wilmer J Cuellar
We describe here the complete genome of Rice hoja blanca tenuivirus The sequenced isolate was obtained by insect vector transmission from a symptomatic rice sample grown in Colombia. Sequence data from the four RNA components were obtained by deep sequencing (Illumina), and infections were confirmed by enzyme-linked immunosorbent assay and Sanger sequencing.
February 15, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29449390/analysis-of-the-complete-genome-sequence-of-cucumber-mosaic-virus-strain-k
#6
Richard Moyle, Lara-Simone Pretorius, Louise S Shuey, Ekaterina Nowak, Peer M Schenk
The complete genome sequence of Cucumber mosaic virus strain K was determined by deep RNA sequencing. The tripartite genome consists of a 3,382-nucleotide (nt) RNA1, a 3,050-nt RNA2, and a 2,218-nt RNA3 segment. Phylogenetic analysis placed RNA1 and RNA2 in subgroup IB. However, RNA3 grouped with subgroup IA isolates, indicating a likely recombination event.
February 15, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29449275/circulating-tumor-dna-reveals-genetics-clonal-evolution-and-residual-disease-in-classical-hodgkin-lymphoma
#7
Valeria Spina, Alessio Bruscaggin, Annarosa Cuccaro, Maurizio Martini, Martina Di Trani, Gabriela Forestieri, Martina Manzoni, Adalgisa Condoluci, Alberto Arribas, Lodovico Terzi-Di-Bergamo, Silvia Laura Locatelli, Elisa Cupelli, Luca Ceriani, Alden A Moccia, Anastasios Stathis, Luca Nassi, Clara Deambrogi, Fary Diop, Francesca Guidetti, Alessandra Cocomazzi, Salvatore Annunziata, Vittoria Rufini, Alessandro Giordano, Antonino Neri, Renzo Boldorini, Bernhard Gerber, Francesco Bertoni, Michele Ghielmini, Georg Stüssi, Armando Santoro, Franco Cavalli, Emanuele Zucca, Luigi Maria Larocca, Gianluca Gaidano, Stefan Hohaus, Carmelo Carlo-Stella, Davide Rossi
The rarity of neoplastic cells in the biopsy imposes major technical hurdles that have so far limited genomic studies in classical Hodgkin lymphoma (cHL). By using a highly sensitive and robust deep-next-generation-sequencing approach for circulating tumor DNA (ctDNA), here we aimed at tracking the genetics of cHL in different clinical phases, and its modifications upon treatment. The analysis was based on specimens collected from 80 newly diagnosed and 32 refractory cHL patients, including longitudinal samples collected under ABVD chemotherapy and longitudinal samples from relapsing patients treated with chemotherapy and immunotherapy...
February 15, 2018: Blood
https://www.readbyqxmd.com/read/29448252/functions-and-roles-of-long-non-coding-rnas-in-human-nasopharyngeal-carcinoma
#8
JingJing Wu, Swei Sunny Hann
Nasopharyngeal carcinoma (NPC) is one of the most common cancers originating in the nasopharynx and occurring at high frequency in South-eastern Asia and North Africa. Long non-coding RNAs (lncRNAs) are a class of non-protein-coding RNA molecules and key regulators of developmental, physiological, and pathological processes in humans. Emerging studies have shown that lncRNAs play critical roles in tumorgenicity and cancer prognosis. With the development of deep sequencing analyses, an extensive amount of functional lncRNAs have been discovered in nasopharyngeal carcinoma tissues and cell lines...
February 9, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29448067/antiviral-resistance-due-to-deletion-in-the-neuraminidase-gene-and-defective-interfering-like-viral-polymerase-basic-2-rna-of-influenza-a-virus-subtype-h3n2
#9
Ramona Trebbien, Claus Bohn Christiansen, Thea Kølsen Fischer
BACKGROUND AND OBJECTIVE: Antiviral treatment of influenza virus infections can lead to drug resistance of virus. This study investigates a selection of mutations in the full genome of H3N2 influenza A virus isolated from a patient in treatment with oseltamivir. STUDY DESIGN: Respiratory samples from a patient were collected before, during, and after antiviral treatment. Whole genome sequencing of the influenza virus by next generation sequencing, and low-frequency-variant analysis was performed...
February 11, 2018: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/29446767/clapo-syndrome-identification-of-somatic-activating-pik3ca-mutations-and-delineation-of-the-natural-history-and-phenotype
#10
Lara Rodriguez-Laguna, Kristina Ibañez, Gema Gordo, Sixto Garcia-Minaur, Fernando Santos-Simarro, Noelia Agra, Elena Vallespín, Victoria E Fernández-Montaño, Rubén Martín-Arenas, Ángela Del Pozo, Héctor González-Pecellín, Rocío Mena, Inmaculada Rueda-Arenas, María V Gomez, Cristina Villaverde, Ana Bustamante, Carmen Ayuso, Víctor L Ruiz-Perez, Julián Nevado, Pablo Lapunzina, Juan C Lopez-Gutierrez, Victor Martinez-Glez
PurposeCLAPO syndrome is a rare vascular disorder characterized by capillary malformation of the lower lip, lymphatic malformation predominant on the face and neck, asymmetry, and partial/generalized overgrowth. Here we tested the hypothesis that, although the genetic cause is not known, the tissue distribution of the clinical manifestations in CLAPO seems to follow a pattern of somatic mosaicism.MethodsWe clinically evaluated a cohort of 13 patients with CLAPO and screened 20 DNA blood/tissue samples from 9 patients using high-throughput, deep sequencing...
February 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29445130/comparative-genomic-inference-suggests-mixotrophic-lifestyle-for-thorarchaeota
#11
Yang Liu, Zhichao Zhou, Jie Pan, Brett J Baker, Ji-Dong Gu, Meng Li
Thorarchaeota are a new archaeal phylum within the Asgard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudflat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, fix inorganic carbon, reduce sulfur/sulfate and produce acetate...
February 14, 2018: ISME Journal
https://www.readbyqxmd.com/read/29444641/oasis-2-improved-online-analysis-of-small-rna-seq-data
#12
Raza-Ur Rahman, Abhivyakti Gautam, Jörn Bethune, Abdul Sattar, Maksims Fiosins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni, Stefan Bonn
BACKGROUND: Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep sequencing. RESULTS: Here we present Oasis 2, which is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy...
February 14, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29440697/ectopic-expression-of-s28a-mutated-histone-h3-modulates-longevity-stress-resistance-and-cardiac-function-in-drosophila
#13
J P Joos, A R Saadatmand, C Schnabel, I Viktorinová, T Brand, M Kramer, S Nattel, D Dobrev, P Tomancak, J Backs, P Kleinbongard, G Heusch, K Lorenz, E Koch, S Weber, A El-Armouche
Histone H3 serine 28 (H3S28) phosphorylation and de-repression of polycomb repressive complex (PRC)-mediated gene regulation is linked to stress conditions in mitotic and post-mitotic cells. To better understand the role of H3S28 phosphorylation in vivo, we studied a Drosophila strain with ectopic expression of constitutively-activated H3S28A, which prevents PRC2 binding at H3S28, thus mimicking H3S28 phosphorylation. H3S28A mutants showed prolonged life span and improved resistance against starvation and paraquat-induced oxidative stress...
February 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29439868/in-depth-genome-analyses-of-viruses-from-vaccine-derived-rabies-cases-and-corresponding-live-attenuated-oral-rabies-vaccines
#14
Florian Pfaff, Thomas Müller, Conrad M Freuling, Christine Fehlner-Gardiner, Susan Nadin-Davis, Emmanuelle Robardet, Florence Cliquet, Vlad Vuta, Peter Hostnik, Thomas C Mettenleiter, Martin Beer, Dirk Höper
Live-attenuated rabies virus strains such as those derived from the field isolate Street Alabama Dufferin (SAD) have been used extensively and very effectively as oral rabies vaccines for the control of fox rabies in both Europe and Canada. Although these vaccines are safe, some cases of vaccine-derived rabies have been detected during rabies surveillance accompanying these campaigns. In recent analysis it was shown that some commercial SAD vaccines consist of diverse viral populations, rather than clonal genotypes...
February 10, 2018: Vaccine
https://www.readbyqxmd.com/read/29436965/gene-to-gene-network-analysis-of-the-mediation-of-plant-innate-immunity-by-the-eliciting-plant-response-like-1-epl1-elicitor-of-trichoderma-formosa
#15
Chi-Hua Cheng, Bing-Nan Shen, Qian-Wen Shang, Li-Yu Liu, Kou-Cheng Peng, Yan-Huey Chen, Fang-Fang Chen, Sin-Fen Hu, Yu-Tai Wang, Hao-Ching Wang, Hsin-Yi Wu, Chaur-Tsuen Lo, Shih-Shun Lin
A new clade, Trichoderma formosa, secretes eliciting plant response-like 1 (Epl1), a small peptide elicitor that stimulates plant immunity. Nicotiana benthamiana pretreated with Epl1 for three days developed immunity against tomato mosaic virus (ToMV) infection. The transcriptome profiles of T. formosa and N. benthamiana were obtained by deep sequencing; the transcript of Epl1 is 736 nt in length and encodes a 12 kDa peptide. Identifying critical genes in Epl1-mediated immunity was challenging due to the high similarity between the transcriptome expression profiles of Epl1-treated and ToMV-infected N...
February 13, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29435569/interpreting-genetic-variants-in-titin-in-patients-with-muscle-disorders
#16
Marco Savarese, Lorenzo Maggi, Anna Vihola, Per Harald Jonson, Giorgio Tasca, Lucia Ruggiero, Luca Bello, Francesca Magri, Teresa Giugliano, Annalaura Torella, Anni Evilä, Giuseppina Di Fruscio, Olivier Vanakker, Sara Gibertini, Liliana Vercelli, Alessandra Ruggieri, Carlo Antozzi, Helena Luque, Sandra Janssens, Maria Barbara Pasanisi, Chiara Fiorillo, Monika Raimondi, Manuela Ergoli, Luisa Politano, Claudio Bruno, Anna Rubegni, Marika Pane, Filippo M Santorelli, Carlo Minetti, Corrado Angelini, Jan De Bleecker, Maurizio Moggio, Tiziana Mongini, Giacomo Pietro Comi, Lucio Santoro, Eugenio Mercuri, Elena Pegoraro, Marina Mora, Peter Hackman, Bjarne Udd, Vincenzo Nigro
Importance: Mutations in the titin gene (TTN) cause a wide spectrum of genetic diseases. The interpretation of the numerous rare variants identified in TTN is a difficult challenge given its large size. Objective: To identify genetic variants in titin in a cohort of patients with muscle disorders. Design, Setting, and Participants: In this case series, 9 patients with titinopathy and 4 other patients with possibly disease-causing variants in TTN were identified...
February 12, 2018: JAMA Neurology
https://www.readbyqxmd.com/read/29434654/quasispecies-variant-of-pre-s-s-gene-in-hbv-related-hepatocellular-carcinoma-with-hbs-antigen-positive-and-occult-infection
#17
Yuri Hatazawa, Yoshihiko Yano, Rina Okada, Toshihito Tanahashi, Hiroki Hayashi, Hirotaka Hirano, Akihiro Minami, Yuki Kawano, Motofumi Tanaka, Takumi Fukumoto, Yoshiki Murakami, Masaru Yoshida, Yoshitake Hayashi
Background: Hepatocellular carcinoma (HCC) can develop in patients who are negative for the hepatitis B surface antigen (HBsAg) in serum but positive for hepatitis B virus (HBV) DNA in the liver, referred to as occult HBV infection (OBI). Previous reports showed that HBV variants in OBI-related HCC are different from those in HBsAg-positive HCC. In the present study, HBV quasispecies based on the pre-S/S gene in OBI-related HCC patients were examined by high throughput sequencing and compared with those in HBsAg-positive HCC...
2018: Infectious Agents and Cancer
https://www.readbyqxmd.com/read/29434616/pollen-from-the-deep-sea-a-breakthrough-in-the-mystery-of-the-ice-ages
#18
REVIEW
María F Sánchez Goñi, Stéphanie Desprat, William J Fletcher, César Morales-Molino, Filipa Naughton, Dulce Oliveira, Dunia H Urrego, Coralie Zorzi
Pollen from deep-sea sedimentary sequences provides an integrated regional reconstruction of vegetation and climate (temperature, precipitation, and seasonality) on the adjacent continent. More importantly, the direct correlation of pollen, marine and ice indicators allows comparison of the atmospheric climatic changes that have affected the continent with the response of the Earth's other reservoirs, i.e., the oceans and cryosphere, without any chronological uncertainty. The study of long continuous pollen records from the European margin has revealed a changing and complex interplay between European climate, North Atlantic sea surface temperatures (SSTs), ice growth and decay, and high- and low-latitude forcing at orbital and millennial timescales...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29434031/a-survey-of-virus-recombination-uncovers-canonical-features-of-artificial-chimeras-generated-during-deep-sequencing-library-preparation
#19
Jean Peccoud, Sébastian Lequime, Isabelle Moltini-Conclois, Isabelle Giraud, Louis Lambrechts, Clément Gilbert
Chimeric reads can be generated by in vitro recombination during the preparation of high-throughput sequencing libraries. Our attempt to detect biological recombination between the genomes of dengue virus (DENV; +ssRNA genome) and its mosquito host using the Illumina Nextera sequencing library preparation kit revealed that most, if not all, detected host-virus chimeras were artificial. Indeed, these chimeras were not more frequent than with control RNA from another species (a pillbug), which was never in contact with DENV RNA prior to the library preparation...
February 6, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29433568/the-peopling-of-the-last-green-sahara-revealed-by-high-coverage-resequencing-of-trans-saharan-patrilineages
#20
Eugenia D'Atanasio, Beniamino Trombetta, Maria Bonito, Andrea Finocchio, Genny Di Vito, Mara Seghizzi, Rita Romano, Gianluca Russo, Giacomo Maria Paganotti, Elizabeth Watson, Alfredo Coppa, Paolo Anagnostou, Jean-Michel Dugoujon, Pedro Moral, Daniele Sellitto, Andrea Novelletto, Fulvio Cruciani
BACKGROUND: Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment. RESULTS: In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations...
February 12, 2018: Genome Biology
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