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Genes and genomes

Małgorzata Dawidowska, Roman Jaksik, Monika Drobna, Bronisława Szarzyńska-Zawadzka, Maria Kosmalska, Łukasz Sędek, Ludomiła Machowska, Anna Lalik, Monika Lejman, Marek Ussowicz, Krzysztof Kałwak, Jerzy R Kowalczyk, Tomasz Szczepański, Michał Witt
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy originating from T-cell precursors. The genetic landscape of T-ALL has been largely characterized by next-generation sequencing. Yet, the transcriptome of miRNAs (miRNome) of T-ALL has been less extensively studied. Using small RNA sequencing, we characterized the miRNome of 34 pediatric T-ALL samples, including the expression of isomiRs and the identification of candidate novel miRNAs (not previously annotated in miRBase). For the first time, we show that immunophenotypic subtypes of T-ALL present different miRNA expression profiles...
February 11, 2019: Neoplasia: An International Journal for Oncology Research
Federico Tondini, Tom Lang, Liang Chen, Markus Herderich, Vladimir Jiranek
Wine fermentations typically involve the yeast Saccharomyces cerevisiae. However, many other yeast species participate to the fermentation process, some with interesting oenological traits. In this study the species Torulaspora delbrueckii, used occasionally in mixed or sequential fermentation with S. cerevisiae to improve wine sensory profile, was investigated to understand the physiological differences between the two. Next generation sequencing was used to characterize the transcriptome of T. delbrueckii and highlight the different genomic response of these yeasts during growth under wine-like conditions...
February 2, 2019: International Journal of Food Microbiology
Corinna Pietsch, Uwe G Liebert
BACKGROUND: Sapovirus is a common cause of self-limiting diarrhea. In immunocompromised individuals chronic infections occur, but are incompletely investigated. OBJECTIVES: To investigate viral evolution in immunocompromised hosts during chronic sapovirus infection. STUDY DESIGN: From January 2010 to September 2018 stool samples of 5333 in-patients were analyzed for the presence of sapovirus RNA by real-time RT-PCR. In follow-up samples of chronic diarrhea cases nucleic acid sequencing of sapovirus genomes was performed...
February 7, 2019: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
Hanae Takatsuki, Chantal Ama Agbemabiese, Toyoko Nakagomi, Sher Bahadur Pun, Punita Gauchan, Hideki Muto, Hiroshi Masumoto, Ryuichiro Atarashi, Osamu Nakagomi, Basu Dev Pandey
Rotavirus A (RVA) causes acute diarrhoea in children and less frequently in adults. However, the knowledge about the genotype distribution of RVA strains circulating in adults is limited particularly in developing countries. This study aimed to characterise the RVA strains detected from adult patients with diarrhoea in Nepal. A total of 47 RVA positive stool samples from adult patients with diarrhoea in Kathmandu, Nepal during 2007-2008 were examined for the G and P genotypes by sequencing. Nearly half (49%) of the samples were genotyped as G9P[8] (n = 23), G1P[8], G2P[4] (n = 5 each), G12P[8] (n = 4), G12P[6] (n = 3), G1P[6] (n = 2), G3P[8] and G9P[6] (n = 1 each)...
February 11, 2019: Infection, Genetics and Evolution
Timothy A Dinh, Mark L Jewell, Matt Kanke, Adam Francisco, Ramja Sritharan, Rigney E Turnham, Seona Lee, Edward R Kastenhuber, Eliane Wauthier, Cynthia D Guy, Raymond S Yeung, Scott W Lowe, Lola M Reid, John D Scott, Anna M Diehl, Praveen Sethupathy
BACKGROUND & AIMS: Fibrolamellar carcinoma is a rare liver cancer that primarily affects adolescents and young adults. It is characterized by a heterozygous ∼400 kb deletion on chromosome 19 that results in a unique DNAJB1-PRKACA fusion. The role of microRNAs (miRNAs) in FLC remains unclear. We identified dysregulated miRNAs in FLC and investigated whether dysregulation of one key miRNA contributes to FLC pathogenesis. METHODS: We analyzed small RNA sequencing (smRNA-seq) data from The Cancer Genome Atlas (TCGA) to identified dysregulated miRNAs in primary FLC tumors and validated the findings in three independent FLC cohorts...
February 11, 2019: Cellular and Molecular Gastroenterology and Hepatology
Dongjuan Yuan, Shiqi Luo, Lian Xu, Xingda Zeng, Zhongdao Wu
MicroRNA plays a vital role in the regulation of host-parasite interaction. In recent years, genomic and transcriptomic resources have become increasingly available for many helminths, but only a limited number of reports in this area are on the regulatory effects of host microRNAs on parasitic nematodes. In this work, we screened increased expression of host microRNAs after nematode infection from miRNA-seq data and predicted target genes by combined bioinformatics analysis and transcriptional profiling. We elucidated regulatory effects of one host miRNA on nematode infection using miRNA inhibitor and adeno-associated virus (AAV)-based TuD miRNA inhibitor...
February 11, 2019: Biochimica et biophysica acta. Gene regulatory mechanisms
Zilan Wen, Tommaso Raffaello, Zhen Zeng, Mirko Pavicic, Fred O Asiegbu
Heterobasidion parviporum Niemelä & Korhonen is a necrotrophic fungal pathogen of Norway spruce (Picea abies). H. parviporum genome encodes numerous necrotrophic small secreted proteins (SSP) which might be important for promoting and sustaining the disease development. However, their transcriptional dynamics and plant defense response during infection are largely unknown. In this study, we identified a necrotrophic SSP named HpSSP35.8 and its coding gene was highly expressed in the pre-symptomatic phase of host (Norway spruce) infection...
February 11, 2019: Fungal Genetics and Biology: FG & B
Claudia M Corbi-Botto, Hernán Morales-Durand, María E Zappa, Sebastián A Sadaba, Pilar Peral-García, Guillermo Giovambattista, Silvina Díaz
Copy number variation (CNV) has been proved to be widespread in human, animal and plant genomes. Together with single nucleotide polymorphisms (SNPs), CVNs play a key role in genetic diversity. In this study, genome-wide detection of CNVs was performed based on SNP data from 24 Criollo Argentino horses genotyped with the GGP Equine70k array. Overall, 165 CNVs meeting stringent quality control criteria were identified and then aggregated into 87 CNV regions (CNVRs), representing a horse genome coverage of 13...
February 11, 2019: Gene
Ronald Y Kwon, Claire J Watson, David Karasik
While genome-wide association studies (GWAS) have revolutionized our understanding of the genetic architecture of skeletal diseases, animal models are required to identify causal mechanisms and to translate underlying biology into new therapies. Despite large-scale knockout mouse phenotyping efforts, the skeletal functions of most genes residing at GWAS-identified loci remain unknown, highlighting a need for complementary model systems to accelerate gene discovery. Over the past several decades, zebrafish (Danio rerio) has emerged as a powerful system for modeling the genetics of human diseases...
February 11, 2019: Bone
Ester Murube, Ana Campa, Juan José Ferreira
A complex landscape of anthracnose resistance genes (Co-) located at the telomeric regions of the bean chromosomes Pv01 and Pv04 has been reported. The aim of this work was to investigate the genetic and physical positions of genes conferring resistance to races 6, 38, 39, 357, 65, and 73 as well as the relationships among the resistance genes identified herein and the previously described Co- genes in these telomeric regions. The linkage analysis using a genetic map of 497 SNPs from the recombinant inbred line population Xana/BAT93 revealed that the gene conferring resistance to race 65 in cultivar Xana (Co-165-X) was located in the Co-1 cluster, at the distal end of chromosome Pv01...
2019: PloS One
Juliah Khayeli Akhwale, Manfred Rohde, Christine Rohde, Boyke Bunk, Cathrin Spröer, Hans-Peter Klenk, Hamadi Iddi Boga, Johannes Wittmann
We report complete genome sequences of eight bacteriophages isolated from Haloalkaline Lake Elmenteita found on the floor of Kenyan Rift Valley. The bacteriophages were sequenced, annotated and a comparative genomic analysis using various Bioinformatics tools carried out to determine relatedness of the bacteriophages to each other, and to those in public databases. Basic genome properties like genome size, percentage coding density, number of open reading frames, percentage GC content and gene organizations revealed the bacteriophages had no relationship to each other...
2019: PloS One
Arpita Das, Krishnendu Pramanik, Rishu Sharma, Saikat Gantait, Joydeep Banerjee
Germin-like proteins (GLPs) are involved in biotic and abiotic stress tolerance in different plant species. Rice (Oryza sativa L.) genome contains about 40 GLP family member proteins in nine chromosomes. Although some of the rice GLP (OsGLP) promoters have been studied through in silico analysis as well as experimentally, studies regarding the distribution pattern of the biotic and abiotic stress associated transcription factor binding sites (TFbs) in the promoter regions of OsGLP genes have not been attempted thoroughly...
2019: PloS One
Keiji Tanimoto, Hitomi Matsuzaki, Eiichi Okamura, Aki Ushiki, Akiyoshi Fukamizu, James Douglas Engel
Long-range associations between enhancers and their target gene promoters have been shown to play critical roles in executing genome function. Recent variations of chromosome capture technology have revealed a comprehensive view of intra- and interchromosomal contacts between specific genomic sites. The locus control region of the β-globin genes (β-LCR) is a super-enhancer that is capable of activating all of the β-like globin genes within the locus in cis through physical interaction by forming DNA loops...
2019: PloS One
Alexander Pearlman, Mohammed Tanjimur Rahman, Kinnari Upadhyay, Johnny Loke, Harry Ostrer
Triple negative breast cancer (TNBC) is an aggressive tumor with propensity to metastasize and poor treatment options. Improving treatment options would be impactful; thus, finding a tumor-specific cell surface protein with metastasis promoting functions that could be knocked out was the goal of this study. The Otoconin 90 gene (OC90), frequently amplified in tumors on chromosome 8q24.22, was identified as a potential therapeutic candidate. Normally OC90 is expressed in the cochlea with no known function in other normal tissues...
2019: PloS One
Caitlin Murphy, Andrea Muscat, David Ashley, Violet Mukaro, Linda West, Yang Liao, David Chisanga, Wei Shi, Ian Collins, Sally Baron-Hay, Sujata Patil, Geoffrey Lindeman, Mustafa Khasraw
BACKGROUND: This study evaluated the feasibility of achieving high response rates in stage II or III breast cancer by tailoring neoadjuvant therapy using clinical and histopathological features and the Oncotype DX Breast Recurrence Score. Genomic determinants of response and resistance were also explored. PATIENTS AND OUTCOME MEASURES: Fifty-one patients were enrolled. The primary cohort comprised 40 patients: 15 human epidermal growth factor receptor type 2 (HER2)-amplified; 15 triple-negative (TNBC); and ten hormone receptor (HR)-positive, HER2-non-amplified tumours; with recurrence scores ≥25...
2019: PloS One
Saúl Jijón-Moreno, Beatriz Eugenia Baca, Diana Carolina Castro-Fernández, Alberto Ramírez-Mata
Azospirillum brasilense is one of the most studied species of diverse agronomic plants worldwide. The benefits conferred to plants inoculated with Azospirillum have been primarily attributed to its capacity to fix atmospheric nitrogen and synthesize phytohormones, especially indole-3-acetic acid (IAA). The principal pathway for IAA synthesis involves the intermediate metabolite indole pyruvic acid. Successful colonization of plants by Azospirillum species is fundamental to the ability of these bacteria to promote the beneficial effects observed in plants...
2019: PloS One
Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma
Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles that can be further analyzed using correlation analysis, co-expression analysis, clustering, differential gene expression (DGE), among many other studies...
February 14, 2019: PLoS Computational Biology
Veroni S Sri Theivakadadcham, Benjamin G Bergey, Emanuel Rosonina
Sequence-specific transcription factors (TFs) represent one of the largest groups of proteins that is targeted for SUMO post-translational modification, in both yeast and humans. SUMO modification can have diverse effects, but recent studies showed that sumoylation reduces the interaction of multiple TFs with DNA in living cells. Whether this relates to a general role for sumoylation in TF binding site selection, however, has not been fully explored because few genome-wide studies aimed at studying such a role have been reported...
February 14, 2019: PLoS Genetics
Marc Parisien, Alexander Samoshkin, Shannon N Tansley, Marjo H Piltonen, Loren J Martin, Nehme El-Hachem, Concetta Dagostino, Massimo Allegri, Jeffrey S Mogil, Arkady Khoutorsky, Luda Diatchenko
Chronic pain is a debilitating and poorly treated condition whose underlying mechanisms are poorly understood. Nerve injury and inflammation cause alterations in gene expression in tissues associated with pain processing, supporting molecular and cellular mechanisms that maintain painful states. However, it is not known whether transcriptome changes can be used to reconstruct a molecular pathophysiology of pain. In the current study, we identify molecular pathways contributing to chronic pain states through the analysis of global changes in the transcriptome of dorsal root ganglia, spinal cord, brain, and blood in mouse assays of nerve injury- and inflammation-induced pain...
January 3, 2019: Pain
Rui M B Maciel, Cleber P Camacho, Ligia Vm Assumpcao, Natassia Elena Bufalo, André L Carvalho, Gisah A de Carvalho, Luciana A Castroneves, Francisco M de Castro, Lucieli Ceolin, Janete Maria Cerutti, Rossana Corbo, Tânia M B L Ferraz, Carla Vaz Ferreira, M Inez C França, Henrique C R Galvão, Fausto Germano-Neto, Hans Graf, Alexander A L Jorge, Ilda S Kunii, Márcio W Lauria, Vera L G Leal, Susan C Lindsey, Delmar Muniz Lourenco-Jr, Lea Maria Zanini Maciel, Patrícia K R Magalhães, João R M Martins, M Cecilia Martins-Costa, Glaucia M F S Mazeto, Anelise Impellizzeri, Célia Regina Nogueira, Edenir I Palmero, Cencita Cordeiro Pessoa, Bibiana Prada, Debora R Siqueira, M Sharmila A Sousa, Rodrigo Toledo, Flávia O F Valente, F Vaisman, Laura Sterian Ward, Shana S Weber, Rita V Weiss, Ji H Yang, Magnus Regio Dias Da Silva, Ana O Hoff, Sergio Pa Toledo, Ana Luiza Maia
Multiple endocrine neoplasia type 2 (MEN2) is an autosomal dominant genetic disease caused by RET gene germline mutations that is characterized by medullary thyroid carcinoma (MTC) associated with other endocrine tumours. Several reports have demonstrated that the RET mutation profile may vary according to geographical area. In this study we collected clinical and molecular data from 554 patients with surgically confirmed MTC from 176 families with MEN2 in 18 different Brazilian centers to compare the type and prevalence of RET mutations with those from other countries...
February 1, 2019: Endocrine Connections
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