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https://www.readbyqxmd.com/read/28107502/rnai-based-functional-genomics-identifies-new-virulence-determinants-in-mucormycosis
#1
Trung Anh Trieu, María Isabel Navarro-Mendoza, Carlos Pérez-Arques, Marta Sanchis, Javier Capilla, Patricia Navarro-Rodriguez, Loida Lopez-Fernandez, Santiago Torres-Martínez, Victoriano Garre, Rosa María Ruiz-Vázquez, Francisco E Nicolás
Mucorales are an emerging group of human pathogens that are responsible for the lethal disease mucormycosis. Unfortunately, functional studies on the genetic factors behind the virulence of these organisms are hampered by their limited genetic tractability, since they are reluctant to classical genetic tools like transposable elements or gene mapping. Here, we describe an RNAi-based functional genomic platform that allows the identification of new virulence factors through a forward genetic approach firstly described in Mucorales...
January 20, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28107465/lead-exposure-induces-weight-gain-in-adult-rats-accompanied-by-dna-hypermethylation
#2
Honglin Sun, Ningjian Wang, Xiaomin Nie, Li Zhao, Qin Li, Zhen Cang, Chi Chen, Meng Lu, Jing Cheng, Hualing Zhai, Fangzhen Xia, Lin Ye, Yingli Lu
OBJECTIVE: Previous studies have revealed the association of lead (Pb) exposure with obesity. DNA methylation alteration has been suggested to be one of the regulatory mechanisms of obesity. We aimed to explore whether Pb exposure is related with weight gain and DNA methylation alteration. METHODS: Male adult 8 week Wistar rats were divided into 5 groups: the normal chow diet (NCD); the NCD+0.05%Pb; the NCD+0.15%Pb; the NCD+0.45%Pb and the high fat diet. Rats were exposed to different dosages of Pb through drinking water for 21 weeks...
2017: PloS One
https://www.readbyqxmd.com/read/28107443/identification-of-the-pla2g6-c-1579g-a-missense-mutation-in-papillon-dog-neuroaxonal-dystrophy-using-whole-exome-sequencing-analysis
#3
Masaya Tsuboi, Manabu Watanabe, Kazumi Nibe, Natsuko Yoshimi, Akihisa Kato, Masahiro Sakaguchi, Osamu Yamato, Miyuu Tanaka, Mitsuru Kuwamura, Kazuya Kushida, Takashi Ishikura, Tomoyuki Harada, James Kenn Chambers, Sumio Sugano, Kazuyuki Uchida, Hiroyuki Nakayama
Whole exome sequencing (WES) has become a common tool for identifying genetic causes of human inherited disorders, and it has also recently been applied to canine genome research. We conducted WES analysis of neuroaxonal dystrophy (NAD), a neurodegenerative disease that sporadically occurs worldwide in Papillon dogs. The disease is considered an autosomal recessive monogenic disease, which is histopathologically characterized by severe axonal swelling, known as "spheroids," throughout the nervous system. By sequencing all eleven DNA samples from one NAD-affected Papillon dog and her parents, two unrelated NAD-affected Papillon dogs, and six unaffected control Papillon dogs, we identified 10 candidate mutations...
2017: PloS One
https://www.readbyqxmd.com/read/28107347/whole-genome-amplification-and-reduced-representation-genome-sequencing-of-schistosoma-japonicum-miracidia
#4
Jonathan A Shortt, Daren C Card, Drew R Schield, Yang Liu, Bo Zhong, Todd A Castoe, Elizabeth J Carlton, David D Pollock
BACKGROUND: In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small amount of DNA obtained from miracidia, the life stage most readily acquired from humans...
January 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28106858/regulation-of-dna-replication-in-early-embryonic-cleavages
#5
REVIEW
Chames Kermi, Elena Lo Furno, Domenico Maiorano
Early embryonic cleavages are characterized by short and highly synchronous cell cycles made of alternating S- and M-phases with virtually absent gap phases. In this contracted cell cycle, the duration of DNA synthesis can be extraordinarily short. Depending on the organism, the whole genome of an embryo is replicated at a speed that is between 20 to 60 times faster than that of a somatic cell. Because transcription in the early embryo is repressed, DNA synthesis relies on a large stockpile of maternally supplied proteins stored in the egg representing most, if not all, cellular genes...
January 19, 2017: Genes
https://www.readbyqxmd.com/read/28106782/from-clinical-standards-to-translating-next-generation-sequencing-research-into-patient-care-improvement-for-hepatobiliary-and-pancreatic-cancers
#6
REVIEW
Ioannis D Kyrochristos, Georgios K Glantzounis, Demosthenes E Ziogas, Ioannis Gizas, Dimitrios Schizas, Efstathios G Lykoudis, Evangelos Felekouras, Anastasios Machairas, Christos Katsios, Theodoros Liakakos, William C Cho, Dimitrios H Roukos
Hepatobiliary and pancreatic (HBP) cancers are associated with high cancer-related death rates. Surgery aiming for complete tumor resection (R0) remains the cornerstone of the treatment for HBP cancers. The current progress in the adjuvant treatment is quite slow, with gemcitabine chemotherapy available only for pancreatic ductal adenocarcinoma (PDA). In the advanced and metastatic setting, only two targeted drugs have been approved by the Food & Drug Administration (FDA), which are sorafenib for hepatocellular carcinoma and erlotinib for PDA...
January 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106529/a-joint-cross-border-investigation-of-a-cluster-of-multidrug-resistant-tuberculosis-in-austria-romania-and-germany-in-2014-using-classic-genotyping-and-whole-genome-sequencing-methods-lessons-learnt
#7
Lena Fiebig, Thomas A Kohl, Odette Popovici, Margarita Mühlenfeld, Alexander Indra, Daniela Homorodean, Domnica Chiotan, Elvira Richter, Sabine Rüsch-Gerdes, Beatrix Schmidgruber, Patrick Beckert, Barbara Hauer, Stefan Niemann, Franz Allerberger, Walter Haas
Molecular surveillance of multidrug-resistant tuberculosis (MDR-TB) using 24-loci MIRU-VNTR in the European Union suggests the occurrence of international transmission. In early 2014, Austria detected a molecular MDR-TB cluster of five isolates. Links to Romania and Germany prompted the three countries to investigate possible cross-border MDR-TB transmission jointly. We searched genotyping databases, genotyped additional isolates from Romania, used whole genome sequencing (WGS) to infer putative transmission links, and investigated pairwise epidemiological links and patient mobility...
January 12, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28106509/potential-epigenetic-biomarkers-of-obesity-related-insulin-resistance-in-human-whole-blood
#8
Samantha E Day, Richard L Coletta, Joon Young Kim, Luis A Garcia, Latoya E Campbell, Tonya R Benjamin, Lori R Roust, Elena A De Filippis, Lawrence J Mandarino, Dawn K Coletta
Obesity can increase the risk of complex metabolic diseases, including insulin resistance. Moreover, obesity can be caused by environmental and genetic factors. However, the epigenetic mechanisms of obesity are not well defined. Therefore, the identification of novel epigenetic biomarkers of obesity allows for a more complete understanding of the disease and its underlying insulin resistance. The aim of our study was to identify DNA methylation changes in whole-blood that were strongly associated with obesity and insulin resistance...
January 20, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28106390/tubulin-binding-and-polymerization-promoting-properties-of-tppp-proteins-are-evolutionarily-conserved
#9
Judit Oláh, Tibor Szénási, Adél Szabó, Kinga Kovács, Péter Lőw, Mauro Stifanic, Ferenc Orosz
Tubulin Polymerization Promoting Proteins (TPPPs) constitute a new eukaryotic protein family. There are three TPPP paralogs in the human genome; denoted as TPPP1, TPPP2 and TPPP3. TPPP1 and TPPP3 are intrinsically unstructured proteins (IUPs) that bind and polymerize tubulin and stabilize microtubules but TPPP2 does not. Vertebrate TPPPs originated from the ancient invertebrate TPPP by two-round whole-genome-duplication thus it was an open question whether the tubulin/microtubule binding function of TPPP1 and TPPP3 is a newly acquired property or it was present in the invertebrate orthologs (generally one TPPP/species)...
January 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28106148/complete-genome-sequencing-elucidates-outbreak-dynamics-of-ca-mrsa-usa300-st8-spa-t008-in-an-academic-hospital-of-paramaribo-republic-of-suriname
#10
Artur J Sabat, Sandra M Hermelijn, Viktoria Akkerboom, Amadu Juliana, John E Degener, Hajo Grundmann, Alexander W Friedrich
We report the investigation of an outbreak situation of methicillin-resistant Staphylococcus aureus (MRSA) that occurred at the Academic Hospital Paramaribo (AZP) in the Republic of Suriname from April to May 2013. We performed whole genome sequencing with complete gap closure for chromosomes and plasmids on all isolates. The outbreak involved 12 patients and 1 healthcare worker/nurse at the AZP. In total 24 isolates were investigated. spa typing, genome-wide single nucleotide polymorphism (SNP) analysis, ad hoc whole genome multilocus sequence typing (wgMLST), stable core genome MLST (cgMLST) and in silico PFGE were used to determine phylogenetic relatedness and to identify transmission...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28105927/candidate-snp-markers-of-aggressiveness-related-complications-and-comorbidities-of-genetic-diseases-are-predicted-by-a-significant-change-in-the-affinity-of-tata-binding-protein-for-human-gene-promoters
#11
Irina V Chadaeva, Mikhail P Ponomarenko, Dmitry A Rasskazov, Ekaterina B Sharypova, Elena V Kashina, Marina Yu Matveeva, Tatjana V Arshinova, Petr M Ponomarenko, Olga V Arkova, Natalia P Bondar, Ludmila K Savinkova, Nikolay A Kolchanov
BACKGROUND: Aggressiveness in humans is a hereditary behavioral trait that mobilizes all systems of the body-first of all, the nervous and endocrine systems, and then the respiratory, vascular, muscular, and others-e.g., for the defense of oneself, children, family, shelter, territory, and other possessions as well as personal interests. The level of aggressiveness of a person determines many other characteristics of quality of life and lifespan, acting as a stress factor. Aggressive behavior depends on many parameters such as age, gender, diseases and treatment, diet, and environmental conditions...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28105923/mosaic-structure-of-mycobacterium-bovis-bcg-genomes-as-a-representation-of-phage-sequences-mobility
#12
Olga L Voronina, Marina S Kunda, Ekaterina I Aksenova, Andrey N Semenov, Natalia N Ryzhova, Vladimir G Lunin, Alexandr L Gintsburg
BACKGROUND: The control of genome stability is relevant for the worldwide BCG vaccine preventing the acute forms of childhood tuberculosis. BCG sub-strains whole genome comparative analysis and revealing the triggers of sub-strains transition were the purpose of our investigation. RESULTS: Whole genome sequencing of three BCG Russia seed lots (1963, 1982, 2006 years) confirmed the stability of vaccine sub-strain genome. Comparative analysis of three Mycobacteruim bovis and nine M...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28105729/whole-genome-grey-and-white-matter-dna-methylation-profiles-in-dorsolateral-prefrontal-cortex
#13
Jose Vicente Sanchez-Mut, Holger Heyn, Enrique Vidal, Raúl Delgado-Morales, Sebastian Moran, Sergi Sayols, Juan Sandoval, Isidre Ferrer, Manel Esteller, Johannes Gräff
The brain's neocortex is anatomically organized into grey and white matter, which are mainly composed by neuronal and glial cells, respectively. The neocortex can be further divided in different Brodmann areas according to their cytoarchitectural organization, which are associated with distinct cortical functions. There is increasing evidence that brain development and function are governed by epigenetic processes, yet their contribution to the functional organization of the neocortex remains incompletely understood...
January 20, 2017: Synapse
https://www.readbyqxmd.com/read/28104664/first-complete-genome-sequence-of-haemophilus-influenzae-serotype-a
#14
Mariam Iskander, Kristy Hayden, Gary Van Domselaar, Raymond Tsang
Haemophilus influenzae is an important human pathogen that primarily infects small children. In recent years, H. influenzae serotype a has emerged as a significant cause of invasive disease among indigenous populations. Here, we present the first complete whole-genome sequence of H. influenzae serotype a.
January 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28104651/draft-genome-sequence-of-the-oleaginous-green-alga-tetradesmus-obliquus-utex-393
#15
B M Carreres, L de Jaeger, J Springer, M J Barbosa, G Breuer, E J van den End, D M M Kleinegris, I Schäffers, E J H Wolbert, H Zhang, P P Lamers, R B Draaisma, V A P Martins Dos Santos, R H Wijffels, G Eggink, P J Schaap, D E Martens
The microalgae Tetradesmus obliquus is able to maintain a high photosynthetic efficiency under nitrogen limitation and is considered a promising green microalgae for sustainable production of diverse compounds, including biofuels. Here, we report the first draft whole-genome shotgun sequencing of T. obliquus The final assembly comprises 108,715,903 bp with over 1,368 scaffolds.
January 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28104650/genome-sequences-of-diverse-human-cytomegalovirus-strains-with-utility-in-drug-screening-and-vaccine-evaluation
#16
Kathleen Corcoran, Carly J Sherrod, Ellen F Perkowski, Jordan Texier, Fengsheng Li, I-Ming Wang, Michael McVoy, Tong-Ming Fu, Dirk P Dittmer
Cytomegalovirus displays genetic heterogeneity, which has implications for antiviral and vaccine development. Many studies have focused on laboratory isolates that have been extensively adapted for growth on fibroblasts. Here, we report whole-genome sequences for 10 human cytomegalovirus (HCMV) strains that readily grow on ARPE-19 human retinal pigment epithelial cells.
January 19, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28104618/hysa-a-hybrid-structural-variant-assembly-approach-using-next-generation-and-single-molecule-sequencing-technologies
#17
Xian Fan, Mark Chaisson, Luay Nakhleh, Ken Chen
Achieving complete, accurate and cost-effective assembly of human genomes is of great importance for realizing the promise of precision medicine. The abundance of repeats and genetic variations in human genomes and the limitations of existing sequencing technologies call for the development of novel assembly methods that can leverage the complementary strengths of multiple technologies. We propose a hybrid structural variant assembly (HySA) approach that integrates sequencing reads from next-generation sequencing and single-molecule sequencing technologies to accurately assemble and detect structural variations in human genomes...
January 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28104394/co-segregation-of-the-m-1555a-g-mutation-in-the-mt-rnr1-gene-and-mutations-in-mt-atp6-gene-in-a-family-with-dilated-mitochondrial-cardiomyopathy-and-hearing-loss-a-whole-mitochondrial-genome-screening
#18
Olfa Alila-Fersi, Imen Chamkha, Imen Majdoub, Lamia Gargouri, Emna Mkaouar-Rebai, Mouna Tabebi, Abdelaziz Tlili, Leila Keskes, Abdelmajid Mahfoudh, Faiza Fakhfakh
Mitochondrial disease refers to a heterogeneous group of disorders resulting in defective cellular energy production due to dysfunction of the mitochondrial respiratory chain, which is responsible for the generation of most cellular energy. Because cardiac muscles are one of the high energy demanding tissues, mitochondrial cardiomyopathies is one of the most frequent mitochondria disorders. Mitochondrial cardiomyopathy has been associated with several point mutations of mtDNA in both genes encoded mitochondrial proteins and mitochondrial tRNA and rRNA...
January 16, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28104386/haemagglutinin-and-neuraminidase-sequencing-when-compared-to-whole-genome-sequencing-proved-sufficient-to-delineate-two-distinct-clusters-of-influenza-a-h1n1-pdm09-in-a-suspected-cross-site-renal-unit-influenza-outbreak
#19
Rebecca Houghton, Joanna Ellis, Monica Galiano, Tristan W Clark, Sarah Wyllie
OBJECTIVES: We describe haemagglutinin (HA) and neuraminidase (NA) sequencing in an apparent cross-site influenza A(H1N1) outbreak in renal transplant and haemodialysis patients, confirmed with whole genome sequencing (WGS). METHODS: Isolates were sequenced from influenza positive individuals. Phylogenetic trees were constructed using HA and NA sequencing and subsequently WGS. Sequence data was analysed to determine genetic relatedness of viruses obtained from inpatient and outpatient cohorts and compared with epidemiological outbreak information...
January 16, 2017: Journal of Infection
https://www.readbyqxmd.com/read/28104311/comprehensive-profiling-of-the-androgen-receptor-in-liquid-biopsies-from-castration-resistant-prostate-cancer-reveals-novel-intra-ar-structural-variation-and-splice-variant-expression-patterns
#20
Bram De Laere, Pieter-Jan van Dam, Tom Whitington, Markus Mayrhofer, Emanuela Henao Diaz, Gert Van den Eynden, Jean Vandebroek, Jurgen Del-Favero, Steven Van Laere, Luc Dirix, Henrik Grönberg, Johan Lindberg
BACKGROUND: Expression of the androgen receptor splice variant 7 (AR-V7) is associated with poor response to second-line endocrine therapy in castration-resistant prostate cancer (CRPC). However, a large fraction of nonresponding patients are AR-V7-negative. OBJECTIVE: To investigate if a comprehensive liquid biopsy-based AR profile may improve patient stratification in the context of second-line endocrine therapy. DESIGN, SETTING, AND PARTICIPANTS: Peripheral blood was collected from patients with CRPC (n=30) before initiation of a new line of systemic therapy...
January 16, 2017: European Urology
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