1,154,868 results match your criteria Genome Medicine [Journal]


Clinical Implications of Single Nucleotide Polymorphisms in Diagnosis of Asthma and its Subtypes.

Yonsei Med J 2019 Jan;60(1):1-9

Department of Interdisciplinary Program in Biomedical Science, Graduate School, Soonchunhyang University, Bucheon, Korea.

For the past three decades, a large number of genetic studies have been performed to examine genetic variants associated with asthma and its subtypes in hopes of gaining better understanding of the mechanisms underlying disease pathology and to identify genetic biomarkers predictive of disease outcomes. Various methods have been used to achieve these objectives, including linkage analysis, candidate gene polymorphism analysis, and genome-wide association studies (GWAS); however, the degree to which genetic variants contribute to asthma pathogenesis has proven to be much less significant than originally expected. Subsequent application of GWAS to well-defined phenotypes, such as occupational asthma and non-steroidal anti-inflammatory drugexacerbated respiratory diseases, has overcome some of these limitations, although with only partial success. Read More

View Article
January 2019

Secretome profile of Cellulomonas sp. B6 growing on lignocellulosic substrates.

J Appl Microbiol 2018 Dec 16. Epub 2018 Dec 16.

Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET). Los Reseros y Nicolas Repetto (1686), Hurlingham, Buenos Aires, Argentina.

Aims: Lignocellulosic biomass deconstruction is a bottleneck for obtaining biofuels and value-added products. Our main goal was to characterize the secretome of a novel isolate, Cellulomonas sp. B6, when grown on residual biomass for the formulation of cost-efficient enzymatic cocktails. Read More

View Article
December 2018

Novel ANO5 mutation c.1067G>T (p.C356F) identified by whole genome sequencing in a big family with atypical gnathodiaphyseal dysplasia.

Head Neck 2018 Dec 15. Epub 2018 Dec 15.

Department of Oral and Maxillofacial Surgery, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou, China.

Background: Gnathodiaphyseal dysplasia (GDD) is a rare skeletal disorder that has not been well studied.

Methods: Sanger sequencing, whole-genome sequencing (WGS), and bioinformatics and structural modeling analyses were performed.

Results: A family with patients with fibro-osseous lesions of the jawbones were initially diagnosed with cherubism. Read More

View Article
December 2018

Genomic insights into the vulnerability of sympatric whitefish species flocks.

Mol Ecol 2018 Dec 16. Epub 2018 Dec 16.

Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047, Kastanienbaum, Switzerland.

The erosion of habitat heterogeneity can reduce species diversity directly but can also lead to the loss of distinctiveness of sympatric species through speciation reversal. We know little about changes in genomic differentiation during the early stages of these processes, which can be mediated by anthropogenic perturbation. Here, we analyse three sympatric whitefish species (Coregonus spp) sampled across two neighbouring and connected Swiss pre-alpine lakes, which have been differentially affected by anthropogenic eutrophication. Read More

View Article
December 2018

House dust mite drives pro-inflammatory eicosanoid reprogramming and macrophage effector functions.

Allergy 2018 Dec 16. Epub 2018 Dec 16.

Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, member of the German Center for Lung Research, 80802, Munich, Germany.

Background: Eicosanoid lipid mediators play key roles in type 2 immune responses, e.g. in allergy and asthma. Read More

View Article
December 2018

Overcoming bioethical, legal, and hereditary barriers to mitochondrial replacement therapy in the USA.

J Assist Reprod Genet 2018 Dec 15. Epub 2018 Dec 15.

Exergen Corporation, Watertown, MA, USA.

The purpose of the paper is to explore novel means to overcome the controversial ban in the USA against mitochondrial replacement therapy, a form of IVF, with the added step of replacing a woman's diseased mutated mitochondria with a donor's healthy mitochondria to prevent debilitating and often fatal mitochondrial diseases. Long proven effective in non-human species, MRT recently performed in Mexico resulted in the birth of a healthy baby boy. We explore the ethics of the ban, the concerns over hereditability of mitochondrial disease and its mathematical basis, the overlooked role of Mitochondrial Eve, the financial burden of mitochondrial diseases for taxpayers, and a woman's reproductive rights. Read More

View Article
December 2018

Genome analysis and -omics approaches provide new insights into the biodegradation potential of Rhodococcus.

Appl Microbiol Biotechnol 2018 Dec 15. Epub 2018 Dec 15.

Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.

The past few years observed a breakthrough of genome sequences of bacteria of Rhodococcus genus with significant biodegradation abilities. Invaluable knowledge from genome data and their functional analysis can be applied to develop and design strategies for attenuating damages caused by hydrocarbon contamination. With the advent of high-throughput -omic technologies, it is currently possible to utilize the functional properties of diverse catabolic genes, analyze an entire system at the level of molecule (DNA, RNA, protein, and metabolite), simultaneously predict and construct catabolic degradation pathways. Read More

View Article
December 2018

Oceanobacillus timonensis sp. nov. and Oceanobacillus senegalensis sp. nov., two new moderately halophilic, Gram-stain positive bacteria isolated from stools sample of healthy young Senegalese.

Antonie Van Leeuwenhoek 2018 Dec 15. Epub 2018 Dec 15.

Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France.

Oceanobacillus timonensis Marseille-P3532 (CSUR P3532, CCUG 70981) and Oceanobacillus senegalensis Marseille-P3587 (CSUR P3587, CCUG 70613), are the type strains of O. timonensis sp. nov. Read More

View Article
December 2018

Recent Incidence Trend of Surgically Resected Esophagogastric Junction Adenocarcinoma and Microsatellite Instability Status in Japanese Patients.

Digestion 2018 Dec 14;99(1):6-13. Epub 2018 Dec 14.

Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation of Cancer Research, Tokyo, Japan.

Background: The incidence trend of esophagogastric junction (EGJ) adenocarcinoma in Japan has not been sufficiently investigated. Little is known about the microsatellite instability (MSI) status of this tumor.

Summary: Previously published studies analyzing the trend of EGJ adenocarcinoma in Japan were reviewed. Read More

View Article
December 2018

Nucleosome Positioning by an Evolutionarily Conserved Chromatin Remodeler Prevents Aberrant DNA Methylation in Neurospora.

Genetics 2018 Dec 15. Epub 2018 Dec 15.

University of Oregon

In the filamentous fungus , constitutive heterochromatin is marked by tri-methylation of histone H3 lysine 9 (H3K9me3) and DNA methylation. We identified mutations in the Neurospora efective n ethylation-1 () gene that cause defects in cytosine methylation and implicate a putative AAA-ATPase chromatin remodeler. Although it was well established that chromatin remodelers can impact transcription by influencing DNA accessibility with nucleosomes, little was known about the role of remodelers on chromatin that is normally not transcribed, including regions of constitutive heterochromatin. Read More

View Article
December 2018

Adaptation of Rabensburg virus (RBGV) to vertebrate hosts by experimental evolution.

Virology 2018 Dec 13;528:30-36. Epub 2018 Dec 13.

The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA; Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, NY, USA.

Rabensburg virus (RBGV; Flaviviridae, Flavivirus) has been classified as both a novel flavivirus and a unique lineage of West Nile virus (WNV). RBGV and WNV share approximately 76% sequence homology, yet RBGV does not replicate to high viral titers within vertebrate cell lines at physiological temperatures and has not been naturally isolated from a vertebrate host. These unique genetic and biological characteristics make RBGV a viable tool to identify the genetic determinants of flavivirus infectivity and fitness in vertebrate hosts. Read More

View Article
December 2018

Non canonical genetic material.

Curr Opin Biotechnol 2018 Dec 13;57:25-33. Epub 2018 Dec 13.

KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, 3000 Leuven, Belgium. Electronic address:

To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pair additional to natural A:T and G:C. Read More

View Article
December 2018

Mechanical regulation of genome architecture and cell-fate decisions.

Authors:
G V Shivashankar

Curr Opin Cell Biol 2018 Dec 13;56:115-121. Epub 2018 Dec 13.

Mechanobiology Institute, National University of Singapore, Singapore & FIRC Institute of Molecular Oncology (IFOM), Milan, Italy. Electronic address:

Landmark experiments in vitro showed that somatic cells can be reprogrammed to stem-cells by the constitutive expression of particular transcription factors. However, in vivo cells naturally exhibit de-differentiation and trans-differentiation programs, thereby suggesting that the signals from the local mechanical microenvironment may be sufficient to induce stem-cell state transitions. In this review, we discuss recent evidence for the biophysical regulation of genome architecture and nuclear programs. Read More

View Article
December 2018

DNA based method for determining source country of the short beaked echidna (Tachyglossus aculeatus) in the illegal wildlife trade.

Forensic Sci Int 2018 Dec 5;295:46-53. Epub 2018 Dec 5.

Australian Centre for Wildlife Genomics, Australian Museum Research Institute, 1 William Street, Sydney, Australia. Electronic address:

The illegal trade in wild animals being sold as 'captive bred' is an emerging issue in the pet and zoo industry and has both animal welfare and conservation implications. DNA based methods can be a quick, inexpensive, and definitive way to determine the source of these animals, thereby assisting efforts to combat this trade. The short beaked echidna (Tachyglossus aculeatus) is currently one of the species suspected to be targeted in this trade. Read More

View Article
December 2018

Emergence in Japan of an isolate of Klebsiella pneumoniae co-harboring bla and rmtB.

J Glob Antimicrob Resist 2018 Dec 13. Epub 2018 Dec 13.

Department of Microbiology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan.

Objectives: The aim of this study was to report that a clinical isolate of K. pneumoniae ST11 harbored both bla and rmtB in Japan.

Methods: A carbapenem and aminoglycoside-resistant Klebsiella pneumoniae was isolated from an inpatient in Japan. Read More

View Article
December 2018

Epidemiological investigation of an Acinetobacter baumannii outbreak using Core Genome Multilocus Sequence Typing.

J Glob Antimicrob Resist 2018 Dec 13. Epub 2018 Dec 13.

National Institute for Infectious Diseases (INMI) L. Spallanzani, Rome, Italy.

Obiectives: Carbapenem-resistant (CR) Acinetobacter baumannii is a serious nosocomial pathogen able to cause a variety of serious, often life-threatening infections and outbreaks. We aimed to investigate the molecular epidemiology of clinical isolates of CR A. baumannii from an outbreak that occurred in the intensive care unit (ICU) of our hospital. Read More

View Article
December 2018

"In Fimo": A Term Proposed for Excrement Examined Experimentally.

Gastroenterology 2018 Dec 13. Epub 2018 Dec 13.

Departments of Chemistry, Microbiology and Immunology, and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. Electronic address:

View Article
December 2018

Hematopoietic tissue of Macrobrachium rosenbergii plays dual roles as a source of hemocyte hematopoiesis and as a defensive mechanism against Macrobrachium rosenbergii nodavirus infection.

Fish Shellfish Immunol 2018 Dec 13. Epub 2018 Dec 13.

Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand; Nakhonsawan Campus, Mahidol University, Nakhonsawan, 60130, Thailand. Electronic address:

White tail disease caused by Macrobrachium rosenbergii nodavirus (MrNV) infection takes place only in nauplii, not adults, of M. rosenbergii prawn. Hemocyte homeostasis and immune-related functions derived from the hematopoietic tissue (Hpt) in adult prawn are presumed to play roles in resisting viral infection. Read More

View Article
December 2018

GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data.

Genomics Proteomics Bioinformatics 2018 Dec 13. Epub 2018 Dec 13.

Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.

Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present the Genome Interaction Tools and Resources (GITAR), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, and visualization, as well as analysis of topologically-associated domains (TADs). Read More

View Article
December 2018

Enlarged and highly repetitive plastome of Lagarostrobos and plastid phylogenomics of Podocarpaceae.

Mol Phylogenet Evol 2018 Dec 13. Epub 2018 Dec 13.

Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei 11529, Taiwan; Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan. Electronic address:

Podocarpaceae is the largest family in cupressophytes (conifers II), but their plastid genomes (plastomes) are poorly studied, with plastome data currently existing for only four of the 19 Podocarpaceous genera. In this study, we sequenced and assembled the complete plastomes from representatives of eight additional genera, including Afrocarpus, Dacrydium, Lagarostrobos, Lepidothamnus, Pherosphaera, Phyllocladus, Prumnopitys, and Saxegothaea. We found that Lagarostrobos, a monotypic genus native to Tasmania, has the largest plastome among any cupressophytes studied to date (151,496 bp). Read More

View Article
December 2018

Imprinted genes influencing the quality of maternal care.

Front Neuroendocrinol 2018 Dec 13. Epub 2018 Dec 13.

Biomedicine Division, School of Biosciences, Cardiff University, Cardiff, UK, CF10 3AX, UK. Electronic address:

In mammals successful rearing imposes a cost on later reproductive fitness specifically on the mother creating the potential for parental conflict. Loss of function of three imprinted genes in the dam result in deficits in maternal care suggesting that, like maternal nutrients, maternal care is a resource over which the parental genomes are in conflict. However, the induction of maternal care is a complex and highly regulated process. Read More

View Article
December 2018

CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines.

iScience 2018 Nov 30. Epub 2018 Nov 30.

Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA. Electronic address:

CellMinerCDB provides a web-based resource (https://discover.nci.nih. Read More

View Article
November 2018

Addressing the Nutritional Phenotype through Personalized Nutrition for Chronic Disease Prevention and Management.

Prog Cardiovasc Dis 2018 Dec 13. Epub 2018 Dec 13.

Internal Medicine-Obesity Medicine, Palo Alto Veterans Affairs Health Care System, Palo Alto, CA, USA; Internal Medicine-Primary Care, San Mateo County Health System, San Mateo, CA, USA.

The primary focus of public health recommendations related to the prevention of food-related chronic disease has been on the adoption of healthy dietary patterns; however, implementation has been challenging. There has been increasing recognition that an individual's diet and environment may impact disease susceptibility by affecting the expression of genes involved in critical metabolic pathways. Precision nutrition (PN) has emerged to translate discoveries about diversity in nutrient metabolism between subgroups and the inter-individual variability in the responses to dietary interventions. Read More

View Article
December 2018

Smc3 is required for mouse embryonic and adult hematopoiesis.

Exp Hematol 2018 Dec 13. Epub 2018 Dec 13.

Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri. Electronic address:

SMC3 encodes a subunit of the cohesin complex that has canonical roles in regulating sister chromatids segregation during mitosis and meiosis. Recurrent heterozygous mutations in SMC3 have been reported in acute myeloid leukemia (AML) and other myeloid malignancies. In this study, we investigated whether the missense mutations in SMC3 might have dominant-negative effects or phenocopy loss-of-function effects by comparing the consequences of Smc3 deficient and haploinsufficient mouse models. Read More

View Article
December 2018

Compound Genomic Alterations of TP53, PTEN, and RB1 Tumor Suppressors in Localized and Metastatic Prostate Cancer.

Eur Urol 2018 Dec 12. Epub 2018 Dec 12.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. Electronic address:

Background: TP53, PTEN, and RB1 tumor suppressor genes (TSGs) are recurrently altered in treatment-resistant prostate cancer. Cooperative loss of two or more TSGs may drive more aggressive disease.

Objective: To determine clinical outcomes of single and compound TSG alterations across the spectrum of prostate cancer. Read More

View Article
December 2018

Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases.

Authors:
Marc S Halfon

Trends Genet 2018 Dec 12. Epub 2018 Dec 12.

Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY, USA; NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA; Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY, USA; Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY, USA; Department of Molecular and Cellular Biology and Program in Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. Electronic address:

Transcriptional enhancers play a major role in regulating metazoan gene expression. Recent developments in genomics and next-generation sequencing have accelerated and revitalized the study of this important class of sequence elements. Increased interest and attention, however, has also led to troubling trends in the enhancer literature. Read More

View Article
December 2018

Genomics, GPCRs and new targets for the control of insect pests and vectors.

Curr Opin Insect Sci 2018 Dec 30;30:99-106. Epub 2018 Aug 30.

Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907-2089, USA.

The pressing need for new pest control products with novel modes of action has spawned interest in small molecules and peptides targeting arthropod GPCRs. Genome sequence data and tools for reverse genetics have enabled the prediction and characterization of GPCRs from many invertebrates. We review recent work to identify, characterize and de-orphanize arthropod GPCRs, with a focus on studies that reveal exciting new functional roles for these receptors, including the regulation of metabolic resistance. Read More

View Article
December 2018

Opening the toolkit for genetic analysis and control of Anopheles mosquito vectors.

Curr Opin Insect Sci 2018 Dec 26;30:8-18. Epub 2018 Jul 26.

Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK.

Anopheles is the only genus of mosquitoes that transmit human malaria and consequently the focus of large scale genome and transcriptome-wide association studies. Genetic tools to define the function of the candidate genes arising from these analyses are vital. Moreover, genome editing offers the potential to modify Anopheles population structure at local and global scale to provide complementary tools towards the ultimate goal of malaria elimination. Read More

View Article
December 2018

Identification of gene-specific DNA methylation signature for Colorectal Cancer.

Cancer Genet 2018 Dec 26;228-229:5-11. Epub 2018 May 26.

Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China. Electronic address:

Background: Colorectal Cancer (CC), a common disease causing approximately million deaths annually, has been the third most frequent type of malignancy. We aimed to identify gene-specific DNA methylation signature to function as prognostic and predictive markers for CC patient survival.

Methods: Expression profiles of gene-specific DNA methylation and the corresponding clinical information of 201 CC patients were downloaded from The Cancer Genome Atlas (TCGA) dataset and differentially expressed gene-specific DNA methylation was identified after tumor subtype classification. Read More

View Article
December 2018

Effect of the chemical environment of the DNA guanine quadruplex on the free energy of binding of Na and K ions.

J Chem Phys 2018 Dec;149(22):225102

Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada.

Guanine quadruplex (G-quadruplex) structures play a vital role in stabilizing the DNA genome and in protecting healthy cells from transforming into cancer cells. The structural stability of G-quadruplexes is greatly enhanced by the binding of monovalent cations such as Na or K into the interior axial channel. We computationally study the free energy of binding of Na and K ions to two intramolecular G-quadruplexes that differ considerably in their degree of rigidity and the presence or absence of terminal nucleotides. Read More

View Article
December 2018

Optimizing denaturing HPLC as a robust technique for identification of Short Tandem Repeats (STR) in forensic medicine.

J Forensic Leg Med 2018 Dec 10;61:108-114. Epub 2018 Dec 10.

Department and Biotechnology Research Center, Semnan University of Medical Sciences, Semnan, Iran. Electronic address:

Introduction: Short Tandem Repeats (STRs) are defined as short lengths of 2-7 base pairs spreading through human genome which due to their highly diverse individually distribution are widely applied for identity detection and other forensic medicine purposes. Burdening considerable costs by the conventional methods such as capillary electrophoresis, we aimed to compare concomitant usage of multiplex PCR and denaturing high-performance liquid chromatography (DHPLC) as cheap, fast, highly accurate, and more accessible methods, with capillary electrophoresis (CE) to evaluate their potential for early screening of STRs.

Materials And Methods: The present study randomly included 20 blood samples from the subjects referred to forensic medicine of Semnan, Iran. Read More

View Article
December 2018
1 Read

Detection of norovirus epidemic genotypes in raw sewage using next generation sequencing.

Environ Int 2018 Dec 12;123:282-291. Epub 2018 Dec 12.

Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Rio de Janeiro, RJ, Brazil.

Noroviruses are a leading cause of epidemic and pandemic acute gastroenteritis (AGE) worldwide, and contaminated food and water are important routes for its transmission. Raw sewage has been used for viral surveillance to monitor the emergence of new norovirus strains with the potential to cause epidemics. In this study, we investigated norovirus occurrence and norovirus RNA levels in 156 samples collected from May 2013 to May 2014, across three different stages (52 samples each) of a wastewater treatment plant (WWTP) in Rio de Janeiro, Brazil. Read More

View Article
December 2018
2 Reads

An update on Drug Repurposing: Re-written saga of the drug's fate.

Biomed Pharmacother 2018 Dec 12;110:700-716. Epub 2018 Dec 12.

Pharamacological Modelling and Simulation Centre, M.S.Ramaiah University of Applied Sciences, Bangalore, Karnataka, India; Department of Pharmacy Practice, Faculty of Pharmacy, M.S.Ramaiah University of Applied Sciences, Bangalore, Karnataka, India.

Drug repurposing is an unconventional drug discovery approach to explore new therapeutic benefits of existing, shelved and the drugs in clinical trials. This approach is currently emerging to overcome the bottleneck constraints faced during traditional drug discovery in grounds of financial support, timeline and resources. In this direction, several efforts were made for the construction of stratagems based on bioinformatics and computational tools to intensify the repurposing process off-late. Read More

View Article
December 2018
1 Read

Molecular alterations in meningiomas: Literature review.

Clin Neurol Neurosurg 2018 Dec 7;176:89-96. Epub 2018 Dec 7.

Departament of Neurology, Laboratory of Molecular and Cellular Biology, LIM15, Faculdade de Medicina, Universidade de São Paulo, SP, Brazil.

Meningiomas, tumors that originate from meningothelial cells, account for approximately 30% of all new diagnoses of central nervous system neoplasms. According to the 2016 WHO classification of central nervous system tumors meningiomas are classified into three grades: I, II, and III. Past studies have shown that the risk of meningiomas recurrence is strongly correlated with the molecular profile of the tumor. Read More

View Article
December 2018
1 Read

Draft genome sequence of human-associated streptogramin resistant Staphylococcus aureus.

J Glob Antimicrob Resist 2018 Dec 12. Epub 2018 Dec 12.

Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, Athens, Georgia, USA. Electronic address:

Objectives: Staphylococcus aureus is one of the leading causes of nosocomial and community-acquired infections. Treatment of those infections with macrolide-lincosamide-streptogramin (MLS) antibiotics has led to resistance to those antibiotics through various mechanisms. S. Read More

View Article
December 2018
1 Read

Draft genome sequence of Escherichia coli ST410 co-harboring bla, bla, bla, aac(3)-IIa, aac(6')-Ib-cr genes with gyrA and parC mutations isolated from pediatric patient in Poland.

J Glob Antimicrob Resist 2018 Dec 12. Epub 2018 Dec 12.

Department of Bacteriology and Biocontamination Control, National Institute of Public Health-National Institute of Hygiene, Warsaw, Poland.

Objectives: Escherichia coli is one of the major agents of nosocomial infections. The aim of this study was to report the first draft genome sequence of an E. coli strain (no. Read More

View Article
December 2018
2 Reads

Genetic susceptibility to Tuberculosis: Interaction between HLA-DQA1 and age of onset.

Infect Genet Evol 2018 Dec 12. Epub 2018 Dec 12.

Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China.

Several genome-wide association studies (GWAS) identified new single nucleotide polymorphisms (SNPs) with susceptibility to Tuberculosis (TB). However, many of them were not replicated across ethnic groups. The cause of this phenomenon of genetic heterogeneity is uncertain. Read More

View Article
December 2018
1 Read

Response to the Letter to the Editor - Necessity of accurate identification of Elizabethkingia species.

Clin Microbiol Infect 2018 Dec 12. Epub 2018 Dec 12.

Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan; Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan. Electronic address:

In addition to Bruker, the latest version of the Vitek MS IVD database-IVD V3.2-was released by bioMérieux in May 2018. The database includes spectra for E. Read More

View Article
December 2018

Genome-wide identification, characterization and expression analysis of the MITF gene in Yesso scallops (Patinopecten yessoensis) with different shell colors.

Gene 2018 Dec 12. Epub 2018 Dec 12.

Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China. Electronic address:

The microphthalmia-associated transcription factor (MITF) is the center of the regulator network of melanin synthesis in vertebrates. However, the role of MITF in shell color formation is poorly studied in mollusks. In the present study, an MITF gene, PyMITF, was first identified at the whole-genome level in Yesso scallop (Patinopecten yessoensis), an evolutionarily and economically important species, the shell color of which shows polymorphism. Read More

View Article
December 2018

Characterization of HPV integration, viral gene expression and E6E7 alternative transcripts by RNA-Seq: A descriptive study in invasive cervical cancer.

Genomics 2018 Dec 12. Epub 2018 Dec 12.

Genetics Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil. Electronic address:

Scarce data are available on the expression of Papillomavirus genome and the frequency of alternatively spliced E6/E7 mRNAs in invasive cervical cancer. We carried out a comprehensive characterization of HPV expression by RNA-Seq analysis in 22 invasive cervical cancer with HPV16 or HPV18, characterizing the presence of integrated/episomal viral DNA, the integration sites in human genome and the proportion of alternative splicing products of E6 and E7 genes. The expression patterns suggested the presence of episomal and/or integrated viral DNA, with integration detected in most tumors, frequently occurring within human genes in HPV18+ and in intergenic regions in HPV16+ tumors. Read More

View Article
December 2018

Assembling a genome for novel nitrogen-fixing bacteria with capabilities for utilization of aromatic hydrocarbons.

Genomics 2018 Dec 12. Epub 2018 Dec 12.

CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, India. Electronic address:

Metagenome from refinery wastewater treatment plant running under nitrogen stress was analyzed for mining of novel aromatic hydrocarbon-degrading bacteria. The sequence data were assembled using metaspade followed by binning using the Metabat tool to assemble genome; where coverage and depth were calculated using bowtie and samtools. The analysis picked a novel genome belonging to family Bradyrhizobiaceae, identified based on 16S rDNA gene which was supported by CheckM and Kraken analysis. Read More

View Article
December 2018

Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform.

Swiss Med Wkly 2018 Dec 15;148:w14693. Epub 2018 Dec 15.

SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Facing multidrug resistant (MDR) bacterial pathogens is one of the most important challenges for our society. The spread of highly virulent and resistant pathogens can be described using molecular typing technologies; in particular, whole genome sequencing (WGS) data can be used for molecular typing purposes with high resolution. WGS data analysis can explain the spatiotemporal patterns of pathogen transmission. Read More

View Article
December 2018
1 Read

Characterization of two steroid hydroxylases from different Streptomyces spp. and their ligand-bound and -unbound crystal structures.

FEBS J 2018 Dec 15. Epub 2018 Dec 15.

Department of Life Science and Biochemical Engineering, Sunmoon University, Asansi, 31460, Republic of Korea.

Bacterial cytochrome P450 (CYP) enzymes are involved in the hydroxylation of various endogenous substrates while using a heme molecule as a cofactor. CYPs have gained biotechnological interest as useful biocatalysts capable of altering chemical structures by adding a hydroxyl group in a regiospecific manner. Here, we identified, purified, and characterized two CYP154C4 proteins from Streptomyces sp. Read More

View Article
December 2018

Sympatric diploid and tetraploid cytotypes of Centaurea stoebe s.l. do not differ in arbuscular mycorrhizal communities and mycorrhizal growth response.

Am J Bot 2018 Dec 14. Epub 2018 Dec 14.

Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague, Czech Republic.

Premise Of The Study: Genome duplication is associated with multiple changes at different levels, including interactions with pollinators and herbivores. Yet little is known whether polyploidy may also shape belowground interactions.

Methods: To elucidate potential ploidy-specific interactions with arbuscular mycorrhizal fungi (AMF), we compared mycorrhizal colonization and assembly of AMF communities in roots of diploid and tetraploid Centaurea stoebe s. Read More

View Article
December 2018
1 Read

Cell-Based Model of the Generation and Maintenance of the Shape and Structure of the Multilayered Shoot Apical Meristem of Arabidopsis thaliana.

Bull Math Biol 2018 Dec 14. Epub 2018 Dec 14.

Department of Mathematics, University of California, Riverside, USA.

One of the central problems in animal and plant developmental biology is deciphering how chemical and mechanical signals interact within a tissue to produce organs of defined size, shape, and function. Cell walls in plants impose a unique constraint on cell expansion since cells are under turgor pressure and do not move relative to one another. Cell wall extensibility and constantly changing distribution of stress on the wall are mechanical properties that vary between individual cells and contribute to rates of expansion and orientation of cell division. Read More

View Article
December 2018

Identification of the gene encoding the TATA box-binding protein-associated factor 1 (TAF1) and its putative role in the heat shock response in the protozoan parasite Entamoeba histolytica.

Parasitol Res 2018 Dec 15. Epub 2018 Dec 15.

Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico.

Transcription factor IID (TFIID) is a cornerstone in the transcription initiation in eukaryotes. It is composed of TBP and approximately 14 different subunits named TBP-associated factors (TAFs). TFIID has a key role in transcription of many genes involved in cell proliferation, cell growth, cell cycle, cell cycle checkpoint, and various other processes as well. Read More

View Article
December 2018
1 Read

Cornification of nail keratinocytes requires autophagy for bulk degradation of intracellular proteins while sparing components of the cytoskeleton.

Apoptosis 2018 Dec 14. Epub 2018 Dec 14.

Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090, Vienna, Austria.

Epidermal keratinocytes undergo cornification to form the cellular building blocks of hard skin appendages such as nails and the protective layer on the surface of the skin. Cornification requires the cross-linking of structural proteins and the removal of other cellular components to form mechanically rigid and inert corneocytes. Autophagy has been proposed to contribute to this intracellular remodelling process, but its molecular targets in keratinocytes, if any, have remained elusive. Read More

View Article
December 2018
1 Read

Full plastome sequence of the fern Vandenboschia speciosa (Hymenophyllales): structural singularities and evolutionary insights.

J Plant Res 2018 Dec 14. Epub 2018 Dec 14.

Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain.

We provide here the first full chloroplast genome sequence, i.e., the plastome, for a species belonging to the fern order Hymenophyllales. Read More

View Article
December 2018

Accuracy of within- and among-family genomic prediction for Fusarium head blight and Septoria tritici blotch in winter wheat.

Theor Appl Genet 2018 Dec 14. Epub 2018 Dec 14.

State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany.

Genomic selection is an approach that uses whole-genome marker data to predict breeding values of genotypes and holds the potential to improve the genetic gain in breeding programs. In this study, two winter wheat populations (DS1 and DS2) consisting of 438 and 585 lines derived from six and eight bi-parental families, respectively, were genotyped with genome-wide single nucleotide polymorphism markers and phenotyped for Fusarium head blight and Septoria tritici blotch severity, plant height and heading date. We used ridge regression-best linear unbiased prediction to investigate the potential of genomic selection under different selection scenarios: prediction across each winter wheat population, within- and among-family prediction in each population, and prediction from DS1 to DS2 and vice versa. Read More

View Article
December 2018

Skewed X-inactivation is common in the general female population.

Eur J Hum Genet 2018 Dec 14. Epub 2018 Dec 14.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

X-inactivation is a well-established dosage compensation mechanism ensuring that X-chromosomal genes are expressed at comparable levels in males and females. Skewed X-inactivation is often explained by negative selection of one of the alleles. We demonstrate that imbalanced expression of the paternal and maternal X-chromosomes is common in the general population and that the random nature of the X-inactivation mechanism can be sufficient to explain the imbalance. Read More

View Article
December 2018
1 Read
  • Page 1 of 23098