209,808 results match your criteria Genomics Insights [Journal]


Sleep Duration and Proteinuria Progression: A Population-Based Cohort Study.

Am J Nephrol 2018 Dec 17;49(1):41-51. Epub 2018 Dec 17.

Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei,

Background: Extensive studies have demonstrated that sleep is an important modulator of cardiovascular and metabolic diseases. However, its impact on renal function remains uncertain.

Methods: A total of 26,249 adults aged ≥20 years were recruited through voluntary health examinations in Taiwan. Read More

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December 2018

A smart nanosensor for the detection of human immunodeficiency virus and associated cardiovascular and arthritis diseases using functionalized graphene-based transistors.

Biosens Bioelectron 2018 Dec 7;126:792-799. Epub 2018 Dec 7.

DBT-National Institute of Animal Biotechnology (DBT-NIAB), Hyderabad 500032, Telangana, India. Electronic address:

Human immunodeficiency virus (HIV), which isa worldwide public health issue, is commonly associated with cardiovascular disorders (CVDs) and rheumatoid arthritis (RA). A smart nanosensor was developed for the detection of HIV and its related diseases (CVDs and RA) using graphene-based field-effect transistors (FETs). In this study, amine-functionalized graphene (afG) was conjugated with antibodies [anti-p24 for HIV, anti-cardiac troponin 1 (anti-cTn1) for CVDs, and anti-cyclic citrullinated peptide (anti-CCP) for RA] to detect various biomarkers. Read More

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December 2018

Extracellular polymeric substances of biofilms: Suffering from an identity crisis.

Water Res 2018 Nov 28;151:1-7. Epub 2018 Nov 28.

Department of Biotechcnology, Delft University of Technology, Delft, the Netherlands. Electronic address:

Microbial biofilms can be both cause and cure to a range of emerging societal problems including antimicrobial tolerance, water sanitation, water scarcity and pollution. The identities of extracellular polymeric substances (EPS) responsible for the establishment and function of biofilms are poorly understood. The lack of information on the chemical and physical identities of EPS limits the potential to rationally engineer biofilm processes, and impedes progress within the water and wastewater sector towards a circular economy and resource recovery. Read More

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November 2018

A mouse model for intellectual disability caused by mutations in the X-linked 2'‑O‑methyltransferase Ftsj1 gene.

Biochim Biophys Acta Mol Basis Dis 2018 Dec 14. Epub 2018 Dec 14.

Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Strasse 8, 17489 Greifswald, Germany.

Mutations in the X chromosomal tRNA 2'‑O‑methyltransferase FTSJ1 cause intellectual disability (ID). Although the gene is ubiquitously expressed affected individuals present no consistent clinical features beyond ID. In order to study the pathological mechanism involved in the aetiology of FTSJ1 deficiency-related cognitive impairment, we generated and characterized an Ftsj1 deficient mouse line based on the gene trapped stem cell line RRD143. Read More

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December 2018

Diverse members of the Xylariales lack canonical mating-type regions.

Fungal Genet Biol 2018 Dec 14. Epub 2018 Dec 14.

Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131 USA. Electronic address:

A survey of genomes reported here for 10 isolates of Monosporascus species and an additional 25 genomes from other members of the Xylariales (representing 15 genera) available in public databases indicated that genes typically associated with MAT1-1 (mat A) or MAT1-2 (mat a) mating types are absent or have diverged greatly relative to counterparts in other Pezizomycotina. This was particularly surprising for isolates known to be homothallic, given that homothallic members of the Pezizomycotina typically possess a MAT1-1-1 (mat A-1) gene and one or both of two other closely-linked mating-type genes, MAT1-1-2 (mat A-2) and MAT1-1-3 (mat A-3), in addition to MAT1-2-1 (mat a-1). We failed to detect candidate genes for either MAT1-1-1 or MAT1-1-2 in any member of the Xylariales. Read More

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December 2018

The problem of genetic code misreading during protein synthesis.

Yeast 2018 Dec 17. Epub 2018 Dec 17.

Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, 21228, United States of America.

Saccharomyces cerevisiae has been an important model for determining the frequency of translational misreading events, those in which a tRNA pairs incorrectly to the mRNA and inserts an amino acid not specified by the codon in the mRNA. Misreading errors have been quantified in vivo using reporter protein systems or mass spectrometry with both approaches converging on a simple model for most misreading. The available data show that misreading tRNAs must form stereotypical base mismatches that correspond to those that can mimic Watson-Crick base pairs when formed in the ribosomal A site. Read More

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December 2018

Association of HLA class I type with prevalence and outcome of patients with acute myeloid leukemia and mutated nucleophosmin.

PLoS One 2018 17;13(12):e0204290. Epub 2018 Dec 17.

Department of Internal Medicine-Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic.

Acute myeloid leukemia with mutated nucleophosmin (NPMc+ AML) forms a distinct AML subgroup with better prognosis which can potentially be associated with immune response against the mutated nucleophosmin (NPM). As the T-cell-mediated immunity involves antigen presentation on HLA class I molecules, we hypothesized that individuals with suitable HLA type could be less prone to develop NPMc+ AML. We compared HLA class I distribution in NPMc+ AML patient cohort (398 patients from 5 centers) with the HLA allele frequencies of the healthy population and found HLA-A*02, B*07, B*40 and C*07 underrepresented in the NPMc+ AML group. Read More

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December 2018
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The CbrB Regulon: Promoter dissection reveals novel insights into the CbrAB expression network in Pseudomonas putida.

PLoS One 2018 17;13(12):e0209191. Epub 2018 Dec 17.

Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/ Consejo Superior de Investigaciones Científicas/ Junta de Andalucía, Seville, Spain.

CbrAB is a high ranked global regulatory system exclusive of the Pseudomonads that responds to carbon limiting conditions. It has become necessary to define the particular regulon of CbrB and discriminate it from the downstream cascades through other regulatory components. We have performed in vivo binding analysis of CbrB in P. Read More

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December 2018

Cell-intrinsic regulation of peripheral memory-phenotype T cell frequencies.

PLoS One 2018 17;13(12):e0200227. Epub 2018 Dec 17.

National Institute of Immunology, New Delhi, India.

Memory T and B lymphocyte numbers are thought to be regulated by recent and cumulative microbial exposures. We report here that memory-phenotype lymphocyte frequencies in B, CD4 and CD8 T-cells in 3-monthly serial bleeds from healthy young adult humans were relatively stable over a 1-year period, while Plasmablast frequencies were not, suggesting that recent environmental exposures affected steady state levels of recently activated but not of memory lymphocyte subsets. Frequencies of memory B and CD4 T cells were not correlated, suggesting that variation in them was unlikely to be determined by cumulative antigenic exposures. Read More

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December 2018

β-actin regulates a heterochromatin landscape essential for optimal induction of neuronal programs during direct reprograming.

PLoS Genet 2018 Dec 17;14(12):e1007846. Epub 2018 Dec 17.

Science Division, Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.

During neuronal development, β-actin serves an important role in growth cone mediated axon guidance. Consistent with this notion, in vivo ablation of the β-actin gene leads to abnormalities in the nervous system. However, whether β-actin is involved in the regulation of neuronal gene programs is not known. Read More

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December 2018

Loss of NFAT2 expression results in the acceleration of clonal evolution in chronic lymphocytic leukemia.

J Leukoc Biol 2018 Dec 17. Epub 2018 Dec 17.

Department of Oncology, Hematology and Immunology, University of Tübingen, Tübingen, Germany.

Chronic lymphocytic leukemia (CLL) can be defined as a clonal expansion of B cells with stereotypic BCRs. Somatic hypermutation of the BCR heavy chains (IGVH) defines a subgroup of patients with a better prognosis. In up to 10% of CLL cases, a transformation to an aggressive B cell lymphoma (Richter's syndrome) with a dismal prognosis can be observed over time. Read More

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December 2018

Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat.

New Phytol 2018 Dec 17. Epub 2018 Dec 17.

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.

Lycophytes are a key group for understanding vascular plant evolution. Lycophyte plastomes are highly distinct, indicating a dynamic evolutionary history, but detailed evaluation is hindered by the limited availability of sequences. Eight diverse plastomes were sequenced to assess variation in structure and functional content across lycophytes. Read More

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December 2018

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Nat Biotechnol 2018 Dec 17. Epub 2018 Dec 17.

US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. Read More

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December 2018
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Predicted glycosyltransferases promote development and prevent spurious cell clumping in the choanoflagellate .

Elife 2018 Dec 17;7. Epub 2018 Dec 17.

Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.

In a previous study we established forward genetics in the choanoflagellate Salpingoeca rosetta and found that a C-type lectin gene is required for rosette development (Levin et al. 2014). Here we report on critical improvements to genetic screens in while also investigating the genetic basis for rosette defect mutants in which single cells fail to develop into orderly rosettes but instead aggregate promiscuously into amorphous clumps of cells. Read More

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December 2018
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Pervasive transcription fine-tunes replication origin activity.

Elife 2018 Dec 17;7. Epub 2018 Dec 17.

Institut Jacques Monod, CNRS UMR 7592, Université Paris-Diderot, Paris, France.

RNA polymerase (RNAPII) transcription occurs pervasively, raising the important question of its functional impact on other DNA-associated processes, including replication. In budding yeast, replication originates from Autonomously Replicating Sequences (ARSs), generally located in intergenic regions. The influence of transcription on ARSs function has been studied for decades, but these earlier studies have neglected the role of non-annotated transcription. Read More

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December 2018

Integrating tumor genomics into studies of the microbiome in colorectal cancer.

Gut Microbes 2018 Dec 17:1-6. Epub 2018 Dec 17.

b Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , MN , USA.

Although the gut microbiome has been linked to colorectal cancer (CRC) development, associations of microbial taxa with CRC status are often inconsistent across studies. We have recently shown that tumor genomics, a factor that is rarely incorporated in analyses of the CRC microbiome, has a strong effect on the composition of the microbiota. Here, we discuss these results in the wider context of studies characterizing interaction between host genetics and the microbiome, and describe the implications of our findings for understanding the role of the microbiome in CRC. Read More

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December 2018

Newborn screening for Prader-Willi syndrome is feasible: Early diagnosis for better outcomes.

Am J Med Genet A 2018 Dec 17. Epub 2018 Dec 17.

Department of Pediatrics, Division of Genetics and Metabolism, University of California, Irvine, California.

Prader-Willi syndrome (PWS), is a complex genetic disease affecting 1/15,000 individuals, characterized by lack of expression of genes on the paternal chromosome 15q11-q13 region. Clinical features include central hypotonia, poor suck, learning and behavior problems, growth hormone deficiency with short stature, hyperphagia, and morbid obesity. Despite significant advances in genetic testing, the mean age for diagnosis in PWS continues to lag behind. Read More

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December 2018
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Reanalysis and optimisation of bioinformatic pipelines is critical for mutation detection.

Hum Mutat 2018 Dec 17. Epub 2018 Dec 17.

Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, Australia.

Rapid advances in genomic technologies have facilitated the identification pathogenic variants causing human disease. We report siblings with developmental and epileptic encephalopathy due to a novel, shared heterozygous pathogenic 13 bp duplication in SYNGAP1 (c.435_447dup, p. Read More

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December 2018

An improved clinical model to predict stimulated C-peptide in children with recent-onset type 1 diabetes.

Pediatr Diabetes 2018 Dec 17. Epub 2018 Dec 17.

The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, Australia.

Background: Stimulated C-peptide measurement after a mixed meal tolerance test (MMTT) is the accepted gold standard for assessing residual beta-cell function in Type 1 diabetes (T1D), however this approach is impractical outside of clinical trials.

Objective: To develop an improved estimate of residual beta-cell function in children with T1D using commonly measured clinical variables.

Subjects/methods: A clinical model to predict 90-minute MMTT stimulated C-peptide in children with recent-onset T1D was developed from the combined AbATE, START, and TIDAL placebo subjects (n = 46) 6 months post-recruitment using multiple linear regression. Read More

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December 2018

PAC1R Genotype to Phenotype Correlations in Autism Spectrum Disorder.

Autism Res 2018 Dec 17. Epub 2018 Dec 17.

Center for Neuroscience Research, Children's Research Institute, Children's National Health System, Washington, DC.

Amygdala dysfunction has been implicated in numerous neurodevelopmental disorders, including autism spectrum disorder (ASD). Previous studies in mice and humans, respectively, have linked Pac1r/PAC1R function to social behavior and PTSD-susceptibility. Based on this connection to social and emotional processing and the central role played by the amygdala in ASD, we examined a putative role for PAC1R in social deficits in ASD and determined the pattern of gene expression in the developing mouse and human amygdala. Read More

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December 2018

Identification of pathogenic YY1AP1 splice variants in siblings with Grange syndrome by whole exome sequencing.

Am J Med Genet A 2018 Dec 17. Epub 2018 Dec 17.

Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany.

Grange syndrome is an autosomal recessive condition characterized by arterial occlusions and hypertension. Syndactyly, brachydactyly, bone fragility, heart defects, and learning disabilities have also been reported. Loss-of-function variants in YY1AP1 have only recently been associated with Grange syndrome. Read More

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December 2018

Bacteriophages That Infect Marine Roseobacters: Genomics and Ecology.

Environ Microbiol 2018 Dec 16. Epub 2018 Dec 16.

Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, USA.

Viruses are the most abundant biological entities in seawater. They influence microbial population dynamics, genetic heterogeneity, and biogeochemical cycles in marine ecosystems. The isolation and characterization of viruses that infect specific hosts have greatly advanced our knowledge of the biological and ecological interactions between viruses and their hosts. Read More

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December 2018

Investigation of deleterious effects of nsSNPs in the POT1 gene: a structural genomics-based approach to understand the mechanism of cancer development.

J Cell Biochem 2018 Dec 16. Epub 2018 Dec 16.

Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.

Protection of telomere 1 (POT1) is one of the key components of shelterin complex, implicated in maintaining the telomere homeostasis, and thus stability of the eukaryotic genome. A large number of non-synonymous single nucleotide polymorphisms (nsSNPs) in the POT1 gene have been reported to cause varieties of human diseases, including cancer. In recent years, a number of mutations in POT1 has been markedly increased, and interpreting the effect of these large numbers of mutations to understand the mechanism of associated diseases seems impossible using experimental approaches. Read More

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December 2018

Models for Cell-Free Synthetic Biology: Make Prototyping Easier, Better, and Faster.

Front Bioeng Biotechnol 2018 29;6:182. Epub 2018 Nov 29.

Micalis Institute, INRA, AgroParisTech, University of Paris-Saclay, Jouy-en-Josas, France.

Cell-free TX-TL is an increasingly mature and useful platform for prototyping, testing, and engineering biological parts and systems. However, to fully accomplish the promises of synthetic biology, mathematical models are required to facilitate the design and predict the behavior of biological components in cell-free extracts. We review here the latest models accounting for transcription, translation, competition, and depletion of resources as well as genome scale models for lysate-based cell-free TX-TL systems, including their current limitations. Read More

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November 2018

The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism.

Mol Autism 2018 10;9:61. Epub 2018 Dec 10.

2Institute for Pediatric Regenerative Medicine and Shriners Hospitals for Children Northern California, 2504 Stockton Blvd, Sacramento, CA 95817 USA.

Background: Gut microbiota has the capacity to impact the regular function of the brain, which can in turn affect the composition of microbiota. Autism spectrum disorder (ASD) patients suffer from gastrointestinal problems and experience changes in gut microbiota; however, it is not yet clear whether the change in the microbiota associated with ASD is a cause or a consequence of the disease.

Methods: We have investigated the species richness and microbial composition in a valproic acid (VPA)-induced rat model autism. Read More

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December 2018

Targeted next-generation sequencing reveals recurrence-associated genomic alterations in early-stage non-small cell lung cancer.

Oncotarget 2018 Nov 20;9(91):36344-36357. Epub 2018 Nov 20.

ACT Genomics, Co. Ltd., Taipei, Taiwan.

Purpose: The identification of genomic alterations related to recurrence in early-stage non-small cell lung cancer (NSCLC) patients may help better stratify high-risk individuals and guide treatment strategies. This study aimed to identify the molecular biomarkers of recurrence in early-stage NSCLC.

Results: Of the 42 tumors evaluable for genomic alterations, TP53 and EGFR were the most frequent alterations with population frequency 52. Read More

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November 2018
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V-ATPases and osteoclasts: ambiguous future of V-ATPases inhibitors in osteoporosis.

Theranostics 2018 26;8(19):5379-5399. Epub 2018 Oct 26.

Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, 28 West Xianning Road, Xi'an 710049, People's Republic of China.

Vacuolar ATPases (V-ATPases) play a critical role in regulating extracellular acidification of osteoclasts and bone resorption. The deficiencies of subunit a3 and d2 of V-ATPases result in increased bone density in humans and mice. One of the traditional drug design strategies in treating osteoporosis is the use of subunit a3 inhibitor. Read More

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October 2018

Antioxidant and angiotensin-I converting enzyme inhibitory activities of phenolic extracts and fractions derived from three phenolic-rich legume varieties.

J Funct Foods 2018 Mar 3;42:289-297. Epub 2018 Feb 3.

Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Mississippi State, MS 39762, United States.

Lentil, black soybean and black turtle bean are commonly consumed legumes of different genera, containing high phenolic contents, which are effective antioxidants and angiotensin-I converting enzyme (ACE) inhibitors. However, these legumes' phenolic compositions and ACE inhibition ability have not been compared. Crude water extract (CE) was semi-purified (SPE) and fractionated using column chromatography. Read More

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Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments.

Algorithms Mol Biol 2018 8;13:17. Epub 2018 Dec 8.

1Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8000 Aarhus C, Denmark.

Background: Motif analysis methods have long been central for studying biological function of nucleotide sequences. Functional genomics experiments extend their potential. They typically generate sequence lists ranked by an experimentally acquired functional property such as gene expression or protein binding affinity. Read More

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December 2018

Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach.

Front Genet 2018 30;9:578. Epub 2018 Nov 30.

Genomics of Gene Expression Laboratory Centro de Investigación Príncipe Felipe, Valencia, Spain.

The Yeast Metabolic Cycle (YMC) is a model system in which levels of around 60% of the yeast transcripts cycle over time. The spatial and temporal resolution provided by the YMC has revealed that changes in the yeast metabolic landscape and chromatin status can be related to cycling gene expression. However, the interplay between histone modifications and transcription factor activity during the YMC is still poorly understood. Read More

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November 2018

Influence of ADAM10 Polymorphisms on Plasma Level of Soluble Receptor for Advanced Glycation End Products and The Association With Alzheimer's Disease Risk.

Front Genet 2018 13;9:540. Epub 2018 Nov 13.

Department of Neurology and Stroke Center, The First Affiliated Hospital of Jinan University, Guangzhou, China.

To determine the role of A disintegrin and metalloproteinase 10 (ADAM10) in genetic susceptibility to Alzheimer's disease (AD) in a representative Chinese sample, we genotyped 362 AD patients and 370 healthy controls for the rs514049A/C and rs653765C/T polymorphisms in the ADAM10 promoter using the SNaPshot technique. We also examined the potential impact of these polymorphisms on the plasma level of soluble receptor for advanced glycation end products (sRAGE), a decoy receptor whose reduction has been associated with a higher risk of AD. Additionally, a meta-analysis was performed using the present study and the largest GWAS from the International Genomics of Alzheimer's Project (IGAP). Read More

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November 2018

Molecular Control by Non-coding RNAs During Fruit Development: From Gynoecium Patterning to Fruit Ripening.

Front Plant Sci 2018 30;9:1760. Epub 2018 Nov 30.

Laboratory of Molecular Genetics of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), University of São Paulo, São Paulo, Brazil.

Fruits are originated from the transition of a quiescent ovary to a fast-growing young fruit. The evolution of reproductive structures such as ovary and fruit has made seed dispersal easier, which is a key process for reproductive success in flowering plants. The complete fruit development and ripening are characterized by a remarkable phenotypic plasticity which is orchestrated by a myriad of genetic factors. Read More

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November 2018

Misconceptions Regarding the Role of Introgression in the Origin of subsp. .

Front Plant Sci 2018 29;9:1750. Epub 2018 Nov 29.

School of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom.

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November 2018

DNA Synthesis Is Activated in Mosquitoes and Human Monocytes During the Induction of Innate Immune Memory.

Front Immunol 2018 30;9:2834. Epub 2018 Nov 30.

Centro de Investigaciones Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico.

Endoreplication is a cell cycle program in which cells replicate their genomes without undergoing mitosis and cytokinesis. For the normal development of many organisms (from fungi to humans) and the formation of their organs, endoreplication is indispensable. The aim of the present study was to explore whether endoreplication and DNA synthesis are relevant processes during the induction of trained innate immunity in human monocytes and in the mosquito cell line. Read More

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November 2018

Immune Response-Dependent Assembly of IMP Dehydrogenase Filaments.

Front Immunol 2018 29;9:2789. Epub 2018 Nov 29.

Department of Oral Biology, University of Florida, Gainesville, FL, United States.

Inosine monophosphate dehydrogenase (IMPDH) catalyzes the conversion of IMP to xanthosine monophosphate, the rate-limiting step in guanosine monophosphate (GMP) synthesis. In cultured cells, IMPDH polymerizes into micron-scale filamentous structures when GMP synthesis is inhibited by depletion of purine precursors or by various drugs, including mycophenolic acid, ribavirin, and methotrexate. IMPDH filaments also spontaneously form in undifferentiated mouse embryonic stem cells and induced pluripotent stem cells, hinting they might function in various highly proliferative cell types. Read More

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November 2018

Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments.

Front Microbiol 2018 29;9:2909. Epub 2018 Nov 29.

Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea.

Candidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylum have remained elusive. Here, we examined the microbial communities of marine sediments of the Ross Sea, Antarctica, and found candidate phylum Atribacteria JS1 lineage was the most abundant candidate phylum accounting for 9. Read More

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November 2018

Infection Results in an Increase in and Genera in the Gut of Mice.

Front Microbiol 2018 29;9:2890. Epub 2018 Nov 29.

Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.

Cystic echinococcosis (CE) is a chronic infectious disease caused by . To confirm whether the infection impacts on the gut microbiota, we established a mouse model of infection in this study whereby BALB/c mice were infected with micro-cysts of . After 4 months of infection, fecal samples were collected for high-throughput sequencing of the hypervariable regions of the 16S rRNA gene. Read More

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November 2018

Gold nanoparticles - an optical biosensor for RNA quantification for cancer and neurologic disorders diagnosis.

Int J Nanomedicine 2018 29;13:8137-8151. Epub 2018 Nov 29.

Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt,

Purpose: The objective of this study is to develop a facile tool for the absolute detection and quantification of nucleic acid transcripts, using a gold nanoparticle-based optical biosensor. Topoisomerase 1 (TOP1) and tyrosyl DNA phosphodiesterase 2 (TDP2) were among the nucleic acid transcripts of choice due to their role as genomic instability biomarkers and their implication in various cancers and neurologic disorders. This opens the door to develop a simple tool that can be used for diagnosing and monitoring treatment response for such diseases, overcoming the requirements for high cost, time, and complexity of the existing technologies for the absolute quantification of transcripts of interest. Read More

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November 2018

Genomewide identification of PPR gene family and prediction analysis on restorer gene in .

J Genet 2018 Dec;97(5):1083-1095

Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, People's Republic of China.

Pentatricopeptide repeat (PPR) gene family plays an essential role in the regulation of plant growth and organelle gene expression. Some PPR genes are related to fertility restoration in plant, but there is no detailed information in . In the present study, we identified 482 and 433 PPR homologues in (D) and (A) genomes, respectively. Read More

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December 2018

Ovarian cancer: An update on imaging in the era of radiomics.

Diagn Interv Imaging 2018 Dec 13. Epub 2018 Dec 13.

Department of Radiology, Hopital Tenon, Assistance publique-Hôpitaux de Paris Sorbonne Universités, Institut des Sciences du Calcul et de Données (ISCD), 75020 Paris, France.

Tumor heterogeneity in ovarian cancer has been reported at the histological and genetic levels and is associated with adverse clinical outcomes. Tumor evaluation using standard computed tomography or magnetic resonance imaging techniques does not account for the intra- or inter-tumoral heterogeneity in advanced ovarian cancer with peritoneal carcinomatosis. As such, computational approaches in assessing tumor heterogeneity have been proposed using radiomics and radiogenomics in order to analyze the whole tumor heterogeneity as opposed to single biopsy sampling. Read More

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December 2018

yylncT Defines a Class of Divergently Transcribed lncRNAs and Safeguards the T-mediated Mesodermal Commitment of Human PSCs.

Cell Stem Cell 2018 Nov 21. Epub 2018 Nov 21.

Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany. Electronic address:

Human protein-coding genes are often accompanied by divergently transcribed non-coding RNAs whose functions, especially in cell fate decisions, are poorly understood. Using an hESC-based cardiac differentiation model, we define a class of divergent lncRNAs, termed yin yang lncRNAs (yylncRNAs), that mirror the cell-type-specific expression pattern of their protein-coding counterparts. yylncRNAs are preferentially encoded from the genomic loci of key developmental cell fate regulators. Read More

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November 2018

Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains.

Mol Cell 2018 Dec 1. Epub 2018 Dec 1.

Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. Electronic address:

Targeting bromodomains (BRDs) of the bromo-and-extra-terminal (BET) family offers opportunities for therapeutic intervention in cancer and other diseases. Here, we profile the interactomes of BRD2, BRD3, BRD4, and BRDT following treatment with the pan-BET BRD inhibitor JQ1, revealing broad rewiring of the interaction landscape, with three distinct classes of behavior for the 603 unique interactors identified. A group of proteins associate in a JQ1-sensitive manner with BET BRDs through canonical and new binding modes, while two classes of extra-terminal (ET)-domain binding motifs mediate acetylation-independent interactions. Read More

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December 2018

Allatostatin-C/AstC-R2 Is a Novel Pathway to Modulate the Circadian Activity Pattern in Drosophila.

Curr Biol 2018 Dec 4. Epub 2018 Dec 4.

Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02454, USA. Electronic address:

Seven neuropeptides are expressed within the Drosophila brain circadian network. Our previous mRNA profiling suggested that Allatostatin-C (AstC) is an eighth neuropeptide and specifically expressed in dorsal clock neurons (DN1s). Our results here show that AstC is, indeed, expressed in DN1s, where it oscillates. Read More

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December 2018

Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity.

Curr Biol 2018 Dec 11. Epub 2018 Dec 11.

Language and Genetics Department, Max Planck Institute for Psycholinguistics, P.O. Box 310, 6500 AH, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands. Electronic address:

One of the features that distinguishes modern humans from our extinct relatives and ancestors is a globular shape of the braincase [1-4]. As the endocranium closely mirrors the outer shape of the brain, these differences might reflect altered neural architecture [4, 5]. However, in the absence of fossil brain tissue, the underlying neuroanatomical changes as well as their genetic bases remain elusive. Read More

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December 2018

Leptin gene polymorphisms are associated with weight gain during lithium augmentation in patients with major depression.

Eur Neuropsychopharmacol 2018 Dec 13. Epub 2018 Dec 13.

Department of Psychiatry and Psychotherapy, Charité University Medicine Berlin, Campus Mitte, Charitéplatz 1, 10117 Berlin, Germany. Electronic address:

Weight gain is a common adverse effect of lithium augmentation. Previous studies indicate an impact of genetic variants at the leptin gene on weight gain as a consequence of psychopharmacological treatment. The primary aim of our study was to identify variants at the leptin locus that might predict lithium-induced weight gain. Read More

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December 2018

Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring.

Trends Microbiol 2018 Nov 22. Epub 2018 Nov 22.

University of Geneva, Department of Genetics and Evolution, 1211 Geneva, Switzerland; ID-Gene ecodiagnostics, Campus Biotech, Avenue Sécheron 15, 1202 Geneva, Switzerland.

Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic ideal. Until now, environmental genomics was mainly used as a replacement of the burdensome morphological identification, to screen known morphologically distinguishable bioindicator taxa. Read More

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November 2018

Assessing copy number aberrations and copy-neutral loss-of-heterozygosity across the genome as best practice: An evidence-based review from the Cancer Genomics Consortium (CGC) working group for chronic lymphocytic leukemia.

Cancer Genet 2018 Dec 16;228-229:236-250. Epub 2018 Oct 16.

Department of Pathology, UMassMemorial Medical Center, Worcester, MA, USA; Quest Diagnostics, Marlborough, MA, USA. Electronic address:

The prognostic role of cytogenetic analysis is well-established in B-cell chronic lymphocytic leukemia (CLL). Approximately 80% of patients have a cytogenetic aberration. Interphase FISH panels have been the gold standard for cytogenetic evaluation, but conventional cytogenetics allows detection of additional abnormalities, including translocations, complex karyotypes and multiple clones. Read More

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December 2018

GGC Repeat Expansion and Exon 1 Methylation of XYLT1 Is a Common Pathogenic Variant in Baratela-Scott Syndrome.

Am J Hum Genet 2018 Dec 4. Epub 2018 Dec 4.

Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA; Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA. Electronic address:

Baratela-Scott syndrome (BSS) is a rare, autosomal-recessive disorder characterized by short stature, facial dysmorphisms, developmental delay, and skeletal dysplasia caused by pathogenic variants in XYLT1. We report clinical and molecular investigation of 10 families (12 individuals) with BSS. Standard sequencing methods identified biallelic pathogenic variants in XYLT1 in only two families. Read More

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December 2018

Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes.

Authors:
Nasim Mavaddat Kyriaki Michailidou Joe Dennis Michael Lush Laura Fachal Andrew Lee Jonathan P Tyrer Ting-Huei Chen Qin Wang Manjeet K Bolla Xin Yang Muriel A Adank Thomas Ahearn Kristiina Aittomäki Jamie Allen Irene L Andrulis Hoda Anton-Culver Natalia N Antonenkova Volker Arndt Kristan J Aronson Paul L Auer Päivi Auvinen Myrto Barrdahl Laura E Beane Freeman Matthias W Beckmann Sabine Behrens Javier Benitez Marina Bermisheva Leslie Bernstein Carl Blomqvist Natalia V Bogdanova Stig E Bojesen Bernardo Bonanni Anne-Lise Børresen-Dale Hiltrud Brauch Michael Bremer Hermann Brenner Adam Brentnall Ian W Brock Angela Brooks-Wilson Sara Y Brucker Thomas Brüning Barbara Burwinkel Daniele Campa Brian D Carter Jose E Castelao Stephen J Chanock Rowan Chlebowski Hans Christiansen Christine L Clarke J Margriet Collée Emilie Cordina-Duverger Sten Cornelissen Fergus J Couch Angela Cox Simon S Cross Kamila Czene Mary B Daly Peter Devilee Thilo Dörk Isabel Dos-Santos-Silva Martine Dumont Lorraine Durcan Miriam Dwek Diana M Eccles Arif B Ekici A Heather Eliassen Carolina Ellberg Christoph Engel Mikael Eriksson D Gareth Evans Peter A Fasching Jonine Figueroa Olivia Fletcher Henrik Flyger Asta Försti Lin Fritschi Marike Gabrielson Manuela Gago-Dominguez Susan M Gapstur José A García-Sáenz Mia M Gaudet Vassilios Georgoulias Graham G Giles Irina R Gilyazova Gord Glendon Mark S Goldberg David E Goldgar Anna González-Neira Grethe I Grenaker Alnæs Mervi Grip Jacek Gronwald Anne Grundy Pascal Guénel Lothar Haeberle Eric Hahnen Christopher A Haiman Niclas Håkansson Ute Hamann Susan E Hankinson Elaine F Harkness Steven N Hart Wei He Alexander Hein Jane Heyworth Peter Hillemanns Antoinette Hollestelle Maartje J Hooning Robert N Hoover John L Hopper Anthony Howell Guanmengqian Huang Keith Humphreys David J Hunter Milena Jakimovska Anna Jakubowska Wolfgang Janni Esther M John Nichola Johnson Michael E Jones Arja Jukkola-Vuorinen Audrey Jung Rudolf Kaaks Katarzyna Kaczmarek Vesa Kataja Renske Keeman Michael J Kerin Elza Khusnutdinova Johanna I Kiiski Julia A Knight Yon-Dschun Ko Veli-Matti Kosma Stella Koutros Vessela N Kristensen Ute Krüger Tabea Kühl Diether Lambrechts Loic Le Marchand Eunjung Lee Flavio Lejbkowicz Jenna Lilyquist Annika Lindblom Sara Lindström Jolanta Lissowska Wing-Yee Lo Sibylle Loibl Jirong Long Jan Lubiński Michael P Lux Robert J MacInnis Tom Maishman Enes Makalic Ivana Maleva Kostovska Arto Mannermaa Siranoush Manoukian Sara Margolin John W M Martens Maria Elena Martinez Dimitrios Mavroudis Catriona McLean Alfons Meindl Usha Menon Pooja Middha Nicola Miller Fernando Moreno Anna Marie Mulligan Claire Mulot Victor M Muñoz-Garzon Susan L Neuhausen Heli Nevanlinna Patrick Neven William G Newman Sune F Nielsen Børge G Nordestgaard Aaron Norman Kenneth Offit Janet E Olson Håkan Olsson Nick Orr V Shane Pankratz Tjoung-Won Park-Simon Jose I A Perez Clara Pérez-Barrios Paolo Peterlongo Julian Peto Mila Pinchev Dijana Plaseska-Karanfilska Eric C Polley Ross Prentice Nadege Presneau Darya Prokofyeva Kristen Purrington Katri Pylkäs Brigitte Rack Paolo Radice Rohini Rau-Murthy Gad Rennert Hedy S Rennert Valerie Rhenius Mark Robson Atocha Romero Kathryn J Ruddy Matthias Ruebner Emmanouil Saloustros Dale P Sandler Elinor J Sawyer Daniel F Schmidt Rita K Schmutzler Andreas Schneeweiss Minouk J Schoemaker Fredrick Schumacher Peter Schürmann Lukas Schwentner Christopher Scott Rodney J Scott Caroline Seynaeve Mitul Shah Mark E Sherman Martha J Shrubsole Xiao-Ou Shu Susan Slager Ann Smeets Christof Sohn Penny Soucy Melissa C Southey John J Spinelli Christa Stegmaier Jennifer Stone Anthony J Swerdlow Rulla M Tamimi William J Tapper Jack A Taylor Mary Beth Terry Kathrin Thöne Rob A E M Tollenaar Ian Tomlinson Thérèse Truong Maria Tzardi Hans-Ulrich Ulmer Michael Untch Celine M Vachon Elke M van Veen Joseph Vijai Clarice R Weinberg Camilla Wendt Alice S Whittemore Hans Wildiers Walter Willett Robert Winqvist Alicja Wolk Xiaohong R Yang Drakoulis Yannoukakos Yan Zhang Wei Zheng Argyrios Ziogas Alison M Dunning Deborah J Thompson Georgia Chenevix-Trench Jenny Chang-Claude Marjanka K Schmidt Per Hall Roger L Milne Paul D P Pharoah Antonis C Antoniou Nilanjan Chatterjee Peter Kraft Montserrat García-Closas Jacques Simard Douglas F Easton

Am J Hum Genet 2018 Dec 5. Epub 2018 Dec 5.

Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK.

Stratification of women according to their risk of breast cancer based on polygenic risk scores (PRSs) could improve screening and prevention strategies. Our aim was to develop PRSs, optimized for prediction of estrogen receptor (ER)-specific disease, from the largest available genome-wide association dataset and to empirically validate the PRSs in prospective studies. The development dataset comprised 94,075 case subjects and 75,017 control subjects of European ancestry from 69 studies, divided into training and validation sets. Read More

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December 2018
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