1,152,559 results match your criteria Genome Biology [Journal]


Potential Role of microRNA-183 as a Tumor Suppressor in Hepatocellular Carcinoma.

Cell Physiol Biochem 2018 Dec 6;51(5):2065-2072. Epub 2018 Dec 6.

Department of General Surgery of East District, The Second Hospital of Hebei Medical University, Shijiazhuang,

Background/aims: Disseminated tumors, known as metastases, are responsible for ninety-percent of mortality due to cancer. Epithelial to mesenchymal transition, a phenomenon required for morphological conversion of non-motile discoid shaped epithelial cells to highly motile spindle-shaped mesenchymal cells, is thought to be a pre-requisite for metastatic progression. Metastasis-associated 1 (MTA1) protein is a prime inducer of EMT and metastatic progression in all solid tumors including hepatocellular carcinoma (HCC). Read More

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December 2018
8 Reads

Reasonable expectations of privacy in non-disclosure of familial genetic risk: What is it reasonable to expect?

Authors:
Victoria Chico

Eur J Med Genet 2018 Dec 3. Epub 2018 Dec 3.

Society and Ethics Research Group, Connecting Science, Wellcome Genome Campus, Cambridge, UK. Electronic address:

Where there is conflict between a patient's interests in non-disclosure of their genetic information to relatives and the relative's interest in knowing the information because it indicates their genetic risk, clinicians have customarily been able to protect themselves against legal action by maintaining confidence even if, professionally, they did not consider this to be the right thing to do. In ABC v St Georges Healthcare NHS Trust ([2017] EWCA Civ 336) the healthcare team recorded their concern about the wisdom of the patient's decision to withhold genetic risk information from his relative, but chose to respect what they considered to be an unwise choice. Even though professional guidance considers that clinicians have the discretion to breach confidence where they believe this to be justified, (Royal College of Physicians, Royal College of Pathologists and the British Society of Human Genetics, 2006; GMC, 2017) clinicians find it difficult to exercise this discretion in line with their convictions against the backdrop of the legal prioritisation of the duty to maintain confidence. Read More

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December 2018

Draft genome analysis of lignocellulolytic enzymes producing Aspergillus terreus with structural insight of β-glucosidases through molecular docking approach.

Int J Biol Macromol 2018 Dec 3. Epub 2018 Dec 3.

Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388110, Gujarat, India.

Members of the genus Aspergillus are extensively studied ascomycetes because of their ability to synthesize high value-added compounds and enzymes of industrial interest. Precise whole genome assembly and gene annotation are significant for gene functional analyses. Here, we report the draft genome sequencing, assembly and whole genome analysis of Aspergillus terreus P14_T3, isolated from rumen sample of cattle fed with coconut-coir. Read More

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December 2018
1 Read

RNA Therapy: Are we using the right Molecules?

Pharmacol Ther 2018 Dec 3. Epub 2018 Dec 3.

Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA.

Small-molecule and protein/antibody drugs mainly act on genome-derived proteins to exert pharmacological effects. RNA based therapies hold the promise to expand the range of druggable targets from proteins to RNAs and the genome, as evidenced by several RNA drugs approved for clinical practice and many others under active trials. While chemo-engineered RNA mimics have found their success in marketed drugs and continue dominating basic research and drug development, these molecules are usually conjugated with extensive and various modifications. Read More

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December 2018
2 Reads

Renoprotective meroterpenoids from the fungus Ganoderma cochlear.

Fitoterapia 2018 Dec 3. Epub 2018 Dec 3.

Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Pharmaceutical Sciences, School of Medicine, Shenzhen University Health Science Center, Shenzhen 518060, People's Republic of China. Electronic address:

Nine multifarious new meroterpenoids, cochlearols E-M (1-9), along with seven known meroterpenoids 10-16, were isolated from the fruiting bodies of Ganoderma cochlear. Racemic 1, 6-8, 10 and 13 were separated by chiral HPLC. The structures were elucidated based on detailed spectroscopic analyses (HRESIMS, 1D/2D-NMR) and calculated electronic circular dichroism (ECD). Read More

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December 2018
1 Read

Nucleoside and N-acetyldopamine derivatives from the insect Aspongopus chinensis.

Fitoterapia 2018 Dec 3. Epub 2018 Dec 3.

Guangdong Key Laboratory for Genome Stability & Disease Prevention, School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen 518060, PR China. Electronic address:

Two new nucleoside derivatives, named asponguanosines A and B (1 and 2), three new N-acetyldopamine analogues, aspongamides C-E (3-5), one new sesquiterpene, aspongnoid D (6), and three known compounds were isolated from the medicinal insect Aspongopus chinensis. Their structures including absolute configurations were assigned by using spectroscopic methods and ECD and C NMR calculations. Biological activities of compounds 3-7 towards human cancer cells, COX-2, ROCK1, and JAK3 were evaluated. Read More

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December 2018
2 Reads

Transgenerational effects in asexually reproduced offspring of Populus.

PLoS One 2018 6;13(12):e0208591. Epub 2018 Dec 6.

Forest & Nature Lab, Department of Environment, Ghent University, Gontrode, Belgium.

The response of trees to a changing climate can be affected by transgenerational phenotypic plasticity, i.e. phenotypic variation that is conserved and transferred to the offspring. Read More

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December 2018
2 Reads

CRISPR/Cas9 mediated knockout of the abdominal-A homeotic gene in fall armyworm moth (Spodoptera frugiperda).

PLoS One 2018 6;13(12):e0208647. Epub 2018 Dec 6.

Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States of America.

The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith), is an important pest of maize in the Americas and has recently been introduced into Africa. Read More

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December 2018
1 Read

Two jatropha karyotypes constructed from meiotic pachytene chromosomes: Pericentric distribution of heterochromatin and variation in repetitive DNAs.

PLoS One 2018 6;13(12):e0208549. Epub 2018 Dec 6.

Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand.

Jatropha (Jatropha curcas) is an oil-bearing plant used for biodiesel production. Construction of its standard karyotype and identification of the euchromatin/heterochromatin distribution associated with gene expression and meiotic recombination are essential to fully characterize its genome. Here, we developed a J. Read More

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December 2018

Gene landscape and correlation between B-cell infiltration and programmed death ligand 1 expression in lung adenocarcinoma patients from The Cancer Genome Atlas data set.

PLoS One 2018 6;13(12):e0208459. Epub 2018 Dec 6.

Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.

Tumor-infiltrating lymphocytes are related to positive clinical prognoses in numerous cancer types. Programmed death ligand 1 (PD-L1), a mediator of the PD-1 receptor, plays an inhibitory role in cancer immune responses. PD-L1 upregulation can impede infiltrating T-cell functions in lung adenocarcinoma (LUAD), a lung cancer subtype. Read More

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December 2018
1 Read

Whole genome variant association across 100 dogs identifies a frame shift mutation in DISHEVELLED 2 which contributes to Robinow-like syndrome in Bulldogs and related screw tail dog breeds.

PLoS Genet 2018 Dec 6;14(12):e1007850. Epub 2018 Dec 6.

Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, United States of America.

Domestic dog breeds exhibit remarkable morphological variations that result from centuries of artificial selection and breeding. Identifying the genetic changes that contribute to these variations could provide critical insights into the molecular basis of tissue and organismal morphogenesis. Bulldogs, French Bulldogs and Boston Terriers share many morphological and disease-predisposition traits, including brachycephalic skull morphology, widely set eyes and short stature. Read More

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December 2018
5 Reads

Tissue Specificity in Trisomy 22 Mosaicism: A Tale of Caution for Interpretation of Chromosomal Microarray Results.

J Assoc Genet Technol 2018 ;44(4):137-140

Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, VT.

Objectives: While the complete form of trisomy 22 is seemingly incompatible with life, the mosaic form is a rare syndrome associated with developmental delays, intellectual disability, and dysmorphic features. Due in part to the difficulty of analyzing chromosomal mosaicism, many instances either go undiagnosed or have their diagnosis delayed. We report a case of mosaic trisomy 22 in a diamnionic-dichorionic twin with marked growth discordance and intra-uterine growth restriction, diagnosed in a 2-year-old with developmental delays, sensorineural hearing loss, cardiac and gastrointestinal abnormalities, and osteopenia of prematurity. Read More

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January 2018
6 Reads

Chlorogenic acid-mediated chemical defense of plants against insect herbivores.

Plant Biol (Stuttg) 2018 Dec 6. Epub 2018 Dec 6.

National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.

Chlorogenic acid is one of the most abundant beneficial polyphenols in plants and is well known as nutritional anti-oxidant in plant based foods. Apart from its dietary antioxidant activity, it has been proven to be an efficient defense molecule against a broad range of insect herbivores. In the last two decades, several reports have shown the effectiveness of chlorogenic acid for insect's growth deterrence. Read More

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December 2018
1 Read

Loop assembly: a simple and open system for recursive fabrication of DNA circuits.

New Phytol 2018 Dec 6. Epub 2018 Dec 6.

Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.

High efficiency methods for DNA assembly have enabled routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customisation, elaborate vector sets or serial manipulations for the different stages of assembly. We have developed Loop assembly based on a recursive approach to DNA fabrication. Read More

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December 2018
1 Read

Insights into the evolution of the suppressors of cytokine signalling (SOCS) gene family in vertebrates.

Mol Biol Evol 2018 Dec 5. Epub 2018 Dec 5.

Scottish Fish Immunology Research Centre, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK.

The SOCS family are key negative regulators of cytokine and growth factor signalling. Typically 8-17 SOCS genes are present in vertebrate species and eight known in mammals, classified as type I (SOCS4-7) and type II (CISH and SOCS1-3) SOCS. It was believed that the type II SOCS were expanded through the two rounds of whole genome duplication (1R and 2R WGDs) from a single CISH/SOCS1-3 precursor. Read More

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December 2018

Advances in Genomic Hepatocellular Carcinoma Research.

Gigascience 2018 Dec 6. Epub 2018 Dec 6.

Graduate School of Integrative Sciences and Engineering, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 117456, Singapore.

Background: Hepatocellular carcinoma (HCC) is the cancer with the second highest mortality in the world due to its late presentation and limited treatment options. As such, there is an urgent need to identify novel biomarkers for early diagnosis and develop novel therapies. The availability of Next Generation Sequencing (NGS) data from tumors of liver cancer patients has provided us with invaluable resources to better understand HCC through the integration of data from different sources to facilitate the identification of promising biomarkers or therapeutic targets. Read More

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December 2018

Evolution of DNA methylation in Papio baboons.

Mol Biol Evol 2018 Dec 5. Epub 2018 Dec 5.

Department of Evolutionary Anthropology, Duke University, Durham, NC.

Changes in gene regulation have long been thought to play an important role in primate evolution. However, although a number of studies have compared genome-wide gene expression patterns across primate species, fewer have investigated the gene regulatory mechanisms that underlie such patterns, or the relative contribution of drift versus selection. Here, we profiled genome-scale DNA methylation levels in blood samples from five of the six extant species of the baboon genus Papio (4-14 individuals per species). Read More

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December 2018

miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants.

Bioinformatics 2018 Dec 6. Epub 2018 Dec 6.

Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P. R. China.

Motivation: Two major challenges arise when employing next generation sequencing (NGS) methods to comprehensively identify microRNAs (miRNAs) in plants: 1) how to minimize the false-positive inheritable to computational predictions; 2) how to minimize the computational time required for analyzing the miRNA transcriptome in plants with complex and large genomes.

Results: We updated miRDeep-P to miRDeep-P2 (miRDP2) by employing a new filtering strategy and overhauling the algorithm. miRDP2 has been tested against miRNA transcriptomes in plants with increasing genome sizes that included Arabidopsis, rice, tomato, maize and wheat. Read More

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December 2018
5 Reads
4.981 Impact Factor

Annotation of the Giardia proteome through structure-based homology and machine learning.

Gigascience 2018 Dec 6. Epub 2018 Dec 6.

Walter & Eliza Hall Institute of Medical Research, Melbourne, Australia.

Background: Large-scale computational prediction of protein structures represents a cost-effective alternative to empirical structure determination with particular promise for non-model organisms and neglected pathogens. Conventional sequence-based tools are insufficient to annotate the genomes of such divergent biological systems. Conversely, protein structure tolerates substantial variation in primary amino acid sequence, and is thus a robust indicator of biochemical function. Read More

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December 2018
2 Reads

New CRISPR-Cas9 vectors for genetic modifications of Bacillus species.

FEMS Microbiol Lett 2018 Dec 6. Epub 2018 Dec 6.

Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.

Genetic manipulation is a fundamental procedure for the study of gene and operon functions and new characteristics acquisition. Modern CRISPR-Cas technology allows genome editing more precise and increases the efficiency of transferring mutations in a variety of hard to manipulate organisms. Here, we describe new CRISPR-Cas vectors for genetic modifications in bacillary species. Read More

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December 2018
1 Read

Comparative genome analysis of Aspergillus flavus clinically isolated in Japan.

DNA Res 2018 Dec 5. Epub 2018 Dec 5.

Medical Mycology Research Center, Chiba University, Chiba City, Chiba, Japan.

Aspergillus flavus is an important zoonotic pathogen and a well-known aflatoxin producer. Aspergillus flavus strains that are prevalent in Japanese environments are reported to be non-aflatoxigenic, although their aflatoxin productivity, especially among clinical isolates, has not been thoroughly investigated to date. In this study, we sequenced the genomes of ten strains of A. Read More

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December 2018
1 Read

Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics.

Bioinformatics 2018 Dec 5. Epub 2018 Dec 5.

Department of Biomedical Data Science, Stanford University.

Summary: Large biobanks linking phenotype to genotype have led to an explosion of genetic association studies across a wide range of phenotypes. Sharing the knowledge generated by these resources with the scientific community remains a challenge due to patient privacy and the vast amount of data. Here we present Global Biobank Engine (GBE), a web-based tool that enables exploration of the relationship between genotype and phenotype in biobank cohorts, such as the UK Biobank. Read More

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December 2018
2 Reads

Whole-genome sequence of the oriental lung fluke Paragonimus westermani.

Gigascience 2018 Dec 6. Epub 2018 Dec 6.

The University of Queensland Diamantina Institute, Brisbane, QLD, Australia.

Background: Foodborne infections caused by lung flukes of the genus Paragonimus are a significant and widespread public health problem in tropical areas. Around 50 Paragonimus species have been reported to infect animals and humans, but Paragonimus westermani is responsible for the bulk of human disease. Despite their medical and economic importance, no genome sequence for any Paragonimus species is available. Read More

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December 2018
2 Reads

Alfred: Interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.

Bioinformatics 2018 Dec 6. Epub 2018 Dec 6.

GeneCore, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany.

Summary/motivation: Harmonizing quality control of large-scale second and third-generation sequencing datasets is key for enabling downstream computational and biological analyses. We present Alfred, an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner, across a wide variety of sequencing assays and technologies. In addition to standard quality control metrics such as GC bias, base composition, insert size and sequencing coverage distributions it supports haplotype-aware and allele-specific feature counting and feature annotation. Read More

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December 2018

A single AT-GC exchange can modulate charge transfer-induced p53-DNA dissociation.

Chem Commun (Camb) 2018 Dec 6. Epub 2018 Dec 6.

Department of Chemistry, Duke University, Durham, North Carolina 27708, USA. and Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA and Department of Physics, Duke University, Durham, North Carolina 27708, USA.

Using molecular dynamics simulations and electronic structure theory, we shed light on the charge dynamics that causes the differential interaction of tumor suppressor protein p53 with the p21 and Gadd45 genes in response to oxidative stress. We show that the sequence dependence of this selectivity results from competing charge transfer to the protein and through the DNA, with implications on the use of genome editing tools to influence the p53 regulatory function. Read More

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December 2018

A reference standard for genome biology.

Authors:

Nat Biotechnol 2018 Dec;36(12):1121

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December 2018

DNA translocation mechanism of an XPD family helicase.

Elife 2018 Dec 6;7. Epub 2018 Dec 6.

Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom.

The XPD family of helicases, that includes human disease-related FANCJ, DDX11 and RTEL1, are Superfamily 2 helicases that contain an iron-sulphur cluster domain, translocate on ssDNA in a 5'-3' direction and play important roles in genome stability. Consequently, mutations in several of these family members in eukaryotes cause human diseases. Family members in bacteria, such as the DinG helicase from , are also involved in DNA repair. Read More

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December 2018
5 Reads

Drought adaptation in by extensive genetic loss-of-function.

Elife 2018 Dec 6;7. Epub 2018 Dec 6.

Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States.

Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments to study natural loss-of-function alleles associated with drought histories in wild . The genes we identified exhibit population genetic signatures of parallel molecular evolution, selection for loss-of-function, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses 7 times more often than expected by chance. Read More

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December 2018
1 Read

General decapping activators target different subsets of inefficiently translated mRNAs.

Elife 2018 Dec 6;7. Epub 2018 Dec 6.

Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States.

The Dcp1-Dcp2 decapping enzyme and the decapping activators Pat1, Dhh1, and Lsm1 regulate mRNA decapping, but their mechanistic integration is unknown. We analyzed the gene expression consequences of deleting or or the C-terminal domain, and found that: i) the Dcp2 C-terminal domain is an effector of both negative and positive regulation; ii) rather than being global activators of decapping, Pat1, Lsm1, and Dhh1 directly target specific subsets of yeast mRNAs and loss of the functions of each of these factors has substantial indirect consequences for genome-wide mRNA expression; and iii) transcripts targeted by Pat1, Lsm1, and Dhh1 exhibit only partial overlap, are generally translated inefficiently, and, as expected, are targeted to decapping-dependent decay. Our results define the roles of Pat1, Lsm1, and Dhh1 in decapping of general mRNAs and suggest that these factors may monitor mRNA translation and target unique features of individual mRNAs. Read More

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December 2018

Biallelic loss of function variants in PPP1R21 cause a neurodevelopmental syndrome with impaired endocytic function.

Hum Mutat 2018 Dec 6. Epub 2018 Dec 6.

Genome Research Division, Human Genetics department, Radboud University Medical Center Nijmegen and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.

Next-generation sequencing has been instrumental in solving the genetic basis of rare inherited diseases, especially neurodevelopmental syndromes. However, functional workup is essential for precise phenotype definition and to understand the underlying disease mechanisms. Using whole exome and whole genome sequencing in 4 independent families with hypotonia, neurodevelopmental delay, facial dysmorphism, loss of white matter and thinning of the corpus callosum, we identified 4 previously unreported homozygous truncating PPP1R21 alleles: c. Read More

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December 2018

Overview of non-coding mutations in chronic lymphocytic leukemia.

Mol Oncol 2018 Dec 6. Epub 2018 Dec 6.

Division of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.

Chronic lymphocytic leukemia (CLL) is the most frequent leukemia type in which the genetic alterations influencing the clinico-biological course are not entirely understood. CLL has a heterogeneous course, with some patients showing an indolent course, and others experiencing an aggressive course. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) studies identified recurrently mutated genes in CLL, and profiled its clonal evolution patterns. Read More

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December 2018
1 Read

High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus.

Proteins 2018 Dec 6. Epub 2018 Dec 6.

Department of Biology, Faculty of Science, Niigata University, Niigata, Japan.

Peptidyl-tRNA hydrolase (Pth) cleaves the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are the products of defective translation, to recycle the tRNA for further rounds of protein synthesis. Pth is ubiquitous in nature, and its activity is essential for bacterial viability. Here, we have determined the crystal structure of Pth from Thermus thermophilus (TtPth) at 1. Read More

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December 2018
2 Reads

Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish.

Mol Ecol 2018 Dec 5. Epub 2018 Dec 5.

Carl von Ossietzky University Oldenburg, Institute for Biology and Environmental Sciences, Carl von Ossietzky Str. 9-11, 26111, Oldenburg, Germany.

Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through non-allelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. Read More

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December 2018

A novel model for predicting non-responsiveness to intravenous immunoglobulins in Kawasaki disease: The Singapore experience.

J Paediatr Child Health 2018 Dec 5. Epub 2018 Dec 5.

Division of Paediatric Cardiology, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore.

Aim: We aimed to assess the utility of four published risk-scoring methods in predicting intravenous immunoglobulins (IVIG) non-responsiveness in Kawasaki disease (KD) patients from Singapore and develop a new predictive model.

Methods: We reviewed the medical records of 215 KD children. The performance of existing scoring methods in identifying non-responsive cases based on sensitivities (SN) and specificities (SP) was evaluated in 122 Singaporean Chinese. Read More

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December 2018
1 Read

A revolutionary tool: CRISPR technology plays an important role in construction of intelligentized gene circuits.

Cell Prolif 2018 Dec 5:e12552. Epub 2018 Dec 5.

Department of Urology, the First Affiliated Hospital of Shenzhen University, Shenzhen, China.

With the development of synthetic biology, synthetic gene circuits have shown great applied potential in medicine, biology, and as commodity chemicals. An ultimate challenge in the construction of gene circuits is the lack of effective, programmable, secure and sequence-specific gene editing tools. The clustered regularly interspaced short palindromic repeat (CRISPR) system, a CRISPR-associated RNA-guided endonuclease Cas9 (CRISPR-associated protein 9)-targeted genome editing tool, has recently been applied in engineering gene circuits for its unique properties-operability, high efficiency and programmability. Read More

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December 2018
4 Reads

Downregulation of fibroblast growth factor 5 inhibits cell growth and invasion of human nonsmall-cell lung cancer cells.

J Cell Biochem 2018 Dec 5. Epub 2018 Dec 5.

Department of Cardio-Thoracic, Wujin People's Hospital of Changzhou, Changzhou, China.

The morbidity and mortality rates of nonsmall-cell lung cancer (NSCLC) have increased in recent years. We aimed to explore the biological role of fibroblast growth factor 5 (FGF5) in NSCLC. We first established that the expression of FGF5 was increased in NSCLC tissues compared with the normal adjacent tissues. Read More

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December 2018

CRISPR/Cas9-Based Chemogenomic Profiling in Mammalian Cells.

Methods Mol Biol 2019 ;1888:153-174

Novartis Institutes for BioMedical Research, Cambridge, MA, USA.

Chemogenomic profiling is a powerful and unbiased approach to elucidate pharmacological targets and the mechanism of bioactive compounds. It is based on identifying cellular hypersensitivity and resistance caused by individual gene modulations with genome-wide coverage. Due to the requirement of bar-coded, genome-wide deletion collections, high-resolution experiments of this nature have historically been limited to fungal systems. Read More

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January 2019
2 Reads

Altered Global mRNA Expressions of Pain and Aggression Related Genes in the Blood of Children with Autism Spectrum Disorders.

J Mol Neurosci 2018 Dec 5. Epub 2018 Dec 5.

Department of Medical Genetics, Erciyes University Medical Faculty, 38039, Kayseri, Turkey.

Autism spectrum disorder (ASD) is characterized by repetitive stereotypic behaviors, restricted interests, social withdrawal, and communication deficits. Aggression and insensitivity to pain are largely unexplained in these cases. We analyzed nine mRNA expressions of the candidate genes related to aggression and insensitivity to pain in the peripheral blood of patients with ASD. Read More

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December 2018
5 Reads

Development of a reverse genetics system for a feline panleukopenia virus.

Virus Genes 2018 Dec 5. Epub 2018 Dec 5.

Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Science, 666 Liuying Xi Road, Changchun, 130122, China.

Feline panleukopenia virus (FPV) infects cats and can be fatal to kittens. There is evidence that canine parvovirus originated from FPV, which makes FPV important in studies of the family Parvoviridae. In the present study, the entire genome of FPV strain HH-1/86 was converted into a full-length infectious clone (pFPV). Read More

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December 2018
1 Read

Nonalcoholic Fatty Liver Disease Demonstrates a Pre-fibrotic and Premalignant Molecular Signature.

Dig Dis Sci 2018 Dec 5. Epub 2018 Dec 5.

Department of Biology, University of Massachusetts Boston, Boston, USA.

Background: Metabolic syndrome contributing to nonalcoholic fatty liver disease (NAFLD) can lead to hepatic dysfunction, steatohepatitis, cirrhosis, and hepatocellular carcinoma.

Aims: In this study, we tested whether diet-induced fatty liver in a mouse model physiologically mimicked human NAFLD, and whether transcriptional alterations in mouse fatty liver signified risk for the development of hepatitis, cirrhosis, and/or hepatocellular carcinoma.

Methods: SAMP6 strain mice were fed a low-fat diet or high-fat diet (HFD) for 6 months. Read More

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December 2018
1 Read

Divergent evolution of rice blast resistance Pi54 locus in the genus Oryza.

Rice (N Y) 2018 Dec 5;11(1):63. Epub 2018 Dec 5.

Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan.

Background: The rice blast resistance gene Pi54 was cloned from Oryza sativa ssp. indica cv. Tetep, which conferred broad-spectrum resistance against Magnaporthe oryzae. Read More

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December 2018
2 Reads

Genome-wide association study of maize plant architecture using F populations.

Plant Mol Biol 2018 Dec 5. Epub 2018 Dec 5.

National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China.

Key Message: Genome-wide association study of maize plant architecture using F populations can better dissect various genetic effects that can provide precise guidance for genetic improvement in maize breeding. Maize grain yield has increased at least eightfold during the past decades. Plant architecture, including plant height, leaf angle, leaf length, and leaf width, has been changed significantly to adapt to higher planting density. Read More

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December 2018
2 Reads

Exploration of Shared Genetic Architecture Between Subcortical Brain Volumes and Anorexia Nervosa.

Mol Neurobiol 2018 Dec 5. Epub 2018 Dec 5.

Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany.

In MRI scans of patients with anorexia nervosa (AN), reductions in brain volume are often apparent. However, it is unknown whether such brain abnormalities are influenced by genetic determinants that partially overlap with those underlying AN. Here, we used a battery of methods (LD score regression, genetic risk scores, sign test, SNP effect concordance analysis, and Mendelian randomization) to investigate the genetic covariation between subcortical brain volumes and risk for AN based on summary measures retrieved from genome-wide association studies of regional brain volumes (ENIGMA consortium, n = 13,170) and genetic risk for AN (PGC-ED consortium, n = 14,477). Read More

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December 2018
1 Read

The first comprehensive description of the expression profile of genes involved in differential body growth and the immune system of the Jeju Native Pig and miniature pig.

Amino Acids 2018 Dec 5. Epub 2018 Dec 5.

Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, 690756, Jeju-Do, Republic of Korea.

Sus scrofa provides a major source of animal protein for humans as well as being an excellent biomedical model. This study was carried out to understand, in detail, the genetic and functional variants of Jeju Native Pigs and miniature pigs through differential expression profiling of the genes controlling their immune response, growth performance, and meat quality. The Illumina HiSeq 2000 platform was used for generating 1. Read More

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December 2018
1 Read

Possibility of numt co-amplification from gigantic genome of Orthoptera: testing efficiency of standard PCR protocol in producing orthologous COI sequences.

Heliyon 2018 Nov 23;4(11):e00929. Epub 2018 Nov 23.

Department of Biology, Faculty of Science, Akdeniz University, 07058, Antalya, Turkey.

Mitochondrial DNA has been the preferential genome biodiversity studies. However, several factors contribute to its inadequacy. Numts constitute one of the main complications that prevent obtaining orthologous mitochondrial sequences. Read More

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November 2018

Breaking point: the genesis and impact of structural variation in tumours.

F1000Res 2018 19;7. Epub 2018 Nov 19.

MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH42XU, UK.

Somatic structural variants undoubtedly play important roles in driving tumourigenesis. This is evident despite the substantial technical challenges that remain in accurately detecting structural variants and their breakpoints in tumours and in spite of our incomplete understanding of the impact of structural variants on cellular function. Developments in these areas of research contribute to the ongoing discovery of structural variation with a clear impact on the evolution of the tumour and on the clinical importance to the patient. Read More

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November 2018

Preliminary insights into the genetics of bank vole tolerance to Puumala hantavirus in Sweden.

Ecol Evol 2018 Nov 26;8(22):11273-11292. Epub 2018 Oct 26.

CBGP, INRA, CIRAD, IRD, Montpellier SupAgro Univ. Montpellier Montpellier France.

Natural reservoirs of zoonotic pathogens generally seem to be capable of tolerating infections. Tolerance and its underlying mechanisms remain difficult to assess using experiments or wildlife surveys. High-throughput sequencing technologies give the opportunity to investigate the genetic bases of tolerance, and the variability of its mechanisms in natural populations. Read More

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November 2018

Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot.

Ecol Evol 2018 Nov 23;8(22):10989-11008. Epub 2018 Oct 23.

Red Sea Research Center, Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal Saudi Arabia.

For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of 47 butterflyfish species (family Chaetodontidae) that includes all shallow water butterflyfish from the coastal waters of the Arabian Peninsula (i.e. Read More

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November 2018

SSR-seq: Genotyping of microsatellites using next-generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring.

Ecol Evol 2018 Nov 25;8(22):10817-10833. Epub 2018 Oct 25.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben Germany.

Microsatellites (or simple sequence repeats, SSR) are widely used markers in population genetics. Traditionally, genotyping was and still is carried out through recording fragment length. Now, next-generation sequencing (NGS) makes it easy to obtain also sequence information for the loci of interest. Read More

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November 2018
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