476,301 results match your criteria Chromosome research : an international journal on the molecular supramolecular and evolutionary aspects of chromosome biology[Journal]


Galactitol catabolism in Sinorhizobium meliloti is dependent on a chromosomally encoded sorbitol dehydrogenase and a pSymB-encoded operon necessary for tagatose catabolism.

Mol Genet Genomics 2019 Mar 16. Epub 2019 Mar 16.

Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.

The legume endosymbiont Sinorhizobium meliloti can utilize a broad range of carbon compounds to support its growth. The linear, six-carbon polyol galactitol is abundant in vascular plants and is metabolized in S. meliloti by the contribution of two loci SMb21372-SMb21377 and SMc01495-SMc01503 which are found on pSymB and the chromosome, respectively. Read More

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http://dx.doi.org/10.1007/s00438-019-01545-zDOI Listing

The E. coli transcriptional regulatory network and its spatial embedding.

Eur Phys J E Soft Matter 2019 Mar 20;42(3):30. Epub 2019 Mar 20.

Computational Systems Biology, Jacobs University Bremen, 28759, Bremen, Germany.

Usually complex networks are studied as graphs consisting of nodes whose spatial arrangement is of no significance. Several real biological networks are, however, embedded in space. In this paper we study the transcription regulatory network (TRN) of E. Read More

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http://dx.doi.org/10.1140/epje/i2019-11794-xDOI Listing

Genome-wide SNP discovery for development of high-density genetic map and QTL mapping of ascochyta blight resistance in chickpea (Cicer arietinum L.).

Theor Appl Genet 2019 Mar 16. Epub 2019 Mar 16.

Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Canada.

Key Message: A high-density linkage map of chickpea using 3430 SNPs was constructed and used to identify QTLs and candidate genes for ascochyta blight resistance in chickpea. Chickpea cultivation in temperate conditions is highly vulnerable to ascochyta blight infection. Cultivation of resistant cultivars in combination with fungicide application within an informed disease management package is the most effective method to control ascochyta blight in chickpeas. Read More

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http://dx.doi.org/10.1007/s00122-019-03322-3DOI Listing

Arterial Spin Labeling for Glioma Grade Discrimination: Correlations with IDH1 Genotype and 1p/19q Status.

Transl Oncol 2019 Mar 14;12(5):749-756. Epub 2019 Mar 14.

Department of Radiology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou 510060, China. Electronic address:

Since accurate grading of gliomas has important clinical value, the aim of this study is to evaluate the diagnostic efficacy of perfusion values derived from arterial spin labeling (ASL) to grade gliomas. In addition, the correlation between perfusion and isocitrate dehydrogenase 1 (IDH1) genotypes and chromosome arms 1p and 19q (1p/19q) status of gliomas was assessed. A total of 52 cases of supratentorial gliomas in adults who received ASL imaging were enrolled in this retrospective study. Read More

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http://dx.doi.org/10.1016/j.tranon.2019.02.013DOI Listing

c-Met expression is a useful marker for prognosis prediction in IDH-mutant lower-grade gliomas and IDH-wildtype glioblastomas.

World Neurosurg 2019 Mar 13. Epub 2019 Mar 13.

Department of Neurosurgery, Fujita Health University, Toyoake, Aichi, Japan.

Objective: c-Met has been shown to be associated with tumor growth in several human cancers. This study aims to evaluate the correlation between the c-Met expression and histopathological/clinical characteristics.

Methods: A total of 153 patients with histologically defined World Health Organization grade II-IV diffuse astrocytic and oligodendroglial tumors were analyzed. Read More

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http://dx.doi.org/10.1016/j.wneu.2019.03.040DOI Listing

Novel Staphylococcal Cassette Chromosome composite island (SCC-CI) with a new subtype of SCCmecVI cassette found in ST5 MRSA in France.

Int J Antimicrob Agents 2019 Mar 13. Epub 2019 Mar 13.

National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France; Department of Clinical Microbiology, Northern Hospital Group, Hospices Civils de Lyon, Lyon, France; International Centre for Research in Infectious diseases, INSERM U1111, University of Lyon, Lyon, France. Electronic address:

An emergent kanamycin-susceptible ST5-MRSA lineage has been identified in France. Whole genome sequencing revealed a 40 kb SCC composite island with a mosaic structure including 3 SCC elements: a ΨSCC, a SCC with a ccrC recombinase, and a novel subtype of SCCmec type VI (VIb). This mosaic structure suggests a high recombination rate of SCC elements from distinct staphylococci species. Read More

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http://dx.doi.org/10.1016/j.ijantimicag.2019.03.015DOI Listing

Impaired EIF2S3 function associated with a novel phenotype of X-linked hypopituitarism with glucose dysregulation.

EBioMedicine 2019 Mar 13. Epub 2019 Mar 13.

Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, United Kingdom. Electronic address:

Background: The heterotrimeric GTP-binding protein eIF2 forms a ternary complex with initiator methionyl-tRNA and recruits it to the 40S ribosomal subunit for start codon selection and thereby initiates protein synthesis. Mutations in EIF2S3, encoding the eIF2γ subunit, are associated with severe intellectual disability and microcephaly, usually as part of MEHMO syndrome.

Methods: Exome sequencing of the X chromosome was performed on three related males with normal head circumferences and mild learning difficulties, hypopituitarism (GH and TSH deficiencies), and an unusual form of glucose dysregulation. Read More

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http://dx.doi.org/10.1016/j.ebiom.2019.03.013DOI Listing

Epicardial fat: the role of testosterone and lipid metabolism in a cohort of patients with Klinefelter syndrome.

Metabolism 2019 Mar 13. Epub 2019 Mar 13.

Centre for Rare Diseases, Policlinico Umberto I, Rome, Italy; Department of Experimental Medicine, Section of Medical Pathophysiology, Food Science and Endocrinology, Sapienza University of Rome, Rome, Italy.

Context: Klinefelter syndrome (KS), in which subjects have additional copies of X chromosomes, is the most common male sex chromosome abnormality, with a prevalence of 1 in 660 and an incidence of about 1 in 500-700 newborns. Its sign and symptoms include infertility, generally low testosterone levels, and an increased prevalence of obesity and metabolic syndrome. Epicardial fat thickness (EFT) reflects visceral adiposity rather than general obesity. Read More

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http://dx.doi.org/10.1016/j.metabol.2019.03.002DOI Listing

Ccne1 Overexpression Causes Chromosome Instability in Liver Cells and Liver Tumor Development in Mice.

Gastroenterology 2019 Mar 13. Epub 2019 Mar 13.

Department of Biochemistry and Molecular Biology; Department of Pediatric and Adolescent Medicine; Department of Pediatrics. Electronic address:

Background & Aims: The CCNE1 locus, which encodes cyclin E1, is amplified in many types of cancer cells and is activated in hepatocellular carcinomas (HCCs) from patients infected with hepatitis B virus or adeno-associated virus type 2, due to integration of the virus nearby. We investigated cell cycle and oncogenic effects of cyclin E1 overexpression in tissues of mice.

Methods: We generated mice with doxycycline-inducible expression of Ccne1 (Ccne1 mice) and activated overexpression of cyclin E1 from age 3 weeks onwards. Read More

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http://dx.doi.org/10.1053/j.gastro.2019.03.016DOI Listing

IKZF1 Deletions with COBL Breakpoints Are Not Driven by RAG-Mediated Recombination Events in Acute Lymphoblastic Leukemia.

Transl Oncol 2019 Mar 13;12(5):726-732. Epub 2019 Mar 13.

Molecular Cancer Study Group, Division of Clinical Research, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, Brazil. Electronic address:

IKZF1 deletion (ΔIKZF1) is an important predictor of relapse in both childhood and adult B-cell precursor acute lymphoblastic leukemia (B-ALL). Previously, we revealed that COBL is a hotspot for breakpoints in leukemia and could promote IKZF1 deletions. Through an international collaboration, we provide a detailed genetic and clinical picture of B-ALL with COBL rearrangements (COBL-r). Read More

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http://dx.doi.org/10.1016/j.tranon.2019.02.002DOI Listing

1q23.1 homozygous deletion and downregulation of Fc receptor-like family genes confer poor prognosis in chronic lymphocytic leukemia.

Clin Exp Med 2019 Mar 15. Epub 2019 Mar 15.

Department of Biology, University of Bari "Aldo Moro", Via G. Orabona No. 4, 70126, Bari, Italy.

The identification of chromosome 1 translocations and deletions is a rare and poorly investigated event in chronic lymphocytic leukemia (CLL). Nevertheless, the identification of novel additional molecular alterations is of great interest, opening to new prognostic and therapeutic strategies for such heterogeneous hematological disease. We here describe a patient affected by CLL with a mutated IGHV status, showing a balanced t(1;3)(q23. Read More

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http://dx.doi.org/10.1007/s10238-019-00551-0DOI Listing

Cell-to-cell variation of chromosomal number in the adult testicular germ cell tumors: a comparison of chromosomal instability among histological components and its putative role in tumor progression.

Virchows Arch 2019 Mar 14. Epub 2019 Mar 14.

Department of Basic Pathology, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan.

By allelotyping analysis, we previously reported a putative progression pathway from germ cell neoplasia in situ (GCNIS) to seminoma, then to embryonal carcinoma in mixed-type testicular germ cell tumors (TGCTs), and detected that loss of heterozygosity events in seminoma components in mixed tumors were more frequent than those in pure seminomas. To elucidate a role of chromosomal instability in the progression of non-seminomatous germ cell tumor (NSGCT), we performed fluorescence in situ hybridization with centromeric probes for chromosomes 1, 7, 8, 12, 17, and X on a cohort of 52 TGCT cases with 103 histologically distinct components: 39 GCNIS lesions (16 and 23 in tumors with and without NSGCT components, respectively), 39 seminomas (27 as pure seminomas and 12 in mixed tumors), and 25 embryonal carcinomas. On a total component basis, both the mean copy number per tumor cell nucleus and the deviations from the modal number of all chromosomes examined significantly increased from GCNIS to seminoma, then to embryonal carcinoma with few exceptions. Read More

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http://dx.doi.org/10.1007/s00428-019-02560-6DOI Listing

Meiotic chromosomes in motion: a perspective from Mus musculus and Caenorhabditis elegans.

Chromosoma 2019 Mar 15. Epub 2019 Mar 15.

Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030, Vienna, Austria.

Vigorous chromosome movement during the extended prophase of the first meiotic division is conserved in most eukaryotes. The movement is crucial for the faithful segregation of homologous chromosomes into daughter cells, and thus for fertility. A prerequisite for meiotic chromosome movement is the stable and functional attachment of telomeres or chromosome ends to the nuclear envelope and their cytoplasmic coupling to the cytoskeletal forces responsible for generating movement. Read More

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http://dx.doi.org/10.1007/s00412-019-00698-5DOI Listing
March 2019
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Elevated signature of a gene module coexpressed with CDC20 marks genomic instability in glioma.

Proc Natl Acad Sci U S A 2019 Mar 15. Epub 2019 Mar 15.

Beijing Key Laboratory of Gene Resource and Molecular Development, Laboratory of Neuroscience and Brain Development, Beijing Normal University, 100875 Beijing, China;

Genomic instability (GI) drives tumor heterogeneity and promotes tumor progression and therapy resistance. However, causative factors underlying GI and means for clinical detection of GI in glioma are inadequately identified. We describe here that elevated expression of a gene module coexpressed with CDC20 (CDC20-M), the activator of the anaphase-promoting complex in the cell cycle, marks GI in glioma. Read More

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http://dx.doi.org/10.1073/pnas.1814060116DOI Listing

suppression during the fetal period optimizes ovarian development by fine-tuning of Notch signaling.

J Cell Sci 2019 Mar 15. Epub 2019 Mar 15.

Department of Pediatrics and Developmental Biology, Tokyo Medical Dental University, Tokyo, Japan.

The nuclear receptor NR5A1 is equally expressed and required for development of the gonadal primordia of both sexes, but after sex determination, it is up-regulated in XY testes and down-regulated in XX ovaries. We have recently demonstrated that this down-regulation is mediated by Forkhead box L2 (FOXL2) and hypothesized that adequate suppression of may be essential for normal ovarian development. Further, analysis of human patients with Disorders/Differences of Sex Development suggests that overexpression of can result in XX (ovo)testicular development. Read More

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http://dx.doi.org/10.1242/jcs.223768DOI Listing

DamID as a versatile tool for understanding gene regulation.

Development 2019 Mar 15;146(6). Epub 2019 Mar 15.

Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London, SW7 2AZ, UK

The interaction of proteins and RNA with chromatin underlies the regulation of gene expression. The ability to profile easily these interactions is fundamental for understanding chromatin biology DNA adenine methyltransferase identification (DamID) profiles genome-wide protein-DNA interactions without antibodies, fixation or protein pull-downs. Recently, DamID has been adapted for applications beyond simple assaying of protein-DNA interactions, such as for studying RNA-chromatin interactions, chromatin accessibility and long-range chromosome interactions. Read More

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http://dx.doi.org/10.1242/dev.173666DOI Listing

Cleaning Genotype Data from Diversity Outbred Mice.

G3 (Bethesda) 2019 Mar 15. Epub 2019 Mar 15.

The Jackson Laboratory.

Data cleaning is an important first step in most statistical analyses, including efforts to map the genetic loci that contribute to variation in quantitative traits. Here we illustrate approaches to quality control and cleaning of array-based genotyping data for multiparent populations (experimental crosses derived from more than two founder strains), using MegaMUGA array data from a set of 291 from Diversity Outbred (DO) mice. Our approach employs data visualizations that can reveal problems at the level of individual mice or with individual SNP markers. Read More

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http://dx.doi.org/10.1534/g3.119.400165DOI Listing

Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus.

BMC Genomics 2019 Mar 15;20(1):218. Epub 2019 Mar 15.

Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.

Background: Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use of anthelmintics has driven the evolution of resistance in a number of species that infect livestock and companion animals, and there are growing concerns regarding the reduced efficacy in some human-infective helminths. Understanding the mechanisms by which resistance evolves is the focus of increasing interest; robust genetic analysis of helminths is challenging, and although many candidate genes have been proposed, the genetic basis of resistance remains poorly resolved. Read More

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http://dx.doi.org/10.1186/s12864-019-5592-6DOI Listing

Supercoil Levels in and Chromosomes Are Regulated by the C-Terminal 35⁻38 Amino Acids of GyrA.

Microorganisms 2019 Mar 15;7(3). Epub 2019 Mar 15.

Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA.

Prokaryotes have an essential gene-gyrase-that catalyzes negative supercoiling of plasmid and chromosomal DNA. Negative supercoils influence DNA replication, transcription, homologous recombination, site-specific recombination, genetic transposition and sister chromosome segregation. Although and Typhimurium are close relatives with a conserved set of essential genes, DNA has a supercoil density 15% higher than , and cannot grow at the supercoil density maintained by wild type (WT) . Read More

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http://dx.doi.org/10.3390/microorganisms7030081DOI Listing

The Emerging Roles of TERRA in Telomere Maintenance and Genome Stability.

Cells 2019 Mar 15;8(3). Epub 2019 Mar 15.

Laboratory of Cell Biology and Molecular Genetics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy.

The finding that transcription occurs at chromosome ends has opened new fields of study on the roles of telomeric transcripts in chromosome end maintenance and genome stability. Indeed, the ends of chromosomes are required to be protected from activation of DNA damage response and DNA repair pathways. Chromosome end protection is achieved by the activity of specific proteins that associate with chromosome ends, forming telomeres. Read More

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http://dx.doi.org/10.3390/cells8030246DOI Listing
March 2019
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Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome.

Genes (Basel) 2019 Mar 14;10(3). Epub 2019 Mar 14.

Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.

In the past decades, the study of microbial life through shotgun metagenomic sequencing has rapidly expanded our understanding of environmental, synthetic, and clinical microbial communities. Here, we review how shotgun metagenomics has affected the field of halophilic microbial ecology, including functional potential reconstruction, virus⁻host interactions, pathway selection, strain dispersal, and novel genome discoveries. However, there still remain pitfalls and limitations from conventional metagenomic analysis being applied to halophilic microbial communities. Read More

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http://dx.doi.org/10.3390/genes10030220DOI Listing

Functional genomics analysis of Phelan-McDermid syndrome 22q13 region during human neurodevelopment.

PLoS One 2019 15;14(3):e0213921. Epub 2019 Mar 15.

Division of Intramural Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America.

Phelan-McDermid syndrome (PMS) is a neurodevelopmental disorder characterized by varying degrees of intellectual disability, severely delayed language development and specific facial features, and is caused by a deletion within chromosome 22q13.3. SHANK3, which is located at the terminal end of this region, has been repeatedly implicated in other neurodevelopmental disorders and deletion of this gene specifically is thought to cause much of the neurologic symptoms characteristic of PMS. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0213921PLOS

Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3K.

PLoS Comput Biol 2019 Mar 15;15(3):e1006402. Epub 2019 Mar 15.

Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America.

The PI3K/AKT signaling pathway plays a role in most cellular functions linked to cancer progression, including cell growth, proliferation, cell survival, tissue invasion and angiogenesis. It is generally recognized that hyperactive PI3K/AKT are oncogenic due to their boost to cell survival, cell cycle entry and growth-promoting metabolism. That said, the dynamics of PI3K and AKT1 during cell cycle progression are highly nonlinear. Read More

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http://dx.doi.org/10.1371/journal.pcbi.1006402DOI Listing

Gelatinous bone marrow transformation and emergence of clonal Philadelphia-negative cytogenetic abnormalities with excess blasts in a patient with chronic myeloid leukemia treated with dasatinib.

Anticancer Drugs 2019 Apr;30(4):416-421

Department of Medicine, The Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases.

Gelatinous bone marrow transformation (GBMT) is a rare pathologic entity of unclear etiology characterized by adipose cell atrophy, focal hematopoietic tissue hypoplasia, and a distinct eosinophilic substance that stains with Alcian blue at pH 2.5. It is traditionally described in the context of malnutrition and cachexia from generalized disease and is important to identify because of its potential reversibility. Read More

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http://dx.doi.org/10.1097/CAD.0000000000000763DOI Listing

Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds.

Metabolomics 2019 Mar 15;15(4):46. Epub 2019 Mar 15.

Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, OT, Germany.

Introduction: To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism.

Objective: This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues.

Methods: The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. Read More

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http://dx.doi.org/10.1007/s11306-019-1503-8DOI Listing
March 2019
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Multiple decay events target mRNA during splicing to regulate the unfolded protein response.

Elife 2019 Mar 15;8. Epub 2019 Mar 15.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, United States.

In the unfolded protein response (UPR), stress in the endoplasmic reticulum (ER) activates a large transcriptional program to increase ER folding capacity. During the budding yeast UPR, Ire1 excises an intron from the mRNA and the exon products of cleavage are ligated, and the translated protein induces hundreds of stress-response genes. Using cells with mutations in RNA repair and decay enzymes, we show that phosphorylation of two different splicing intermediates is required for their degradation by the 5'→3' exonuclease Xrn1 to enact opposing effects on the UPR. Read More

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http://dx.doi.org/10.7554/eLife.42262DOI Listing

Impressionist portraits of mitotic exit: APC/C, K11-linked ubiquitin chains and Cezanne.

Cell Cycle 2019 Mar 15. Epub 2019 Mar 15.

a Lineberger Comprehensive Cancer Center.

The Anaphase-Promoting Complex/Cyclosome (APC/C) is an E3 ubiquitin ligase and key regulator of cell cycle progression. By triggering the degradation of mitotic cyclins, APC/C controls cell cycle-dependent oscillations in Cyclin Dependent Kinase (CDK) activity. Thus, the dynamic activities of both APC/C and CDK sit at the core of the cell cycle oscillator. Read More

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http://dx.doi.org/10.1080/15384101.2019.1593646DOI Listing

Cornelia de Lange syndrome, related disorders, and the Cohesin complex: Abstracts from the 8th biennial scientific and educational symposium 2018.

Am J Med Genet A 2019 Mar 15. Epub 2019 Mar 15.

Research Department, Cornelia de Lange Syndrome Foundation, Avon, Connecticut.

Cornelia de Lange Syndrome (CdLS), due to mutations in genes of the cohesin protein complex, is described as a disorder of transcriptional regulation. Phenotypes in this expanding field include short stature, microcephaly, intellectual disability, variable facial features and organ involvement, resulting in overlapping presentations, including established syndromes and newly described conditions. Individuals with all forms of CdLS have multifaceted complications, including neurodevelopmental, feeding, craniofacial, and communication. Read More

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http://dx.doi.org/10.1002/ajmg.a.61108DOI Listing

Discovery of early life stress interacting and sex-specific quantitative trait loci impacting cocaine responsiveness.

Br J Pharmacol 2019 Mar 15. Epub 2019 Mar 15.

Department of Psychological & Brain Sciences, University of California Santa Barbara, Santa Barbara, CA, 93106.

Background And Purpose: Addiction vulnerability involves complex gene X environment interactions leading to a pathological response to drugs. Identification of the genes mediating these interactions is an important step in understanding the underlying neurobiology and rarely have such analyses examined sex-specific influences. To dissect this interaction, we examined the impact of prenatal stress (PNS) on cocaine responsiveness in male and female mice of the BXD recombinant inbred panel. Read More

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http://dx.doi.org/10.1111/bph.14661DOI Listing

Role of a novel race-related tumor suppressor microRNA located in frequently deleted chromosomal locus 8p21 in prostate cancer progression.

Carcinogenesis 2019 Mar 15. Epub 2019 Mar 15.

Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, CA.

The prostate cancer (PCa) genome is characterized by deletions of chromosome 8p21-22 region that increase significantly with tumor grade and are associated with poor prognosis. We proposed and validated a novel, paradigm shifting hypothesis that this region is associated with a set of microRNA genes - miRs-3622, -3622b, -383- that are lost in PCa and play important mechanistic roles in PCa progression and metastasis. Extending our hypothesis, in this study, we evaluated the role of a microRNA gene located in chr8p- miR-4288- by employing clinical samples and cell lines. Read More

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http://dx.doi.org/10.1093/carcin/bgz058DOI Listing

The biological function of long noncoding RNA FAL1 in oesophageal carcinoma cells.

Artif Cells Nanomed Biotechnol 2019 Dec;47(1):896-903

a Department of Oncology , Heze municipal hospital , Heze , Shandong , China.

Long non-coding RNAs (lncRNAs) have been reported to be involved in the pathogenesis of a variety of malignancies, including oesophageal cancer. Alterations of the lncRNA focally amplified lncRNA on chromosome 1 (FAL1) are present in epithelial tumours. However, its expression pattern and function in oesophageal cancer are poorly addressed. Read More

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https://www.tandfonline.com/doi/full/10.1080/21691401.2019.1
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http://dx.doi.org/10.1080/21691401.2019.1573738DOI Listing
December 2019
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Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer.

Genes Chromosomes Cancer 2019 Mar 15. Epub 2019 Mar 15.

Larner College of Medicine, University of Vermont, Burlington, Vermont.

Cells establish and sustain structural and functional integrity of the genome to support cellular identity and prevent malignant transformation. In this review, we present a strategic overview of epigenetic regulatory mechanisms including histone modifications and higher order chromatin organization (HCO) that are perturbed in breast cancer onset and progression. Implications for dysfunctions that occur in hormone regulation, cell cycle control, and mitotic bookmarking in breast cancer are considered, with an emphasis on epithelial-to-mesenchymal transition and cancer stem cell activities. Read More

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http://dx.doi.org/10.1002/gcc.22731DOI Listing

Stringent response leads to continued cell division and a temporal re-start of DNA replication after initial shutdown in Vibrio cholerae.

Mol Microbiol 2019 Mar 15. Epub 2019 Mar 15.

LOEWE Center for Synthetic Microbiology - SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany.

Vibrio cholerae is an aquatic bacterium with the potential to infect humans and cause the cholera disease. While most bacteria have single chromosomes, the V. cholerae genome is encoded on two replicons of different size. Read More

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http://dx.doi.org/10.1111/mmi.14241DOI Listing

Phenotypic spectrum of NRXN1 mono- and bi-allelic deficiency: a systematic review.

Clin Genet 2019 Mar 14. Epub 2019 Mar 14.

Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy.

Neurexins are presynaptic cell adhesion molecules critically involved in synaptogenesis and vesicular neurotransmitter release. They are encoded by three genes (NRXN1-3), each yielding a longer alpha (α) and a shorter beta (β) transcript. Deletions spanning the promoter and the initial exons of the NRXN1 gene, located in chromosome 2p16. Read More

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http://dx.doi.org/10.1111/cge.13537DOI Listing

The roles of homologous recombination and the immune system in the genomic evolution of cancer.

J Transl Sci 2019 Apr 1;5(2). Epub 2018 Oct 1.

Harvard (Dana Farber) Cancer Institute, Boston, MA, USA.

A variety of factors, whether extracellular (mutagens/carcinogens and viruses in the environment, chronic inflammation and radiation associated with the environment and/or electronic devices/machines) and/or intracellular (oxidative metabolites of food, oxidative stress due to inflammation, acid production, replication stress, DNA replication/repair errors, and certain hormones, cytokines, growth factors), pose a constant threat to the genomic integrity of a living cell. However, in the normal cellular environment multiple biological pathways including DNA repair, cell cycle, apoptosis and the immune system work in a precise, regulated (tightly controlled), timely and concerted manner to ensure genomic integrity, stability and proper functioning of a cell. If damage to DNA takes place, it is efficiently and accurately repaired by the DNA repair systems. Read More

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http://dx.doi.org/10.15761/JTS.1000282DOI Listing

Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon ( L.).

Front Genet 2019 27;10:68. Epub 2019 Feb 27.

Department of Genetics, SalmoBreed AS, Bergen, Norway.

Amoebic gill disease (AGD) is one of the most important parasitic diseases of farmed Atlantic salmon. It is a source of major economic loss to the industry and poses significant threats to animal welfare. Previous studies have shown that resistance against this disease has a moderate, heritable genetic component, although the genes and the genetic pathways that contribute to this process have yet to be elucidated. Read More

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http://dx.doi.org/10.3389/fgene.2019.00068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400892PMC
February 2019

Identification and Functional Characterization of Promoter Binding Protein-Like Gene in Wheat ( L.).

Front Plant Sci 2019 22;10:212. Epub 2019 Feb 22.

College of Life Sciences, Northwest A&F University, Yangling, China.

Wheat ( L.) is one of the most important crops in the world. promoter binding protein-like (SPL) proteins are plant-specific transcript factors and play critical roles in plant growth and development. Read More

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http://dx.doi.org/10.3389/fpls.2019.00212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6401658PMC
February 2019

Does Leave an Epigenetic Imprint on the Brain?

Front Neurosci 2019 27;13:173. Epub 2019 Feb 27.

Neuroscience Institute, Georgia State University, Atlanta, GA, United States.

The words "sex" and "gender" are often used interchangeably in common usage. In fact, the Merriam-Webster dictionary offers "sex" as the definition of gender. The authors of this review are neuroscientists, and the words "sex" and "gender" mean very different things to us: sex is based on biological factors such as sex chromosomes and gonads, whereas gender has a social component and involves differential expectations or treatment by conspecifics, based on an individual's perceived sex. Read More

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http://dx.doi.org/10.3389/fnins.2019.00173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400866PMC
February 2019

Multi-allelic QTL analysis of protein content in a bi-parental population of cultivated tetraploid potato.

Euphytica 2019 8;215(2):14. Epub 2019 Jan 8.

1Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.

Protein content is a key quality trait for the potato starch industry. The objective of this study was to identify allele-specific quantitative trait loci (QTLs) for tuber protein content in cultivated potato ( L.) at the tetraploid level. Read More

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http://dx.doi.org/10.1007/s10681-018-2331-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390886PMC
January 2019

Low C6orf141 Expression is Significantly Associated with a Poor Prognosis in Patients with Oral Cancer.

Sci Rep 2019 Mar 14;9(1):4520. Epub 2019 Mar 14.

Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.

C6orf141 (Chromosome 6 open reading frame 141) is a novel gene, and its role in oral cancer progression remains unclear. C6orf141 expression in oral squamous cell carcinoma (OSCC) and adjacent normal tissues from 428 patients was examined through immunohistochemistry (IHC). Our results revealed that C6orf141 expression was significantly reduced in OSCC compared with adjacent normal tissues. Read More

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http://dx.doi.org/10.1038/s41598-019-41194-1DOI Listing

Assessing the role of Rv1222 (RseA) as an anti-sigma factor of the Mycobacterium tuberculosis extracytoplasmic sigma factor SigE.

Sci Rep 2019 Mar 14;9(1):4513. Epub 2019 Mar 14.

Department of Biology, University of Padova, Padova, Italy.

σ is one of the 13 sigma factors encoded by the Mycobacterium tuberculosis chromosome, and its involvement in stress response and virulence has been extensively characterized. Several sigma factors are post-translationally regulated by proteins named anti-sigma factors, which prevent their binding to RNA polymerase. Rv1222 (RseA), whose gene lays immediately downstream sigE, has been proposed in the past as the σ-specific anti sigma factor. Read More

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http://dx.doi.org/10.1038/s41598-019-41183-4DOI Listing

Rapid and reversible suppression of ALT by DAXX in osteosarcoma cells.

Sci Rep 2019 Mar 14;9(1):4544. Epub 2019 Mar 14.

Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.

Many tumors maintain chromosome-ends through a telomerase-independent, DNA-templated mechanism called alternative lengthening of telomeres (ALT). While ALT occurs in only a subset of tumors, it is strongly associated with mutations in the genes ATRX and DAXX, which encode components of an H3.3 histone chaperone complex. Read More

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http://dx.doi.org/10.1038/s41598-019-41058-8DOI Listing
March 2019
5.078 Impact Factor

Biallelic loss-of-function LACC1/FAMIN Mutations Presenting as Rheumatoid Factor-Negative Polyarticular Juvenile Idiopathic Arthritis.

Sci Rep 2019 Mar 14;9(1):4579. Epub 2019 Mar 14.

Department of Immunology, Hospital Clínic-IDIBAPS, Barcelona, Spain.

Juvenile idiopathic arthritis (JIA) is a complex rheumatic disease with both autoimmune and autoinflammatory components. Recently, familial cases of systemic-onset JIA have been attributed to mutations in LACC1/FAMIN. We describe three affected siblings from a Moroccan consanguineous family with an early-onset chronic, symmetric and erosive arthritis previously diagnosed as rheumatoid factor (RF)-negative polyarticular JIA. Read More

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http://dx.doi.org/10.1038/s41598-019-40874-2DOI Listing

Convergent Evolution of Copy Number Alterations in Multi-Centric Hepatocellular Carcinoma.

Sci Rep 2019 Mar 14;9(1):4611. Epub 2019 Mar 14.

Institute of Pathology, University Hospital Basel and University of Basel, Schoenbeinstrasse 40, 4056, Basel, Switzerland.

In the recent years, new molecular methods have been proposed to discriminate multicentric hepatocellular carcinomas (HCC) from intrahepatic metastases. Some of these methods utilize sequencing data to assess similarities between cancer genomes, whilst other achieved the same results with transcriptome and methylome data. Here, we attempt to classify two HCC patients with multi-centric disease using the recall-rates of somatic mutations but find that difficult because their tumors share some chromosome-scale copy-number alterations (CNAs) but little-to-no single-nucleotide variants. Read More

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http://dx.doi.org/10.1038/s41598-019-40843-9DOI Listing

Identification of QTL underlying the leaf length and area of different leaves in barley.

Sci Rep 2019 Mar 14;9(1):4431. Epub 2019 Mar 14.

College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.

Leaf is the main organ of photosynthesis, which significantly impacts crop yield. A high-density linkage map containing 1894 single nucleotide polymorphism (SNP) and 68 simple sequence repeats (SSR) markers was used to identify quantitative trait locus (QTL) for flag leaf length (FLL), second leaf length (SLL), third leaf length (TLL), fourth leaf length (FOLL), flag leaf area (FLA), second leaf area (SLA), third leaf area (TLA) and fourth leaf area (FOLA). In total, 57 QTLs underlying the top four leaf length and area traits were identified and mapped on chromosome 2H, 3H, 4H and 7H. Read More

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http://dx.doi.org/10.1038/s41598-019-40703-6DOI Listing

Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins.

Sci Rep 2019 Mar 14;9(1):4577. Epub 2019 Mar 14.

Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå, Sweden.

In specific cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have limited understanding of many loops identified by Chromosome Conformation Capture (such as Hi-C) analyses. In efforts to elucidate their characteristics and functions, we have identified highly interacting regions (HIRs) using intra-chromosomal Hi-C datasets with a new computational method based on looking at the eigenvector that corresponds to the smallest eigenvalue (here unity). Analysis of these regions using ENCODE data shows that they are in general enriched in bound factors involved in DNA damage repair and have actively transcribed genes. Read More

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http://dx.doi.org/10.1038/s41598-019-40770-9DOI Listing

Chromosome and plasmid-borne P promoters differ in sensitivity to critically low temperatures.

Sci Rep 2019 Mar 14;9(1):4486. Epub 2019 Mar 14.

Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland.

Temperature shifts trigger genome-wide changes in Escherichia coli's gene expression. We studied if chromosome integration impacts on a gene's sensitivity to these shifts, by comparing the single-RNA production kinetics of a P promoter, when chromosomally-integrated and when single-copy plasmid-borne. At suboptimal temperatures their induction range, fold change, and response to decreasing temperatures are similar. Read More

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http://dx.doi.org/10.1038/s41598-019-39618-zDOI Listing

A reference-grade wild soybean genome.

Nat Commun 2019 Mar 14;10(1):1216. Epub 2019 Mar 14.

Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3. Read More

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http://dx.doi.org/10.1038/s41467-019-09142-9DOI Listing
March 2019
10.742 Impact Factor

The genomic history of the Iberian Peninsula over the past 8000 years.

Authors:
Iñigo Olalde Swapan Mallick Nick Patterson Nadin Rohland Vanessa Villalba-Mouco Marina Silva Katharina Dulias Ceiridwen J Edwards Francesca Gandini Maria Pala Pedro Soares Manuel Ferrando-Bernal Nicole Adamski Nasreen Broomandkhoshbacht Olivia Cheronet Brendan J Culleton Daniel Fernandes Ann Marie Lawson Matthew Mah Jonas Oppenheimer Kristin Stewardson Zhao Zhang Juan Manuel Jiménez Arenas Isidro Jorge Toro Moyano Domingo C Salazar-García Pere Castanyer Marta Santos Joaquim Tremoleda Marina Lozano Pablo García Borja Javier Fernández-Eraso José Antonio Mujika-Alustiza Cecilio Barroso Francisco J Bermúdez Enrique Viguera Mínguez Josep Burch Neus Coromina David Vivó Artur Cebrià Josep Maria Fullola Oreto García-Puchol Juan Ignacio Morales F Xavier Oms Tona Majó Josep Maria Vergès Antònia Díaz-Carvajal Imma Ollich-Castanyer F Javier López-Cachero Ana Maria Silva Carmen Alonso-Fernández Germán Delibes de Castro Javier Jiménez Echevarría Adolfo Moreno-Márquez Guillermo Pascual Berlanga Pablo Ramos-García José Ramos-Muñoz Eduardo Vijande Vila Gustau Aguilella Arzo Ángel Esparza Arroyo Katina T Lillios Jennifer Mack Javier Velasco-Vázquez Anna Waterman Luis Benítez de Lugo Enrich María Benito Sánchez Bibiana Agustí Ferran Codina Gabriel de Prado Almudena Estalrrich Álvaro Fernández Flores Clive Finlayson Geraldine Finlayson Stewart Finlayson Francisco Giles-Guzmán Antonio Rosas Virginia Barciela González Gabriel García Atiénzar Mauro S Hernández Pérez Armando Llanos Yolanda Carrión Marco Isabel Collado Beneyto David López-Serrano Mario Sanz Tormo António C Valera Concepción Blasco Corina Liesau Patricia Ríos Joan Daura María Jesús de Pedro Michó Agustín A Diez-Castillo Raúl Flores Fernández Joan Francès Farré Rafael Garrido-Pena Victor S Gonçalves Elisa Guerra-Doce Ana Mercedes Herrero-Corral Joaquim Juan-Cabanilles Daniel López-Reyes Sarah B McClure Marta Merino Pérez Arturo Oliver Foix Montserrat Sanz Borràs Ana Catarina Sousa Julio Manuel Vidal Encinas Douglas J Kennett Martin B Richards Kurt Werner Alt Wolfgang Haak Ron Pinhasi Carles Lalueza-Fox David Reich

Science 2019 03;363(6432):1230-1234

Department of Genetics, Harvard Medical School, Boston, MA, USA.

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia's ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. Read More

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http://dx.doi.org/10.1126/science.aav4040DOI Listing

Generation of Highly Biomimetic Quality Control Materials for Noninvasive Prenatal Testing Based on Enzymatic Digestion of Matched Mother-Child Cell Lines.

Clin Chem 2019 Mar 14. Epub 2019 Mar 14.

National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China;

Background: Noninvasive prenatal testing (NIPT) based on cell-free DNA (cfDNA) is widely used. However, biomimetic quality control materials that have properties identical to clinical samples and that are applicable to a wide range of methodologies are still not available to support assay development, internal quality control, and proficiency testing.

Methods: We developed a set of dual enzyme-digested NIPT quality control materials (DENQCMs) that comprise simulated human plasma and mixtures of mother cell line-derived cfDNA based on DNA fragmentation factor digestion (D-cfDNA) and the matched child cell line-derived cfDNA based on micrococcal nuclease digestion (M-cfDNA). Read More

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http://dx.doi.org/10.1373/clinchem.2018.299602DOI Listing