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Neonatal genomics

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https://www.readbyqxmd.com/read/29674529/draft-genome-sequences-of-five-neonatal-meningitis-causing-escherichia-coli-isolates-sp-4-sp-5-sp-13-sp-46-and-sp-65
#1
Aixia Xu, James R Johnson, Shiowshuh Sheen, Christopher Sommers
Neonatal meningitis-causing Escherichia coli isolates (SP-4, SP-5, SP-13, SP-46, and SP-65) were recovered between 1989 and 1997 from infants in the Netherlands. Here, we report the draft genome sequences of these five E. coli isolates, which are currently being used to validate food safety processing technologies.
April 19, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29666266/dna-methylation-and-transcriptome-aberrations-mediated-by-er%C3%AE-in-mouse-seminal-vesicles-following-developmental-des-exposure
#2
Yin Li, Katherine J Hamilton, Tianyuan Wang, Laurel A Coons, Wendy N Jefferson, Ruifang Li, Yu Wang, Sara A Grimm, J Tyler Ramsey, Liwen Liu, Kevin E Gerrish, Carmen J Williams, Paul A Wade, Kenneth S Korach
Early transient developmental exposure to an endocrine active compound, diethylstilbestrol (DES), a synthetic estrogen, causes late-stage effects in the reproductive tract of adult mice. Estrogen receptor alpha (ERα) plays a role in mediating these developmental effects. However, the developmental mechanism is not well known in male tissues. Here, we present genome-wide transcriptome and DNA methylation profiling of the seminal vesicles (SVs) during normal development and after DES exposure. ERα mediates aberrations of the mRNA transcriptome in SVs of adult mice following neonatal DES exposure...
April 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29660755/-beckwith-wiedemann-syndrome-bws-current-status-of-diagnosis-and-clinical-management-summary-of-the-first-international-consensus-statement
#3
Miriam Elbracht, Dirk Prawitt, Rebekka Nemetschek, Christian Kratz, Thomas Eggermann
Beckwith-Wiedemann syndrome (BWS) belongs to the group of imprinting disorders and is characterized by variable clinical features, including overgrowth, macroglossia, abdominal wall defect, neonatal hypoglycemia, body asymmetry and an increased risk for embryonal tumors. In the majority of cases, molecular alterations of the Imprinting Center (IC) regions in the chromosomal region 11p15.5 can be detected, and a correlation of single clinical features with specific genomic and epigenetic changes is obvious. Therefore, the detailed molecular diagnosis is a prerequisite for a precise prediction of the tumor risk and the tumor spectrum...
April 16, 2018: Klinische Pädiatrie
https://www.readbyqxmd.com/read/29649453/potential-role-of-omics-technique-in-prenatal-diagnosis-of-congenital-heart-defects
#4
REVIEW
Lizhu Chen, Johnny Guan, Qiuju Wei, Zhengwei Yuan, Mo Zhang
Congenital heart defect (CHD) is one of the most common birth defects and is the leading cause of neonatal death. Currently, there are no biomarkers available for prenatal diagnosis of CHD. Clinical strategies to diagnose CHD mostly depend on fetal echocardiography. Recent advances in "omics" techniques have opened up new possibilities for biomarker discoveries. In this review, we discuss recent advances in prenatal detection of CHD using biomarkers obtained by "omics" approaches, including genomics, proteomics, metabolomics, and others...
April 10, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29642382/a-low-glycaemic-index-diet-in-pregnancy-induces-dna-methylation-variation-in-blood-of-newborns-results-from-the-rolo-randomised-controlled-trial
#5
Aisling A Geraghty, Alexandra Sexton-Oates, Eileen C O'Brien, Goiuri Alberdi, Peter Fransquet, Richard Saffery, Fionnuala M McAuliffe
The epigenetic profile of the developing fetus is sensitive to environmental influence. Maternal diet has been shown to influence DNA methylation patterns in offspring, but research in humans is limited. We investigated the impact of a low glycaemic index dietary intervention during pregnancy on offspring DNA methylation patterns using a genome-wide methylation approach. Sixty neonates were selected from the ROLO (Randomised cOntrol trial of LOw glycaemic index diet to prevent macrosomia) study: 30 neonates from the low glycaemic index intervention arm and 30 from the control, whose mothers received no specific dietary advice...
April 6, 2018: Nutrients
https://www.readbyqxmd.com/read/29626210/the-life-cycle-of-non-polio-enteroviruses-and-how-to-target-it
#6
REVIEW
Jim Baggen, Hendrik Jan Thibaut, Jeroen R P M Strating, Frank J M van Kuppeveld
The genus Enterovirus (EV) of the family Picornaviridae includes poliovirus, coxsackieviruses, echoviruses, numbered enteroviruses and rhinoviruses. These diverse viruses cause a variety of diseases, including non-specific febrile illness, hand-foot-and-mouth disease, neonatal sepsis-like disease, encephalitis, paralysis and respiratory diseases. In recent years, several non-polio enteroviruses (NPEVs) have emerged as serious public health concerns. These include EV-A71, which has caused epidemics of hand-foot-and-mouth disease in Southeast Asia, and EV-D68, which recently caused a large outbreak of severe lower respiratory tract disease in North America...
April 6, 2018: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29624006/intrinsic-and-extrinsic-molecular-determinants-or-modulators-for-epigenetic-remodeling-and-reprogramming-of-somatic-cell-derived-genome-in-mammalian-nuclear-transferred-oocytes-and-resultant-embryos
#7
M Samiec, M Skrzyszowska
The efficiency of somatic cell cloning in mammals remains disappointingly low. Incomplete and aberrant reprogramming of epigenetic memory of somatic cell nuclei in preimplantation nuclear- transferred (NT) embryos is one of the most important factors that limit the cloning effectiveness. The extent of epigenetic genome-wide alterations, involving histone or DNA methylation and histone deacetylation, that are mediated by histone-lysine methyltransferases (HMTs) or DNA methyltransferases (DNMTs) and histone deacetylases (HDACs) can be modulated/reversed via exogenous inhibitors of these enzymes throughout in vitro culture of nuclear donor cells, nuclear recipient oocytes and/or cloned embryos...
March 2018: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/29614566/-spectrum-of-mutations-in-benign-familial-neonatal-infantile-epilepsy
#8
Q Zeng, Y H Zhang, X L Yang, L H Pu, J Zhang, A J Liu, Z X Yang, X Y Liu, X R Wu
Objective: To investigate the spectrum of mutations in families with benign familial neonatal-infantile epilepsy (BFNIE) . Methods: Clinical data and peripheral blood DNA samples of all BFNIE probands and their family members were collected from Peking University First Hospital between December 2012 and April 2016. Clinical phenotypes of affected members were analyzed. Genomic DNA was extracted from peripheral blood samples with standard protoco1. Mutations in PRRT2 were screened using Sanger sequencing. For families that PRRT2 mutations were not detected by Sanger sequencing, candidate gene mutations were further screened by next-generation sequencing for epilepsy...
April 2, 2018: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29611334/conditional-ablation-of-the-prorenin-receptor-in-nephron-progenitor-cells-results-in-developmental-programming-of-hypertension
#9
Renfang Song, Laura Kidd, Adam Janssen, Ihor V Yosypiv
Nephron induction during kidney development is driven by reciprocal interactions between progenitor cells (NPCs) of the cap mesenchyme (CM) and the ureteric bud (UB). The prorenin receptor (PRR) is a receptor for renin and prorenin, and an accessory subunit of the vacuolar proton pump V-ATPase. Previously, we demonstrated that conditional ablation of the PRR in Six2+ NPCs in mice (Six2PRR -/- ) causes early neonatal death. Here, we identified genes that are regulated by PRR in Six2+ NPCs FACS-isolated from Six2PRR -/- and control kidneys on embryonic day E15...
April 2018: Physiological Reports
https://www.readbyqxmd.com/read/29610688/prenatal-identification-and-molecular-characterization-of-two-simultaneous-de-novo-interstitial-duplications-of-chromosomal-regions-7p22-1p21-1-and-15q24-1
#10
Sabrina C Burn, Kali Swift, Maria Palmquist
The occurrence of simultaneous de novo chromosomal aberrations is extremely rare. Here, we describe two, previously unreported, simultaneous de novo interstitial duplications of chromosomes 7p and 15q. Amniocentesis was completed for a healthy gravida 4 para 3 woman due to her advanced maternal age and concurrent ultrasound findings of partial vermian agenesis, choroid-plexus cysts, and hypoplastic nasal bone. Cytogenetic analysis of cultured amniocytes by conventional chromosome analysis, comparative genomic hybridization, and fluorescence in situ hybridization revealed two interstitial duplications of the chromosomal regions 7p22...
2018: Case Reports in Genetics
https://www.readbyqxmd.com/read/29601581/widespread-domain-like-perturbations-of-dna-methylation-in-whole-blood-of-down-syndrome-neonates
#11
Peter Henneman, Arjan Bouman, Adri Mul, Lia Knegt, Anne-Marie van der Kevie-Kersemaekers, Nitash Zwaveling-Soonawala, Hanne E J Meijers-Heijboer, A S Paul van Trotsenburg, Marcel M Mannens
INTRODUCTION: Down syndrome (DS) is the most frequent genetic cause of intellectual disability. Despite the fact that more than 50 years have passed since the discovery of its genetic aberrations, the exact pathogenesis of the DS phenotype has remained largely unexplained. It was recently hypothesized that the DS pathogenesis involves complex (epi)genetic, molecular and cellular determinants. To date, many reports have addressed epigenetic aberrations associated with DS at different developmental stages/ages and tissue types, but to our best knowledge not in DS newborns...
2018: PloS One
https://www.readbyqxmd.com/read/29599516/enterobacter-bugandensis-a-novel-enterobacterial-species-associated-with-severe-clinical-infection
#12
Niladri Bhusan Pati, Swapnil Prakash Doijad, Tilman Schultze, Gopala Krishna Mannala, Yancheng Yao, Sangeeta Jaiswal, Daniel Ryan, Mrutyunjay Suar, Konrad Gwozdzinski, Boyke Bunk, Mobarak Abu Mraheil, Mohamed A Marahiel, Julian D Hegemann, Cathrin Spröer, Alexander Goesmann, Linda Falgenhauer, Torsten Hain, Can Imirzalioglu, Stephen E Mshana, Jörg Overmann, Trinad Chakraborty
Nosocomial pathogens can cause life-threatening infections in neonates and immunocompromised patients. E. bugandensis (EB-247) is a recently described species of Enterobacter, associated with neonatal sepsis. Here we demonstrate that the extended spectrum ß-lactam (ESBL) producing isolate EB-247 is highly virulent in both Galleria mellonella and mouse models of infection. Infection studies in a streptomycin-treated mouse model showed that EB-247 is as efficient as Salmonella Typhimurium in inducing systemic infection and release of proinflammatory cytokines...
March 29, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29599079/efficient-in-vivo-liver-directed-gene-editing-using-crispr-cas9
#13
Kshitiz Singh, Hanneke Evens, Nisha Nair, Melvin Y Rincón, Shilpita Sarcar, Ermira Samara-Kuko, Marinee K Chuah, Thierry VandenDriessche
In vivo tissue-specific genome editing at the desired loci is still a challenge. Here, we report that AAV9-delivery of truncated guide RNAs (gRNAs) and Cas9 under the control of a computationally designed hepatocyte-specific promoter lead to liver-specific and sequence-specific targeting in the mouse factor IX (F9) gene. The efficiency of in vivo targeting was assessed by T7E1 assays, site-specific Sanger sequencing, and deep sequencing of on-target and putative off-target sites. Though AAV9 transduction was apparent in multiple tissues and organs, Cas9 expression was restricted mainly to the liver, with only minimal or no expression in other non-hepatic tissues...
March 6, 2018: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/29597895/in-vivo-genome-editing-partially-restores-alpha1-antitrypsin-in-a-murine-model-of-aat-deficiency
#14
Chun-Qing Song, Dan Wang, Tingting Jiang, Kevin O'Connor, Qiushi Tang, Lingling Cai, Xiangrui Li, Zhiping Weng, Hao Yin, Guangping Gao, Christian Mueller, Terence R Flotte, Wen Xue
CRISPR genome editing holds promise in the treatment of genetic diseases that currently lack effective long-term therapies. Patients with Alpha-1 Antitrypsin (AAT) deficiency develop progressive lung disease due to the loss of AAT's antiprotease function and liver disease due to a toxic gain of function of the common mutant allele. However, it remains unknown whether CRISPR-mediated AAT correction in the liver, where AAT is primarily expressed, can correct either or both defects. Here we show that AAV delivery of CRISPR can effectively correct Z-AAT mutation in the liver of a transgenic mouse model...
March 29, 2018: Human Gene Therapy
https://www.readbyqxmd.com/read/29593030/stem-cell-properties-of-normal-human-keratinocytes-determine-transformation-responses-to-hpv16-dna
#15
Yvon Woappi, Maria Hosseinipour, Kim E Creek, Lucia Pirisi
Human papillomavirus (HPV) infection of the genital tract is common, however only about 10-15% of infections persist, and approximately 10-15% of these persistent infections result in cancer. Basal epidermal stem cells are the presumed target cells for HPV infection, providing a reservoir of latently infected cells that persist over time and initiate lesions. Yet, it is not known whether stem cell density has any influence on transformation of human keratinocytes by HPV. We explored the relationship between stem cell properties of normal human keratinocytes and their susceptibility to transformation by HPV16 DNA...
March 28, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29588851/vancomycin-resistant-enterococcus-faecium-sequence-type-796-rapid-international-dissemination-of-a-new-epidemic-clone
#16
Andrew A Mahony, Andrew H Buultjens, Susan A Ballard, Elizabeth A Grabsch, Shirley Xie, Torsten Seemann, Rhonda L Stuart, Despina Kotsanas, Allen Cheng, Helen Heffernan, Sally A Roberts, Geoffrey W Coombs, Narin Bak, John K Ferguson, Glen C Carter, Benjamin P Howden, Timothy P Stinear, Paul D R Johnson
Background: Vancomycin-resistant Enterococcus faecium (VRE) is a leading cause of hospital-acquired infections. New, presumably better-adapted strains of VRE appear unpredictably; it is uncertain how they spread despite improved infection control. We aimed to investigate the relatedness of a novel sequence type (ST) of vanB E. faecium - ST796 - very near its time of origin from hospitals in three Australian states and New Zealand. Methods: Following near-simultaneous outbreaks of ST796 in multiple institutions, we gathered then tested colonization and bloodstream infection isolates' antimicrobial resistance (AMR) phenotypes, and phylogenomic relationships using whole genome sequencing (WGS)...
2018: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/29577422/notch4-is-a-possible-novel-susceptibility-gene-for-dilated-cardiomyopathy-in-the-chinese-population-a-case-control-study
#17
Xiaoqing Shi, Yang Zhang, Bingjie Li, Mengle Peng, Yingying Yuan, Ximing Wang, Xinqiang Li, Dongze Yu, Yongzhe Li, Dongchun Qin
BACKGROUND: The incidence of dilated cardiomyopathy (DCM) has increased in recent years, and many studies have sought to further improve the general understanding of this condition. Previous studies have demonstrated that some single nucleotide polymorphisms (SNPs) associated with systemic lupus erythematosus also affect susceptibility to DCM, suggesting that immune-related diseases may share similar genetic susceptibility. Recent large-scale and genome-wide association studies have identified NCR3, NOTCH4, CYP1A2, ITGA1, OPRM1, ST8SIA2, and LINC00704 as genetic risk factors associated with cardiac manifestations of neonatal lupus...
March 26, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29563294/divergent-pathogenic-properties-of-circulating-coxsackievirus-a6-associated-with-emerging-hfmd
#18
Shao-Hua Wang, Ao Wang, Pan-Pan Liu, Wen-Yan Zhang, Juan Du, Shuang Xu, Guan-Chen Liu, Bai-Song Zheng, Chen Huan, Ke Zhao, Xiao-Fang Yu
Coxsackievirus A6 (CV-A6) is an emerging pathogen associated with hand, foot, and mouth disease (HFMD). Its genetic characterization and pathogenic properties are largely unknown. Here, we report 39 circulating CV-A6 strains isolated in 2013 from HFMD patients in Northeast China. Three major clusters of CV-A6 were identified and related to CV-A6 mostly from Shanghai, indicating that domestic CV-A6 strains were responsible for HFMD emerging in Northeast China. Four full-length CV-A6 genomes representing each cluster were sequenced and analyzed further...
March 21, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29557107/array-comparative-genomic-hybridization-as-the-first-line-investigation-for-neonates-with-congenital-heart-disease-experience-in-a-single-tertiary-center
#19
Bo Geum Choi, Su Kyung Hwang, Jung Eun Kwon, Yeo Hyang Kim
BACKGROUND AND OBJECTIVES: The purpose of the present study was to investigate the advantages and disadvantages of verifying genetic abnormalities using array comparative genomic hybridization (a-CGH) immediately after diagnosis of congenital heart disease (CHD). METHODS: Among neonates under the age of 28 days who underwent echocardiography from January 1, 2014 to April 30, 2016, neonates whose chromosomal and genomic abnormalities were tested using a-CGH in cases of an abnormal finding on echocardiography were enrolled...
March 2018: Korean Circulation Journal
https://www.readbyqxmd.com/read/29555974/successful-knock-in-of-hypertrophic-cardiomyopathy-mutation-r723g-into-the-myh7-gene-mimics-hcm-pathology-in-pigs
#20
J Montag, B Petersen, A K Flögel, E Becker, A Lucas-Hahn, G J Cost, C Mühlfeld, T Kraft, H Niemann, B Brenner
Familial Hypertrophic Cardiomyopathy (HCM) is the most common inherited cardiac disease. About 30% of the patients are heterozygous for mutations in the MYH7 gene encoding the ß-myosin heavy chain (MyHC). Hallmarks of HCM are cardiomyocyte disarray and hypertrophy of the left ventricle, the symptoms range from slight arrhythmias to sudden cardiac death or heart failure. To gain insight into the underlying mechanisms of the diseases' etiology we aimed to generate genome edited pigs with an HCM-mutation. We used TALEN-mediated genome editing and successfully introduced the HCM-point mutation R723G into the MYH7 gene of porcine fibroblasts and subsequently cloned pigs that were heterozygous for the HCM-mutation R723G...
March 19, 2018: Scientific Reports
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