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Neonatal genomics

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https://www.readbyqxmd.com/read/28733429/proteogenomic-analysis-and-discovery-of-immune-antigens-in-mycobacterium-vaccae
#1
Jianhua Zheng, Lihong Chen, Liguo Liu, Haifeng Li, Bo Liu, Dandan Zheng, Tao Liu, Jie Dong, Lilian Sun, Yafang Zhu, Jian Yang, Xiaobing Zhang, Qi Jin
Tuberculosis (TB) is one of the leading causes of death worldwide, especially in developing countries. Neonatal BCG vaccination occurs in various regions, but the level of protection varies in different populations. Recently, Mycobacterium vaccae is found to be an immunomodulating therapeutic agent that could confer a significant level of protection against TB. It is the only vaccine in a phase III trial from WHO to assess its efficacy and safety in preventing TB disease in people with latent TB infection. However, the mechanism of immunotherapy of M...
July 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28729278/high-quality-genome-sequence-of-the-highly-resistant-bacterium-staphylococcus-haemolyticus-isolated-from-a-neonatal-bloodstream-infection
#2
Farideh Hosseinkhani, Mohammad Emaneini, Willem van Leeuwen
Using Illumina HiSeq and PacBio technologies, we sequenced the genome of the multidrug-resistant bacterium Staphylococcus haemolyticus, originating from a bloodstream infection in a neonate. The sequence data can be used as an accurate reference sequence.
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28728135/prostate-cancer-risk-and-dna-methylation-signatures-in-aging-rats-following-developmental-bpa-exposure-a-dose-response-analysis
#3
Gail S Prins, Shu-Hua Ye, Lynn Birch, Xiang Zhang, Ana Cheong, Han Lin, Esther Calderon-Gierszal, Jacob Groen, Wen-Yang Hu, Shuk-Mei Ho, Richard B van Breemen
BACKGROUND: Previous studies have uncovered heightened prostatic susceptibility to hormone-induced neoplasia from early-life exposure to low-dose bisphenol A (BPA). However, significant data gaps remain that are essential to address for biological relevance and necessary risk assessment. OBJECTIVES: A complete BPA dose-response analysis of prostate lesions across multiple prostatic lobes was conducted that included internal BPA dosimetry, progression to adenocarcinoma with aging and mechanistic connections to epigenetically reprogramed genes...
July 11, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28727969/fetal-dysmorphology-still-an-essential-art-analysis-of-the-limitations-of-microarray-in-a-fetal-population-and-a-look-toward-the-genome-sequencing-era
#4
E Fletcher, M Porteous, K J McKenzie, E J Maher, M J Evans
Cytogenomic microarray allows assessment of the genome at higher resolutions than traditional karyotyping. The objective of this study is to evaluate the utility of microarray in a routine fetal autopsy setting before the advent of routine fetal exome/genome sequencing and the issues these technologies may generate. A systematic review of fetal postmortems at 12-24 weeks gestation between January 2011 and December 2014 was undertaken. Cases where there was no consent for audit, research, or genetic testing were excluded as were cases referred to the Procurator Fiscal, stillbirths, and neonatal deaths...
July 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28726280/an-efficient-study-design-to-test-parent-of-origin-effects-in-family-trios
#5
Xiaobo Yu, Gao Chen, Rui Feng
Increasing evidence has shown that genes may cause prenatal, neonatal, and pediatric diseases depending on their parental origins. Statistical models that incorporate parent-of-origin effects (POEs) can improve the power of detecting disease-associated genes and help explain the missing heritability of diseases. In many studies, children have been sequenced for genome-wide association testing. But it may become unaffordable to sequence their parents and evaluate POEs. Motivated by the reality, we proposed a budget-friendly study design of sequencing children and only genotyping their parents through single nucleotide polymorphism array...
July 20, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28722566/molecular-epidemiology-of-staphylococcus-aureus-skin-and-soft-tissue-infections-in-the-lao-people-s-democratic-republic
#6
Alicia D Yeap, Kate Woods, David A B Dance, Bruno Pichon, Sayaphet Rattanavong, Viengmon Davong, Rattanaphone Phetsouvanh, Paul N Newton, Nandini Shetty, Angela M Kearns
This is the first report of the molecular epidemiology of Staphylococcus aureus from skin and soft tissue infections (SSTI) in Laos. We selected a random sample of 96 S. aureus SSTI isolates received by the Microbiology Laboratory, Mahosot Hospital, Vientiane, between July 2012 and June 2014, including representation from seven referral hospitals. Isolates underwent susceptibility testing by Clinical and Laboratory Standards Institute methods, spa typing and DNA microarray analysis, with whole genome sequencing for rare lineages...
May 30, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28719906/a-common-ancestral-asn242ser-mutation-in-tmem67-identified-in-multiple-iranian-families-with-joubert-syndrome
#7
MohammadReza Dehghani, Majid Mojarad, Ehsan Ghayoor Karimiani, Mohammad Yahya Vahidi Mehrjardi, Afsaneh Sahebalzamani, Farah Ashrafzadeh, Mehran Beiraghi Toosi, Atiyeh Eslahi, Najmeh Ahangari, Seyed Mojtaba Yassini, Afsaneh Hassanbeigi, Azam Rasti, Seyed Mehdi Kalantar, Reza Maroofian
BACKGROUND: Joubert syndrome (JS) is a clinically and genetically heterogeneous group of rare neurodevelopmental disorder characterised by peculiar midbrain-hindbrain malformation, known as the "molar tooth" sign. JS can manifest a broad range of signs and symptoms. The most common features of JS are hypotonia, ataxia, developmental delay/intellectual disability, abnormal eye movements, and neonatal breathing abnormalities. To date, 29 genes have been shown to cause JS. METHODS: We employed whole-genome single nucleotide polymorphism genotyping in a group of Iranian families with JS and Sanger sequencing of a known mutation associated with JS located in a single homozygous regions shared by affected members of the families...
July 19, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28719641/inversion-of-the-imprinting-control-region-of-the-peg3-domain
#8
Joomyeong Kim, Hongzhi He, Hana Kim
The imprinting of the mouse Peg3 domain is controlled through a 4-kb genomic region encompassing the bidirectional promoter and 1st exons of Peg3 and Usp29. In the current study, this ICR was inverted to test its orientation dependency for the transcriptional and imprinting control of the Peg3 domain. The inversion resulted in the exchange of promoters and 1st exons between Peg3 and Usp29. Paternal transmission of this inversion caused 10-fold down-regulation of Peg3 and 2-fold up-regulation of Usp29 in neonatal heads, consistent with its original promoter strength in each direction...
2017: PloS One
https://www.readbyqxmd.com/read/28712937/returning-ex-patriot-chinese-to-guangdong-china-increase-the-risk-for-local-transmission-of-zika-virus
#9
Jiufeng Sun, De Wu, Haojie Zhong, Dawei Guan, Huan Zhang, Qiqi Tan, Huiqiong Zhou, Meng Zhang, Dan Ning, Baohuan Zhang, Changwen Ke, Tie Song, Jinyan Lin, Yonghui Zhang, Marion Koopmans, George F Gao
OBJECTIVES: Rapid transmission and linkage to microcephaly and Guillain-Barre syndrome have made Zika virus (ZIKV) infection become a serious threat to global public health. The epidemiology, virological characteristics and genetic evolution of introduced ZIKV to Guangdong, China, were investigated. METHODS: Analyses of the epidemiological characteristics and genetic diversity of ZIKV isolates were performed. RESULTS: Nineteen confirmed ZIKV infection cases were imported from Venezuela and Samoa...
July 14, 2017: Journal of Infection
https://www.readbyqxmd.com/read/28711508/virulent-and-pathogenic-features-on-the-cronobacter-sakazakii-polymyxin-resistant-pmr-mutant-strain-s-3
#10
Xuerui Bao, Ling Yang, Lequn Chen, Bing Li, Lin Li, Yanyan Li, Zhenbo Xu
Cronobacter sakazakii is a well-known opportunistic pathogen responsible for necrotizing enterocolitis, meningitis and septicaemia in the premature, immunocompromised infants and neonates. This pathogen possesses various virulence factors and regulatory systems, and pmrA/pmrB regulatory system has been identified in a variety of bacterial species. The current study aims to investigate role of pmrA gene in the pathogenicity and virulence characteristics of Cronobacter sakazakii using whole genome sequencing and RNA-seq...
July 12, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28694793/comparative-genomic-characterization-of-the-highly-persistent-and-potentially-virulent-cronobacter-sakazakii-st83-cc65-strain-h322-and-other-st83-strains
#11
Hannah R Chase, Gopal R Gopinath, Athmanya K Eshwar, Andrea Stoller, Claudia Fricker-Feer, Jayanthi Gangiredla, Isha R Patel, Hediye N Cinar, HyeJin Jeong, ChaeYoon Lee, Flavia Negrete, Samantha Finkelstein, Roger Stephan, Ben D Tall, Angelika Lehner
Cronobacter (C.) sakazakii is an opportunistic pathogen and has been associated with serious infections with high mortality rates predominantly in pre-term, low-birth weight and/or immune compromised neonates and infants. Infections have been epidemiologically linked to consumption of intrinsically and extrinsically contaminated lots of reconstituted powdered infant formula (PIF), thus contamination of such products is a challenging task for the PIF producing industry. We present the draft genome of C. sakazakii H322, a highly persistent sequence type (ST) 83, clonal complex (CC) 65, serotype O:7 strain obtained from a batch of non-released contaminated PIF product...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28689251/genome-wide-analysis-of-dna-methylation-in-hyperoxia-exposed-newborn-rat-lung
#12
Chung-Ming Chen, Yi-Chun Liu, Yue-Jun Chen, Hsiu-Chu Chou
PURPOSE: Oxygen therapy is often required to treat newborn infants with respiratory disorders. Prolonged exposure of neonatal rats to hyperoxia reduced alveolar septation, increased terminal air space size, and increased lung fibrosis; these conditions are very similar to those of human bronchopulmonary dysplasia. Epigenetic regulation of gene expression plays a crucial role in bronchopulmonary dysplasia development. METHOD: We reared Sprague-Dawley rat pups in either room air (RA, n = 24) or an atmosphere containing 85% O2 (n = 26) from Postnatal Days 1 to 14...
July 8, 2017: Lung
https://www.readbyqxmd.com/read/28687920/complete-genome-sequence-and-phylogenetic-analysis-of-senecavirus-a-isolated-in-northeast-china-in-2016
#13
Haiwei Wang, Chen Li, Bo Zhao, Tiangang Yuan, Decheng Yang, Guohui Zhou, Li Yu
Senecavirus A (SVA) is associated with vesicular disease in swine and the acute death of neonatal piglets. Here, senecavirus A was isolated from a pig displaying vesicular disease in Northeast China. The virus was designated as SVA/HLJ/CHA/2016 and its full-length nucleotide sequence was determined and analyzed in comparison with other known SVA strains. The complete genome sequence of SVA/HLJ/CHA/2016 shares high nucleotide identities, of 93.8 to 99%, with previously reported SVA full-length genomes. Phylogenetic analysis of both the SVA full-length genomes and the VP1 genes revealed that the SVA/HLJ/CHA/2016 strain is closely related to the 2015 US strains, instead of other China isolates...
July 7, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28686619/rare-variants-of-small-effect-size-in-neuronal-excitability-genes-influence-clinical-outcome-in-japanese-cases-of-scn1a-truncation-positive-dravet-syndrome
#14
Michael F Hammer, Atsushi Ishii, Laurel Johnstone, Alexander Tchourbanov, Branden Lau, Ryan Sprissler, Brian Hallmark, Miao Zhang, Jin Zhou, Joseph Watkins, Shinichi Hirose
Dravet syndrome (DS) is a rare, devastating form of childhood epilepsy that is often associated with mutations in the voltage-gated sodium channel gene, SCN1A. There is considerable variability in expressivity within families, as well as among individuals carrying the same primary mutation, suggesting that clinical outcome is modulated by variants at other genes. To identify modifier gene variants that contribute to clinical outcome, we sequenced the exomes of 22 individuals at both ends of a phenotype distribution (i...
2017: PloS One
https://www.readbyqxmd.com/read/28667116/a-third-type-of-resistance-of-codling-moth-against-cydia-pomonella-granulovirus-cpgv-shows-a-mixture-of-a-z-linked-and-autosomal-inheritance-pattern
#15
A J Sauer, S Schulze-Bopp, E Fritsch, K Undorf-Spahn, J A Jehle
Different isolates of Cydia pomonella granulovirus (CpGV) are worldwide used to control codling moth larvae (Cydia pomonella; CM) in pome fruit production. Two types of dominantly inherited field resistances of CM to CpGV have been recently identified: Z-chromosomal type I resistance and autosomal type II resistance. In the present study, a CpGV-resistant CM field population (termed SA-GO) from North-East Germany was investigated. SA-GO individuals showed cross-resistance to CpGV isolates of genome group A (CpGV-M) and genome group E (CpGV-S), whereas genome group B (CpGV-E2) was still infective...
June 30, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28659227/the-role-of-genetic-liability-in-the-association-of-urbanicity-at-birth-and-during-upbringing-with-schizophrenia-in-denmark
#16
D Paksarian, B B Trabjerg, K R Merikangas, O Mors, A D Børglum, D M Hougaard, J J McGrath, C B Pedersen, P B Mortensen, E Agerbo
BACKGROUND: Studies have indicated that the association of urbanicity at birth and during upbringing with schizophrenia may be driven by familial factors such as genetic liability. We used a population-based nested case-control study to assess whether polygenic risk score (PRS) for schizophrenia was associated with urbanicity at birth and at age 15, and to assess whether PRS and parental history of mental disorder together explained the association between urbanicity and schizophrenia...
June 29, 2017: Psychological Medicine
https://www.readbyqxmd.com/read/28646206/crispr-cas9-mediated-genome-editing-via-postnatal-administration-of-aav-vector-cures-haemophilia-b-mice
#17
Tsukasa Ohmori, Yasumitsu Nagao, Hiroaki Mizukami, Asuka Sakata, Shin-Ichi Muramatsu, Keiya Ozawa, Shin-Ichi Tominaga, Yutaka Hanazono, Satoshi Nishimura, Osamu Nureki, Yoichi Sakata
Haemophilia B, a congenital haemorrhagic disease caused by mutations in coagulation factor IX gene (F9), is considered an appropriate target for genome editing technology. Here, we describe treatment strategies for haemophilia B mice using the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system. Administration of adeno-associated virus (AAV) 8 vector harbouring Staphylococcus aureus Cas9 (SaCas9) and single guide RNA (sgRNA) to wild-type adult mice induced a double-strand break (DSB) at the target site of F9 in hepatocytes, sufficiently developing haemophilia B...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630471/candidatus-mycoplasma-girerdii-replicates-diversifies-and-co-occurs-with-trichomonas-vaginalis-in-the-oral-cavity-of-a-premature-infant
#18
Elizabeth K Costello, Christine L Sun, Erica M Carlisle, Michael J Morowitz, Jillian F Banfield, David A Relman
Genital mycoplasmas, which can be vertically transmitted, have been implicated in preterm birth, neonatal infections, and chronic lung disease of prematurity. Our prior work uncovered 16S rRNA genes belonging to a novel, as-yet-uncultivated mycoplasma (lineage 'Mnola') in the oral cavity of a premature neonate. Here, we characterize the organism's associated community, growth status, metabolic potential, and population diversity. Sequencing of genomic DNA from the infant's saliva yielded 1.44 Gbp of high-quality, non-human read data, from which we recovered three essentially complete (including 'Mnola') and three partial draft genomes (including Trichomonas vaginalis)...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630186/loss-of-c-5-sterol-desaturase-activity-results-in-increased-resistance-to-azole-and-echinocandin-antifungals-in-a-clinical-isolate-of-candida-parapsilosis
#19
Jeffrey M Rybak, C Michael Dickens, Josie E Parker, Kelly Caudle, Kayihura Manigaba, Sarah G Whaley, Andrew Nishimoto, Arturo Luna-Tapia, Sujoy Roy, Qing Zhang, Katherine S Barker, Glen E Palmer, Thomas R Sutter, Ramin Homayouni, Nathan P Wiederhold, Steven L Kelly, P David Rogers
Among emerging non-albicans Candida species, C. parapsilosis is of particular concern as a cause of nosocomial bloodstream infections in neonatal and intensive care unit patients. While fluconazole and echinocandins are considered effective treatment of such infections, recent reports of fluconazole and echinocandin resistance in C. parapsilosis indicate a growing problem. The present study describes a novel mechanism of antifungal resistance in this organism affecting the susceptibility of azole and echinocandin antifungals in a clinical isolate obtained from a patient with prosthetic valve endocarditis...
June 19, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28630177/integrated-genome-and-transcriptome-sequencing-identifies-a-noncoding-mutation-in-the-genome-replication-factor-donson-as-the-cause-of-microcephaly-micromelia-syndrome
#20
Gilad D Evrony, Dwight R Cordero, Jun Shen, Jennifer N Partlow, Timothy W Yu, Rachel E Rodin, R Sean Hill, Michael E Coulter, Anh-Thu N Lam, Divya Jayaraman, Dianne Gerrelli, Diana G Diaz, Chloe Santos, Victoria Morrison, Antonella Galli, Ulrich Tschulena, Stefan Wiemann, M Jocelyne Martel, Betty Spooner, Steven C Ryu, Princess C Elhosary, Jillian M Richardson, Danielle Tierney, Christopher A Robinson, Rajni Chibbar, Dana Diudea, Rebecca Folkerth, Sheldon Wiebe, A James Barkovich, Ganeshwaran H Mochida, James Irvine, Edmond G Lemire, Patricia Blakley, Christopher A Walsh
While next-generation sequencing has accelerated the discovery of human disease genes, progress has been largely limited to the "low hanging fruit" of mutations with obvious exonic coding or canonical splice site impact. In contrast, the lack of high-throughput, unbiased approaches for functional assessment of most noncoding variants has bottlenecked gene discovery. We report the integration of transcriptome sequencing (RNA-seq), which surveys all mRNAs to reveal functional impacts of variants at the transcription level, into the gene discovery framework for a unique human disease, microcephaly-micromelia syndrome (MMS)...
June 19, 2017: Genome Research
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