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Neonatal genomics

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https://www.readbyqxmd.com/read/28646206/crispr-cas9-mediated-genome-editing-via-postnatal-administration-of-aav-vector-cures-haemophilia-b-mice
#1
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
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/28619811/full-genome-sequence-of-listeria-monocytogenes-strain-h34-isolated-from-a-newborn-with-sepsis-in-uruguay
#5
Francis Muchaamba, Claudia Guldimann, Taurai Tasara, María Inés Mota, Valeria Braga, Gustavo Varela, Gabriela Algorta, Jochen Klumpp, Marco Jermini, Roger Stephan
The foodborne pathogen Listeria monocytogenes causes severe disease mainly in the vulnerable populations of the young, old, pregnant, and immunocompromised. Here, we present the genome sequence of L. monocytogenes H34, a serotype 1/2b, lineage I, sequence type 489 (ST489) strain, isolated from a neonatal sepsis case in Uruguay.
June 15, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28612095/maternal-fetal-vitamin-d-receptor-polymorphisms-significantly-associated-with-preterm-birth
#6
Talya Rosenfeld, Hagit Salem, Gheona Altarescu, Sorina Grisaru-Granovsky, Aharon Tevet, Ruth Birk
PURPOSE: Preterm birth (PTB) is a complex trait with strong genetic background, whose etiology is not fully understood. It was recently suggested that pregnancy duration is affected by fetal genetic variation even more than by the maternal genome. Vitamin D receptor (VDR) is involved in embryonic implantation and fertility. We studied the association between both maternal and neonatal vitamin D receptor (VDR) genetic variation and PTB. METHODS: Maternal and fetal (umbilical cord) DNA was isolated from Jewish Israeli idiopathic preterm newborns (24-36 weeks, n = 146) and control term newborns (>37 weeks, n = 229)...
June 13, 2017: Archives of Gynecology and Obstetrics
https://www.readbyqxmd.com/read/28595673/neonatal-dna-methylation-and-early-onset-conduct-problems-a-genome-wide-prospective-study
#7
Charlotte A M Cecil, Esther Walton, Sara R Jaffee, Tom O'Connor, Barbara Maughan, Caroline L Relton, Rebecca G Smith, Wendy McArdle, Tom R Gaunt, Isabelle Ouellet-Morin, Edward D Barker
Early-onset conduct problems (CP) are a key predictor of adult criminality and poor mental health. While previous studies suggest that both genetic and environmental risks play an important role in the development of early-onset CP, little is known about potential biological processes underlying these associations. In this study, we examined prospective associations between DNA methylation (cord blood at birth) and trajectories of CP (4-13 years), using data drawn from the Avon Longitudinal Study of Parents and Children...
June 9, 2017: Development and Psychopathology
https://www.readbyqxmd.com/read/28585265/past-present-and-future-of-epigenetics-in-brain-sexual-differentiation
#8
REVIEW
Nancy G Forger
Sexual differentiation has long been considered "epigenetic," although the meaning of that word has shifted over time. Here we track the evolution of ideas about epigenetics in sexual differentiation, and identify principles that have emerged from recent studies. Experiments manipulating a particular epigenetic mechanism during neonatal life demonstrate a role for both histone acetylation and DNA methylation in the development of sex differences in the brain and behavior of rodents. In addition, hormone-dependent sex differences in the number of neurons of a particular phenotype may be programmed by differences in DNA methylation early in life...
June 6, 2017: Journal of Neuroendocrinology
https://www.readbyqxmd.com/read/28582313/outbreaks-in-the-neonatal-icu-a-review-of-the-literature
#9
Julia Johnson, Caroline Quach
PURPOSE OF REVIEW: Neonates in the neonatal ICU (NICU) are uniquely vulnerable to colonization and infection with pathogens such as multidrug resistant Gram-negative bacteria, which in turn are associated with increased infection-related morbidities and higher case-fatality rates. We reviewed the English, French, and German language literature published between 2015 and 2017, for reports of NICU outbreaks. RECENT FINDINGS: A total of 39 outbreaks in NICUs were reported with Gram-negative bacteria (n = 21; 54%) causing most, and extended spectrum beta-lactamase-producing organisms being the most frequent resistance mechanism reported (n = 5)...
June 2, 2017: Current Opinion in Infectious Diseases
https://www.readbyqxmd.com/read/28581886/enhanced-immunization-techniques-to-obtain-highly-specific-monoclonal-antibodies
#10
Rodrigo de Almeida, Cecília Naomi Nakamura, Marina de Lima Fontes, Elenice Deffune, Sérgio Luis Felisbino, Ramon Kaneno, Wagner José Fávaro, Athanase Billis, Marcel Otávio Cerri, Ana Marisa Fusco-Almeida, Maria José Mendes-Giannini, Andrei Moroz
Despite fast advances in genomics and proteomics, monoclonal antibodies (mAbs) are still a valuable tool for areas such as the evolution of basic research in stem cells and cancer, for immunophenotyping cell populations, diagnosing and prognosis of diseases, and for immunotherapy. To summarize different subtractive immunization approaches successfully employed for the production of highly specific antibodies, we identified scientific articles in NCBI PubMed using the following search terms: subtractive immunization, monoclonal antibody, tolerization, neonatal, high-zone tolerance, masking immunization...
June 5, 2017: MAbs
https://www.readbyqxmd.com/read/28576875/genome-editing-of-factor-x-in-zebrafish-reveals-unexpected-tolerance-of-severe-defects-in-the-common-pathway
#11
Zhilian Hu, Yang Liu, Michael C Huarng, Marzia Menegatti, Deepak Reyon, Megan S Rost, Zachary G Norris, Catherine E Richter, Alexandra N Stapleton, Neil C Chi, Flora Peyvandi, J Keith Joung, Jordan A Shavit
Deficiency of factor X (F10) in humans is a rare bleeding disorder with a heterogeneous phenotype and limited therapeutic options. Targeted disruption of F10 and other common pathway factors in mice results in embryonic/neonatal lethality with rapid resorption of homozygous mutants, hampering further studies. Several of these mutants also display yolk sac vascular defects, suggesting a role for thrombin signaling in vessel development. The zebrafish is a vertebrate model that demonstrates conservation of the mammalian hemostatic and vascular systems...
June 2, 2017: Blood
https://www.readbyqxmd.com/read/28572454/neurodevelopmental-protein-musashi-1-interacts-with-the-zika-genome-and-promotes-viral-replication
#12
Pavithra L Chavali, Lovorka Stojic, Luke W Meredith, Nimesh Joseph, Michael S Nahorski, Thomas J Sanford, Trevor R Sweeney, Ben A Krishna, Myra Hosmillo, Andrew E Firth, Richard Bayliss, Carlo L Marcelis, Susan Lindsay, Ian Goodfellow, C Geoffrey Woods, Fanni Gergely
A recent outbreak of Zika virus in Brazil has led to a simultaneous increase in reports of neonatal microcephaly. Zika targets cerebral neural precursors, a cell population essential for cortical development, but the cause of this neurotropism remains obscure. Here we report that the neural RNA-binding protein Musashi-1 (MSI1) interacts with the Zika genome and enables viral replication. Zika infection disrupts the binding of MSI1 to its endogenous targets, thereby deregulating expression of factors implicated in neural stem cell function...
June 1, 2017: Science
https://www.readbyqxmd.com/read/28561420/cab4b-the-first-human-platelet-antigen-carried-by-gpix-discovered-in-a-context-of-severe-neonatal-thrombocytopenia
#13
V Jallu, T Beranger, F Bianchi, C Casale, C Chenet, N Ferre, S Philippe, J Quesne, C Martageix, R Petermann
BACKGROUND: After 3 miscarriages, a 39-year-old woman gave birth at 1 year interval to 2 severely thrombocytopenic neonates (4 and 33 G/L) with intracranial haemorrhages. Transfusion of platelets concentrates corrected thrombocytopenias. The outcome was favourable for the 1(st) child but the second one died 10 days after caesarean delivery (31 WG + 6 days). METHODS: Serological studies were performed using MAIPA and flow cytometry techniques. Human platelet antigens (HPA) genotyping was done by using the BioArray HPA BeadChip and PCR-SSP techniques...
May 31, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28553280/atypical-porcine-pestivirus-as-a-novel-type-of-pestivirus-in-pigs-in-china
#14
Jin Yuan, Zhiyong Han, Jun Li, Yunzhen Huang, Jiongfeng Yang, Hongxing Ding, Jingyuan Zhang, Mengjiao Zhu, Yangyi Zhang, Jiedan Liao, Mingqiu Zhao, Jinding Chen
Pestiviruses are highly variable RNA viruses. A growing number of novel pestiviruses has been discovered in domestic and wild species in the last two decades. Recently, a novel atypical porcine pestivirus (APPV) linked with the development of congenital tremor (CT) in neonatal pigs was described in Europe and the Americas. Here, the first Asian APPV complete polyprotein coding sequence was assembled from serum samples from newborn piglets affected with CT in Southern China, and termed APPV_GD. 14 organ samples from affected piglets were analyzed by quantitative RT-PCR (qRT-PCR) to investigate the tissue tropism of APPV, and 135 serum samples from pigs from 10 farms were used for identifying APPV in adult pigs...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28550974/eliminating-hiv-1-packaging-sequences-from-lentiviral-vector-proviruses-enhances-safety-and-expedites-gene-transfer-for-gene-therapy
#15
Conrad A Vink, John R Counsell, Dany P Perocheau, Rajvinder Karda, Suzanne M K Buckley, Martijn H Brugman, Melanie Galla, Axel Schambach, Tristan R McKay, Simon N Waddington, Steven J Howe
Lentiviral vector genomic RNA requires sequences that partially overlap wild-type HIV-1 gag and env genes for packaging into vector particles. These HIV-1 packaging sequences constitute 19.6% of the wild-type HIV-1 genome and contain functional cis elements that potentially compromise clinical safety. Here, we describe the development of a novel lentiviral vector (LTR1) with a unique genomic structure designed to prevent transfer of HIV-1 packaging sequences to patient cells, thus reducing the total HIV-1 content to just 4...
May 17, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28550066/rapid-whole-genome-sequencing-identifies-a-novel-homozygous-npc1-variant-associated-with-niemann-pick-type-c1-disease-in-a-7-week-old-male-with-cholestasis
#16
Amber Hildreth, Kristen Wigby, Shimul Chowdhury, Shareef Nahas, Jaime Barea, Paulina Ordonez, Serge Batalov, David M Dimmock, Rcigm Investigators, Stephen F Kingsmore
Niemann-Pick Type C disease (NPC; OMIM #257220) is an inborn error of intracellular cholesterol trafficking. It is an autosomal recessive disorder caused predominantly by mutations in NPC1. While characterized as a progressive neurological disorder, it can also cause cholestasis and liver dysfunction due to intrahepatocyte lipid accumulation. We report a 7 week old who was admitted with neonatal cholestasis, who was diagnosed with a novel homozygous stop-gain variant in NPC1 by rapid whole genome sequencing (WGS)...
May 26, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28546117/analysis-on-pathogenic-and-virulent-characteristics-of-the-cronobacter-sakazakii-strain-baa-894-by-whole-genome-sequencing-and-its-demonstration-in-basic-biology-science
#17
Xuerui Bao, Ling Yang, Lequn Chen, Bing Li, Lin Li, Yanyan Li, Zhenbo Xu
Cronobacter sakazakii is an opportunistic pathogen responsible for necrotizing enterocolitis, meningitis and septicaemia especially to infant and neonate, with high lethality ranging in 40%-80%. This strain is able to survive in infant milk formula and possesses capability of pathogenicity and virulence, biofilm formation, and high resistance to elevated osmotic, low pH, heat, oxidation, and desiccasion. This study is aims to investigate the molecular characteristics of Cronobacter sakazakii BAA 894, including mechanisms of its invasion and adherence, biofilm formation, unusual resistance to environmental stress employing whole genome sequencing and comparative genomics...
May 22, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28505178/a-reverse-dot-blot-assay-for-the-screening-of-twenty-mutations-in-four-genes-associated-with-nshl-in-a-chinese-population
#18
Siping Li, Qi Peng, Shengyun Liao, Wenrui Li, Qiang Ma, Xiaomei Lu
BACKGROUND: Congenital deafness is one of the most distressing disorders affecting humanity and exhibits a high incidence worldwide. Most cases of congenital deafness in the Chinese population are caused by defects in a limited number of genes. A convenient and reliable method for detecting common deafness-related gene mutations in the Chinese population is required. METHODS: We developed a PCR-reverse dot blot (RDB) assay for screening 20 hotspot mutations of GJB2, GJB3, SLC26A4, and MT-RNR1, which are common non-syndromic hearing loss (NSHL)-associated genes in the Chinese population...
2017: PloS One
https://www.readbyqxmd.com/read/28501220/7-8-hydroxy-2-deoxyguanosine-2-deoxiguanosine-ratio-determined-in-hydrolysates-of-brain-dna-by-ultrachromatrography-coupled-to-tandem-mass-spectrometry
#19
Isabel Torres-Cuevas, Miguel Aupi, Miguel Angel Asensi, Máximo Vento, Ángel Ortega, Javier Escobar
7,8-hydroxy-2'-deoxyguanosine (8-OHdG) is an abundant DNA lesion formed by oxidation of the nucleoside 2'-deoxyguanosine (2-dG) and one of the most studied and accepted oxidative stress biomarkers. 8-OHdG has a strong carcinogenic potential, and prolonged oxidative stress heightens pathological conditions and especially cancer risk. Our aim was to develop, validate and apply a reliable method to assess DNA oxidation in genomic cellular DNA of sensible target organs such as brain. A procedure to isolate and digest the DNA of brain tissue properly for further detection of 8-OHdG and 2-dG by Ultra Performance Liquid Chromatography-tandem Mass Spectrometry (UPLC-MS/MS) was optimized...
August 1, 2017: Talanta
https://www.readbyqxmd.com/read/28497003/achondroplasia-and-biliary-atresia-a-rare-association-and-review-of-literature
#20
Ranjit I Kylat
Achondroplasia (ACH) occurs in most cases as de novo mutations of the gene-encoding fibroblast growth factor receptor 3 (FGFR3). Biliary atresia (BA) is a progressive neonatal inflammatory and fibro-obliterative cholangiopathy affecting the extra- and intrahepatic biliary tree to varying degrees, and it results in obstruction to bile flow and cholestatic jaundice in neonates. BA is thought to be a multifactorial disease, genome association studies have shown abnormalities in susceptibility genes, and levels of fibroblast growth factor 21 (FGF21) and fibroblast growth factor 23 (FGF23) have been noted to be increased...
June 2017: Journal of Pediatric Genetics
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