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Neonatal genomics

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https://www.readbyqxmd.com/read/27913251/unmapped-reads-from-cattle-rnaseq-data-a-source-for-missing-and-misassembled-sequences-in-the-reference-assemblies-and-for-detection-of-pathogens-in-the-host
#1
Tahir Usman, Frieder Hadlich, Wiebke Demasius, Rosemarie Weikard, Christa Kühn
Usually, reads from transcriptome sequencing data unmapped to the target species reference genome are disregarded. A recent RNAseq project on the new fatal disease Bovine Neonatal Pancytopenia had indicated an unexplained immune response signature to a double stranded RNA virus. To unravel its background, contigs were de novo assembled from unmapped RNAseq reads and aligned against the bovine genome assemblies and multispecies NCBI databases. Lack of genuine virus sequence contigs rejected the hypothesis of a live virus being causal for the unexplained immune response...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27910939/real-time-pcr-based-serotyping-of-streptococcus-agalactiae
#2
Kathleen M Breeding, Bhavana Ragipani, Kun-Uk David Lee, Martin Malik, Tara M Randis, Adam J Ratner
Group B Streptococcus (GBS) is an encapsulated, gram-positive pathogen that is an important cause of neonatal invasive infections, including sepsis and meningitis. There are ten known GBS serotypes based on distinct capsule compositions (Ia, Ib, II-IX), and current candidate capsular polysaccharide conjugate vaccines target only a subset of these. Serotyping of GBS isolates is important for understanding local epidemiology and for monitoring for serotype replacement or capsular switching. However, serotyping generally requires either latex agglutination, multiplex PCR with analysis of band sizes, or analysis of whole genome sequences-all techniques that are either expensive or not widely available...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910039/silencing-genes-in-the-heart
#3
Henry Fechner, Roland Vetter, Jens Kurreck, Wolfgang Poller
Silencing of cardiac genes by RNA interference (RNAi) has developed into a powerful new method to treat cardiac diseases. Small interfering (si)RNAs are the inducers of RNAi, but cultured primary cardiomyocytes and heart are highly resistant to siRNA transfection. This can be overcome by delivery of small hairpin (sh)RNAs or artificial microRNA (amiRNAs) by cardiotropic adeno-associated virus (AAV) vectors. Here we describe as example of the silencing of a cardiac gene, the generation and cloning of shRNA, and amiRNAs directed against the cardiac protein phospholamban...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27905109/a-lethal-neonatal-phenotype-of-mitochondrial-short-chain-enoyl-coa-hydratase-1-deficiency
#4
F Al Mutairi, H E Shamseldin, M Alfadhel, R J Rodenburg, F S Alkuraya
Short-chain enoyl-CoA hydratase (SCEH) is a mitochondrial enzyme involved in the oxidation of fatty acids and the catabolic pathway of valine and, to a lesser extent, isoleucine. Deficiency of this enzyme was recently shown to cause an early childhood Leigh syndrome phenotype. The few reported patients were compound heterozygotes for two missense or missense with truncating variants in ECHS1 that encodes SCEH. We describe two siblings with severe refractory lactic acidosis and death within the first 2 days of life...
October 13, 2016: Clinical Genetics
https://www.readbyqxmd.com/read/27903736/t-and-b-cell-markers-in-dried-blood-spots-of-neonates-with-congenital-cytomegalovirus-infection-b-cell-numbers-at-birth-are-associated-with-long-term-outcomes
#5
Roberta Rovito, Marjolein J Korndewal, Menno C van Zelm, Dimitrios Ziagkos, Els Wessels, Mirjam van der Burg, Aloys C M Kroes, Anton W Langerak, Ann C T M Vossen
Congenital CMV infection (cCMV) is the most common congenital infection that can cause long-term impairment (LTI). The pathogenesis of LTI is not completely understood. Fetal immunity may play a role in controlling the infection and preventing LTI, although immune activation may also contribute to fetal immunopathology. In this study, we analyzed various molecular markers of T and B cell numbers in neonatal dried blood spots of 99 children with cCMV and 54 children without cCMV: δRec-ψJα signal joints on TCR excision circles, intron recombination signal sequence k-deleting element signal joints on Igκ-deleting recombination excision circles, genomic intron recombination signal sequence k-deleting element coding joint, genomic Vδ1-Jδ1, and Vδ2-Jδ1 rearrangements...
November 30, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27900365/genome-sequencing-in-a-case-of-niemann-pick-type-c
#6
Max Dougherty, John Lazar, Jason C Klein, Karina Diaz, Theodore Gobillot, Eli Grunblatt, Nicholas Hasle, Daniel Lawrence, Megan Maurano, Maria Nelson, Gregory Olson, Sanjay Srivatsan, Jay Shendure, C Dirk Keene, Thomas Bird, Marshall S Horwitz, Desiree A Marshall
Adult-onset Niemann-Pick disease type C (NPC) is an infrequent presentation of a rare neurovisceral lysosomal lipid storage disorder caused by autosomal recessive mutations in NPC1 (∼95%) or NPC2 (∼5%). Our patient was diagnosed at age 33 when he presented with a 10-yr history of difficulties in judgment, concentration, speech, and coordination. A history of transient neonatal jaundice and splenomegaly with bone marrow biopsy suggesting a lipid storage disorder pointed to NPC; biochemical ("variant" level cholesterol esterification) and ultrastructural studies in adulthood confirmed the diagnosis...
November 2016: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27899417/emerging-roles-of-glis3-in-neonatal-diabetes-type-1-and-type-2-diabetes
#7
Xianjie Wen, Yisheng Yang
GLI-similar 3 (GLIS3), a member of the Krüppel-like zinc finger protein subfamily, is predominantly expressed in the pancreas, thyroid, and kidney. Glis3 mRNA can be initially detected in mouse pancreas at embryonic day 11.5 and is largely restricted to β cells, pancreatic polypeptide-expressing cells, as well as ductal cells at later stage of pancreas development. Mutations in GLIS3 cause a neonatal diabetes syndrome, characterized by neonatal diabetes, congenital hypothyroidism, and polycystic kidney. Importantly, genome-wide association studies showed that variations of GLIS3 are strongly associated with both type 1 diabetes (T1D) and type 2 diabetes (T2D) in multiple populations...
November 29, 2016: Journal of Molecular Endocrinology
https://www.readbyqxmd.com/read/27888796/altered-dna-methylation-in-neonates-born-large-for-gestational-age-is-associated-with-cardiometabolic-risk-in-children
#8
Xian-Hua Lin, Dan-Dan Wu, Ling Gao, Jun-Yu Zhang, Hai-Tao Pan, Hui Wang, Cheng Li, Ping Zhang, Meng-Xi Guo, Yan-Ting Wu, Ya-Jing Tan, Li Jin, Yu-Qian Xiang, Ju-Xue Li, Jian-Zhong Sheng, He-Feng Huang
BACKGROUND: Infants being born Large-for-gestational-age (LGA) are prone to developing cardiometabolic disease. However, the underlying mechanisms remain unclear. RESULTS: Clinical investigation showed that children born LGA had significantly higher serum level of total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-c), and insulin, ratio of TC/high-density lipoprotein-cholesterol (HDL-c) compared to children born appropriate for gestational age (AGA)...
November 18, 2016: Oncotarget
https://www.readbyqxmd.com/read/27881546/draft-genome-sequences-of-two-haemophilus-quentini-isolates-recovered-from-two-different-patients-blood-cultures
#9
Alireza Eshaghi, Deidre Soares, Raymond Tsang, David Richardson, Julianne V Kus, Samir N Patel
Here, we present the draft genome sequences of two strains (K068 and C860) of the genospecies "Haemophilus quentini" The isolates were recovered from blood cultures of a newborn neonate and an elderly patient with septicemia in Ontario, Canada.
November 23, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27861552/pathoadaptive-mutations-of-escherichia-coli-k1-in-experimental-neonatal-systemic-infection
#10
Alex J McCarthy, David Negus, Patricia Martin, Catarina Pechincha, Eric Oswald, Richard A Stabler, Peter W Taylor
Although Escherichia coli K1 strains are benign commensals in adults, their acquisition at birth by the newborn may result in life-threatening systemic infections, most commonly sepsis and meningitis. Key features of these infections, including stable gastrointestinal (GI) colonization and age-dependent invasion of the bloodstream, can be replicated in the neonatal rat. We previously increased the capacity of a septicemia isolate of E. coli K1 to elicit systemic infection following colonization of the small intestine by serial passage through two-day-old (P2) rat pups...
2016: PloS One
https://www.readbyqxmd.com/read/27854133/focusing-on-developmental-origins-and-disease-inception-for-the-prevention-of-pulmonary-hypertension
#11
Bradley A Maron, Steven H Abman
Despite the growing armamentarium of therapies, pulmonary vascular disease continues to cause significant morbidity and mortality in neonates, children and adults in diverse clinical settings. To address this challenge, a strategic shift is underway that emphasizes disease recognition prior to the onset of clinical signs and symptoms when substantial pulmonary vascular remodeling is already present. Specifically, there is growing interest regarding the i) molecular events that define pulmonary vascular disease inception, ii) range of early cardiopulmonary hemodynamic measures that are associated with adverse outcome, and iii) widening utility of exercise for risk-stratification...
November 17, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27834717/draft-genome-sequence-of-an-extended-spectrum-%C3%AE-lactamase-positive-hypervirulent-klebsiella%C3%A2-pneumoniae-strain-with-novel-sequence-type-2318-isolated-from-a-neonate
#12
Chaitra Shankar, Sridhar Santhanam, Manish Kumar, Vijay Gupta, Naveen Kumar Devanga Ragupathi, Balaji Veeraraghavan
Antimicrobial resistance among hypervirulent Klebsiella pneumoniae is increasingly reported. Here, we report the draft genome sequence of a hypervirulent K. pneumoniae strain isolated from a neonate with sepsis belonging to novel sequence type 2318 (ST2318).
November 10, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27831749/crispr-cas-loci-profiling-of-cronobacter-sakazakii-pathovars
#13
Pauline Ogrodzki, Stephen James Forsythe
AIM:  Cronobacter sakazakii sequence types 1, 4, 8 and 12 are associated with outbreaks of neonatal meningitis and necrotizing enterocolitis infections. However clonality results in strains which are indistinguishable using conventional methods. This study investigated the use of clustered regularly interspaced short palindromic repeats (CRISPR)-cas loci profiling for epidemiological investigations. MATERIALS & METHODS: Seventy whole genomes of C. sakazakii strains from four clonal complexes which were widely distributed temporally, geographically and origin of source were profiled...
November 10, 2016: Future Microbiology
https://www.readbyqxmd.com/read/27827000/the-role-of-alternative-gjb2-transcription-in-screening-for-neonatal-sensorineural-deafness-in-austria
#14
Thomas Parzefall, Trevor Lucas, Martin Koenighofer, Reinhard Ramsebner, Alexandra Frohne, Shelly Czeiger, Wolf-Dieter Baumgartner, Christian Schoefer, Wolfgang Gstoettner, Klemens Frei
CONCLUSION: Alterations within a novel putative Exon 1a within the gap junction beta 2 (GJB2) gene may play a role in the development of genetic hearing impairment in Austria. OBJECTIVES: Mutations in the GJB2 gene are the most common cause of hereditary sensorineural deafness. Genome-wide screening for alternative transcriptional start sites in the human genome has revealed the presence of an additional GJB2 exon (E1a). This study tested the hypothesis of whether alternative GJB2 transcription involving E1a may play a role in the development of congenital sensorineural deafness in Austria...
November 9, 2016: Acta Oto-laryngologica
https://www.readbyqxmd.com/read/27813676/differential-gene-dosage-effects-of-diabetes-associated-gene-glis3-in-pancreatic-%C3%AE-cell-differentiation-and-function
#15
Yisheng Yang, Sean P Bush, Xianjie Wen, Wei Cao, Lawrence Chan
Mutations of GLI-similar 3 (GLIS3) underlie a neonatal diabetes syndrome. Genome-wide association studies revealed that GLIS3 variants are associated with both common type 1 and type 2 diabetes. Global Glis3-deficient (Glis3(-/-)) mice die of severe diabetes shortly after birth. GLIS3 controls islet differentiation by transactivating neurogenin 3 (Ngn3). To unravel the function of Glis3 in adults, we generated inducible global Glis3-deficient mice (Glis3(fl/fl)/RosaCre(ERT2)). Tamoxifen (TAM)-treated Glis3(fl/fl)/RosaCre(ERT2) mice developed severe diabetes, which was reproduced in TAM-treated β cell-specific Glis3(fl/fl)/Pdx1Cre(ERT) mice, but not in TAM-treated Glis3(fl/fl)/MipCre(ERT) mice...
November 4, 2016: Endocrinology
https://www.readbyqxmd.com/read/27811114/complete-genome-sequence-of-the-neonatal-meningitis-causing-escherichia-coli-strain-nmec-o18
#16
Bryon A Nicholson, Yvonne M Wannemuehler, Catherine M Logue, Ganwu Li, Lisa K Nolan
Neonatal meningitis Escherichia coli (NMEC) is a common agent of neonatal bacterial meningitis, causing high neonatal mortality and neurologic sequelae in its victims. Here, we present the complete genome sequence of NMEC O18 (also known as NMEC 58), a highly virulent (O18ac:K1, ST416) strain.
November 3, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27809765/impact-of-neonatal-iron-deficiency-on-hippocampal-dna-methylation-and-gene-transcription-in-a-porcine-biomedical-model-of-cognitive-development
#17
Kyle M Schachtschneider, Yingkai Liu, Laurie A Rund, Ole Madsen, Rodney W Johnson, Martien A M Groenen, Lawrence B Schook
BACKGROUND: Iron deficiency is a common childhood micronutrient deficiency that results in altered hippocampal function and cognitive disorders. However, little is known about the mechanisms through which neonatal iron deficiency results in long lasting alterations in hippocampal gene expression and function. DNA methylation is an epigenetic mark involved in gene regulation and altered by environmental factors. In this study, hippocampal DNA methylation and gene expression were assessed via reduced representation bisulfite sequencing and RNA-seq on samples from a previous study reporting reduced hippocampal-based learning and memory in a porcine biomedical model of neonatal iron deficiency...
November 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27795246/draft-whole-genome-sequence-of-a-haemophilus-quentini-strain-isolated-from-an-infant-in-the-united-kingdom
#18
Alasdair T M Hubbard, Sian E W Davies, Laura Baxter, Sarah Thompson, Mark M Collery, Daniel C Hand, Colin G Fink, D John I Thomas
Haemophilus quentini is a rare and distinct genospecies of Haemophilus that has been suggested as a cause of neonatal bacteremia and urinary tract infections in men. We present the draft whole-genome sequence of H. quentini MP1 isolated from an infant in the United Kingdom, aiding future identification and detection of this pathogen.
October 6, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27788041/fetal-dysmorphology-still-an-essential-art-analysis-of-the-limitations-of-microarray-in-a-fetal-population-and-a-look-toward-the-genome-sequencing-era
#19
Elaine Fletcher, Mary Porteous, Eddy Maher, Kathryn J McKenzie, Margaret 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 post mortems performed between Jan 2011 - Dec 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...
October 27, 2016: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/27767922/serotype-iv-sequence-type-468-group-b-streptococcus-neonatal-invasive-disease-minnesota-usa
#20
Sarah Teatero, Patricia Ferrieri, Nahuel Fittipaldi
To further understand the emergence of serotype IV group B Streptococcus (GBS) invasive disease, we used whole-genome sequencing to characterize 3 sequence type 468 strains isolated from neonates in Minnesota, USA. We found that strains of tetracycline-resistant sequence type 468 GBS have acquired virulence genes from a putative clonal complex 17 GBS donor by recombination.
November 2016: Emerging Infectious Diseases
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