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DNA Sequencing

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https://www.readbyqxmd.com/read/28817723/sequence-analysis-of-the-rifampicin-resistance-determining-region-rrdr-of-rpob-gene-in-multidrug-resistance-confirmed-and-newly-diagnosed-tuberculosis-patients-of-punjab-pakistan
#1
Salma Hameed, Kartyk Moganeradj, Nasir Mahmood, Timothy D McHugh, Muhammad Nawaz Chaudhry, Catherine Arnold
Molecular screening of new patients suspected for TB could help in the effective control of TB in Pakistan as it is a high TB burden country. It will be informative to understand the prevalence of multi drug resistance for a better drug regimen management in this geographical area. The Rifampicin resistance determining region (RRDR) sequencing was used to identify mutations associated with drug resistance in DNA extracts from 130 known multidrug resistant (MDR) cultured strains and compared with mutations observed in DNA extracts directly from 86 sputum samples from consecutive newly diagnosed cases in Lahore, Pakistan...
2017: PloS One
https://www.readbyqxmd.com/read/28817651/comparative-genetic-analysis-of-the-45s-rdna-intergenic-spacers-from-three-saccharum-species
#2
Yongji Huang, Fan Yu, Xueting Li, Ling Luo, Jiayun Wu, Yongqing Yang, Zuhu Deng, Rukai Chen, Muqing Zhang
The 45S ribosomal DNA (rDNA) units are separated by an intergenic spacer (IGS) containing the signals for transcription and processing of rRNAs. For the first time, we sequenced and analyzed the entire IGS region from three original species within the genus Saccharum, including S. spontaneum, S. robustum, and S. officinarum in this study. We have compared the IGS organization within three original species of the genus Saccharum. The IGS of these three original species showed similar overall organizations comprised of putative functional elements needed for rRNA gene activity as well as a non-transcribed spacer (NTS), a promoter region, and an external transcribed spacer (ETS)...
2017: PloS One
https://www.readbyqxmd.com/read/28817493/dna-methylation-of-the-glucocorticoid-receptor-gene-promoter-in-the-placenta-is-associated-with-blood-pressure-regulation-in-human-pregnancy
#3
Sulistyo E Dwi Putra, Christoph Reichetzeder, Martin Meixner, Karsten Liere, Torsten Slowinski, Berthold Hocher
BACKGROUND: Blood pressure (BP) regulation during pregnancy is influenced by hormones of placental origin. It was shown that the glucocorticoid system is altered in hypertensive pregnancy disorders such as preeclampsia. Epigenetic mechanism might influence the activity of genes involved in placental hormone/hormone receptor synthesis/action during pregnancy. METHOD: In the current study, we analyzed the association of 5'-C-phosphate-G-3' (CpG) site methylation of different glucocorticoid receptor gene (NR3C1) promoter regions with BP during pregnancy...
August 16, 2017: Journal of Hypertension
https://www.readbyqxmd.com/read/28817385/novel-molecular-defects-associated-with-very-early-onset-inflammatory-bowel
#4
Sara Ciullini Mannurita, Eleonora Gambineri
PURPOSE OF REVIEW: Immune dysregulation disorders present with common clinical features of multiorgan autoimmunity. Gastrointestinal involvement is the hallmark of an impaired immune homeostasis. This review will give an overview on the novel phenotypes, highlighting the major points that will help to enable early diagnosis and treatment. RECENT FINDINGS: The rapid progress on DNA sequencing technologies have led to the identification of monogenic defects that adversely impact the control of immune homeostasis...
August 16, 2017: Current Opinion in Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28817345/reverse-transcription-quantitative-polymerase-chain-reaction-for-detection-of-and-differentiation-between-rna-and-dna-of-hiv-1-based-lentiviral-vectors
#5
Melanie Pavlovic, Nina Koehler, Martina Anton, Anna Dinkelmeier, Maren Haase, Thorsten Stellberger, Ulrich Busch, Armin E Baiker
The purpose of the described method is the detection of and differentiation between RNA and DNA of human immunodeficiency virus (HIV)-derived lentiviral vectors (LV) in cell culture supernatants and swab samples. For the analytical surveillance of genetic engineering, operations methods for the detection of the HIV-1-based LV generations are required. Furthermore, for research issues, it is important to prove the absence of LV particles for downgrading experimental settings in terms of the biosafety level. Here, a quantitative polymerase chain reaction method targeting the long terminal repeat U5 subunit and the start sequence of the packaging signal ψ is described...
August 2017: Human Gene Therapy Methods
https://www.readbyqxmd.com/read/28817168/infection-with-a-novel-derogenid-trematode-in-a-flap-necked-chameleon-chamaeleo-dilepis
#6
Nancy B Collicutt, Nicole I Stacy, Heather Stockdale Walden, April Childress, Jennifer Dill, Marita Anderson, James F X Wellehan
A 2-year-old female Flap-necked chameleon (Chamaeleo dilepis) was presented with a history of anorexia. On physical examination, three 11×4×2 mm, light tan-pink, raised, gelatinous, freely movable, poorly demarcated, raised nodules were identified within the oral cavity. An impression smear contained multiple, light blue to green structures exhibiting an 18×35 μm, elliptical-shaped anterior portion and a single 1×150 μm filament with a tapered end. Initial differential etiologies included trematode ova, flagellate protozoa, fungal sporangia, plant material, and sperm...
August 17, 2017: Veterinary Clinical Pathology
https://www.readbyqxmd.com/read/28817112/monoallelic-and-biallelic-creb3l1-variant-causes-mild-and-severe-osteogenesis-imperfecta-respectively
#7
Rachel B Keller, Thao T Tran, Shawna M Pyott, Melanie G Pepin, Ravi Savarirayan, George McGillivray, Deborah A Nickerson, Michael J Bamshad, Peter H Byers
PurposeOsteogenesis imperfecta (OI) is a heritable skeletal dysplasia. Dominant pathogenic variants in COL1A1 and COL1A2 explain the majority of OI cases. At least 15 additional genes have been identified, but those still do not account for all OI phenotypes that present. We sought the genetic cause of mild and lethal OI phenotypes in an unsolved family.MethodsWe performed exome sequencing on seven members of the family, both affected and unaffected.ResultsWe identified a variant in cyclic AMP responsive element binding protein 3-like 1 (CREB3L1) in a consanguineous family...
August 17, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28817111/prospective-cohort-study-for-identification-of-underlying-genetic-causes-in-neonatal-encephalopathy-using-whole-exome-sequencing
#8
Theodora U J Bruun, Caro-Lyne DesRoches, Diane Wilson, Vann Chau, Tadashi Nakagawa, Masahiro Yamasaki, Shinya Hasegawa, Toshiyuki Fukao, Christian Marshall, Saadet Mercimek-Andrews
PurposeNeonatal encephalopathy, which is characterized by a decreased level of consciousness, occurs in 1-7/1,000 live-term births. In more than half of term newborns, there is no identifiable etiological factor. To identify underlying genetic defects, we applied whole-exome sequencing (WES) in term newborns with neonatal encephalopathy as a prospective cohort study.MethodsTerm newborns with neonatal encephalopathy and no history of perinatal asphyxia were included. WES was performed using patient and both parents' DNA...
August 17, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28816587/dna-methylation-independent-growth-restriction-and-altered-developmental-programming-in-a-mouse-model-of-preconception-male-alcohol-exposure
#9
Richard C Chang, William M Skiles, S Chronister Sarah, Haiqing Wang, Gabrielle I Sutton, Yudhishtar S Bedi, Matthew Snyder, Charles R Long, Michael C Golding
The preconception environment is a significant modifier of dysgenesis and the development of environmentally-induced disease. To date, Fetal Alcohol Spectrum Disorders (FASDs) have been exclusively associated with maternal exposures, yet emerging evidence suggests male-inherited alterations in the developmental program of sperm may be relevant to the growth-restriction phenotypes of this condition. Using a mouse model of voluntary consumption, we find chronic preconception male ethanol exposure associates with fetal growth restriction, decreased placental efficiency, abnormalities in cholesterol trafficking, sex-specific alterations in the genetic pathways regulating hepatic fibrosis, and disruptions in the regulation of imprinted genes...
August 17, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28815871/clinical-and-molecular-characterization-of-de-novo-loss-of-function-variants-in-hnrnpu
#10
Magalie S Leduc, Hsiao-Tuan Chao, Chunjing Qu, Magdalena Walkiewicz, Rui Xiao, Pilar Magoulas, Shujuan Pan, Joke Beuten, Weimin He, Jonathan A Bernstein, Christian P Schaaf, Fernando Scaglia, Christine M Eng, Yaping Yang
DNA alterations in the 1q43-q44 region are associated with syndromic neurodevelopmental disorders characterized by global developmental delay, intellectual disability, dysmorphic features, microcephaly, seizures, and agenesis of the corpus callosum. HNRNPU is located within the 1q43-q44 region and mutations in the gene have been reported in patients with early infantile epileptic encephalopathy. Here, we report on the clinical presentation of four patients with de novo heterozygous HNRNPU loss-of-function mutations detected by clinical whole exome sequencing: c...
August 16, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28815820/functional-analysis-of-the-biosynthetic-gene-cluster-required-for-immunity-and-secretion-of-a-novel-lactococcus-specific-bacteriocin-lactococcin-z
#11
G M Daba, N Ishibashi, T Zendo, K Sonomoto
AIMS: Characterization of the biosynthesis (secretion and immunity) of lactococcin Z. METHODS AND RESULTS: Lactococcin Z is produced by Lactococcus lactis QU 7. DNA sequence analysis revealed that the lactococcin Z gene cluster (approximately 5.1 kb) includes four genes encoding putative biosynthetic proteins; LczB (self-immunity protein), LczC (an ABC transporter), and LczD (a transport accessory protein), besides the previously identified LczA. LczB showed 25...
August 17, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28815618/effect-on-gene-expression-of-three-allelic-variants-in-gata-motifs-of-abo-rhd-and-rhce-regulatory-elements
#12
Katie Fennell, Roser Hoffman, Ken Yoshida, Sadahiko Iwamoto, Lavendri Govender, Kuben Vather, Ashika Sookraj, Ute Jentsch, Chantale Pambrun, Catherine McAuley, Margaret A Keller, Gorka Ochoa-Garay
BACKGROUND: Only a few genetic variants have been reported in regulatory elements of blood group genes. Most of them affect GATA motifs, binding sites for the GATA-1 transcription factor. STUDY DESIGN AND METHODS: Samples from two patients and one donor with unusual or discrepant serology for ABO, RhD, and RhCE antigens were analyzed by DNA sequencing. Analyzed regions included the coding sequence and portions of regulatory elements. The effect of some variants on gene expression was evaluated in reporter gene assays...
August 16, 2017: Transfusion
https://www.readbyqxmd.com/read/28815558/sequence-variants-in-esr1-and-oxtr-are-associated-with-mayer-rokitansky-k%C3%A3-ster-hauser-syndrome
#13
Sara Yvonne Brucker, Liliane Frank, Simone Eisenbeis, Melanie Henes, Diethelm Wallwiener, Olaf Riess, Barbara Van Eijck, Dorit Schöller, Michael Bonin, Kristin Katharina Rall
INTRODUCTION: Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS) is characterized by congenital absence of the uterus and the upper two-thirds of the vagina in otherwise phenotypically normal females. It is found isolated or associated with renal, skeletal and other malformations. Despite of ongoing research, the etiology is mainly unknown. For a long time, the hypothesis of deficient hormone receptors as cause for MRKHS exists, and is supported by previous findings of our group. The aim of the present study was to identify unknown genetic causes for MRKHS and to compare them with data banks including a review of the literature...
August 16, 2017: Acta Obstetricia et Gynecologica Scandinavica
https://www.readbyqxmd.com/read/28815537/from-heterochromatin-to-long-noncoding-rnas-in-drosophila-expanding-the-arena-of-gene-function-and-regulation
#14
Subhash C Lakhotia
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815535/history-discovery-and-classification-of-lncrnas
#15
Julien Jarroux, Antonin Morillon, Marina Pinskaya
The RNA World Hypothesis suggests that prebiotic life revolved around RNA instead of DNA and proteins. Although modern cells have changed significantly in 4 billion years, RNA has maintained its central role in cell biology. Since the discovery of DNA at the end of the nineteenth century, RNA has been extensively studied. Many discoveries such as housekeeping RNAs (rRNA, tRNA, etc.) supported the messenger RNA model that is the pillar of the central dogma of molecular biology, which was first devised in the late 1950s...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815508/multipart-dna-assembly-using-site-specific-recombinases-from-the-large-serine-integrase-family
#16
Femi J Olorunniji, Christine Merrick, Susan J Rosser, Margaret C M Smith, W Marshall Stark, Sean D Colloms
Assembling multiple DNA fragments into functional plasmids is an important and often rate-limiting step in engineering new functions in living systems. Bacteriophage integrases are enzymes that carry out efficient recombination reactions between short, defined DNA sequences known as att sites. These DNA splicing reactions can be used to assemble large numbers of DNA fragments into a functional circular plasmid in a method termed serine integrase recombinational assembly (SIRA). The resulting DNA assemblies can easily be modified by further recombination reactions catalyzed by the same integrase in the presence of its recombination directionality factor (RDF)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28815506/preparing-fosmid-mate-paired-libraries-using-cre-loxp-recombination
#17
Ze Peng, Jeff L Froula, Jan-Fang Cheng
Fosmid end sequencing has been widely utilized in genome sequence assemblies and genome structural variation studies. We have developed a new approach to construct fosmid paired-end libraries that is suitable for Illumina sequencing platform. This approach employs a newly modified fosmid vector (pFosClip) which contains two loxP sites with identical orientation and two inverse Illumina adaptor priming sites flanking the cloning site. DNA prepared from the fosmid library constructed with pFosClip can be treated with the Cre recombinase to remove most of the vector DNA, leaving only 107 bp of the vector sequence with insert DNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28815505/preparing-mate-paired-illumina-libraries-using-cre-recombinase
#18
Ze Peng, Nandita Nath, Zhiying Zhao, Jeff L Froula, Jan-Fang Cheng, Feng Chen
Large insert mate pair reads have been used in de novo assembly and discovery of structural variants. We developed a new approach, Cre-LoxP inverse PCR paired end (CLIP-PE), which exploits the advantages of (1) Cre-LoxP recombination system to efficiently circularize large DNA fragments, (2) inverse PCR to enrich for the desired products that contain both ends of the large DNA fragments, and (3) use of restriction enzymes to introduce a recognizable junction site between ligated fragment ends. We have successfully created CLIP-PE libraries of up to 22 kb jumping pairs and demonstrated their ability to improve genome assemblies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28815504/purification-and-in-vitro-characterization-of-zinc-finger-recombinases
#19
Femi J Olorunniji, Susan J Rosser, W Marshall Stark
Zinc finger recombinases (ZFRs) are designer site-specific recombinases that have been adapted for a variety of genome editing purposes. Due to their modular nature, ZFRs can be customized for targeted sequence recognition and recombination. There has been substantial research on the in vivo properties and applications of ZFRs; however, in order to fully understand and customize them, it will be necessary to study their properties in vitro. Experiments in vitro can allow us to optimize catalytic activities, improve target specificity, measure and minimize off-target activity, and characterize key steps in the recombination pathway that might be modified to improve performance...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28815464/inherited-nonsyndromic-ichthyoses-an-update-on-pathophysiology-diagnosis-and-treatment
#20
REVIEW
Anders Vahlquist, Judith Fischer, Hans Törmä
Hereditary ichthyoses are due to mutations on one or both alleles of more than 30 different genes, mainly expressed in the upper epidermis. Syndromic as well as nonsyndromic forms of ichthyosis exist. Irrespective of etiology, virtually all types of ichthyosis exhibit a defective epidermal barrier that constitutes the driving force for hyperkeratosis, skin scaling, and inflammation. In nonsyndromic forms, these features are most evident in severe autosomal recessive congenital ichthyosis (ARCI) and epidermolytic ichthyosis, but to some extent also occur in the common type of non-congenital ichthyosis...
August 16, 2017: American Journal of Clinical Dermatology
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