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DNA Sequencing

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https://www.readbyqxmd.com/read/29166670/age-related-differences-in-the-respiratory-microbiota-of-chickens
#1
Laura Glendinning, Gerry McLachlan, Lonneke Vervelde
In this era of next generation sequencing technologies it is now possible to characterise the chicken respiratory microbiota without the biases inherent to traditional culturing techniques. However, little research has been performed in this area. In this study we characterise and compare buccal, nasal and lung microbiota samples from chickens in three different age groups using 16S rRNA gene analysis. Buccal and nasal swabs were taken from birds aged 2 days (n = 5), 3 weeks (n = 5) and 30 months (n = 6). Bronchoalveolar lavage (BAL) samples were also collected alongside reagent only controls...
2017: PloS One
https://www.readbyqxmd.com/read/29166270/detection-of-yersinia-enterocolitica-species-in-pig-tonsils-and-raw-pork-meat-by-the-real-time-pcr-and-culture-methods
#2
M A Stachelska
The aim of the present study was to establish a rapid and accurate real-time PCR method to detect pathogenic Yersinia enterocolitica in pork. Yersinia enterocolitica is considered to be a crucial zoonosis, which can provoke diseases both in humans and animals. The classical culture methods designated to detect Y. enterocolitica species in food matrices are often very time-consuming. The chromosomal locus _tag CH49_3099 gene, that appears in pathogenic Y. enterocolitica strains, was applied as DNA target for the 5' nuclease PCR protocol...
September 26, 2017: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/29165844/oral-microbiomes-from-hunter-gatherers-and-traditional-farmers-reveal-shifts-in-commensal-balance-and-pathogen-load-linked-to-diet
#3
Florent Lassalle, Matteo Spagnoletti, Matteo Fumagalli, Liam Shaw, Mark Dyble, Catherine Walker, Mark G Thomas, Andrea Bamberg Migliano, Francois Balloux
Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in close proximity in the Philippines...
November 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29165730/what-else-is-in-salviae-officinalis-folium-comprehensive-species-identification-of-plant-raw-material-by-dna-metabarcoding
#4
Corinna Schmiderer, Brigitte Lukas, Joana Ruzicka, Johannes Novak
Quality control of drugs consists of identifying the raw material to avoid unwanted admixtures or exchange of material as well as looking for abiotic and biotic contaminations. So far, identity and microbial contamination are analyzed by separate processes and separate methods. Species identification by their DNA ("DNA barcoding") has the potential to supplement existing methods of identification. The introduction of next-generation sequencing methods offers completely new approaches like the identification of whole communities in one analysis, termed "DNA metabarcoding"...
November 17, 2017: Planta Medica
https://www.readbyqxmd.com/read/29165665/novel-structural-features-drive-dna-binding-properties-of-cmr-a-crp-family-protein-in-tb-complex-mycobacteria
#5
Sridevi Ranganathan, Jonah Cheung, Michael Cassidy, Christopher Ginter, Janice D Pata, Kathleen A McDonough
Mycobacterium tuberculosis (Mtb) encodes two CRP/FNR family transcription factors (TF) that contribute to virulence, Cmr (Rv1675c) and CRPMt (Rv3676). Prior studies identified distinct chromosomal binding profiles for each TF despite their recognizing overlapping DNA motifs. The present study shows that Cmr binding specificity is determined by discriminator nucleotides at motif positions 4 and 13. X-ray crystallography and targeted mutational analyses identified an arginine-rich loop that expands Cmr's DNA interactions beyond the classical helix-turn-helix contacts common to all CRP/FNR family members and facilitates binding to imperfect DNA sequences...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165662/increased-global-dna-hypomethylation-in-distant-metastatic-and-dedifferentiated-thyroid-cancer
#6
E N Klein Hesselink, Carles Zafon, Núria Villalmanzo, Carmela Iglesias, B M van Hemel, M S Klein Hesselink, Cristina Montero-Conde, Raquel Buj, Dídac Mauricio, Miguel A Peinado, Manel Puig-Domingo, Garcilaso Riesco-Eizaguirre, Jordi L Reverter, Mercedes Robledo, T P Links, Mireia Jordà
Introduction: Global DNA hypomethylation is a major event for the development and progression of cancer, although the significance in thyroid cancer remains unclear. Therefore, we aimed to investigate its role in thyroid cancer progression and its potential as a prognostic marker. Methods: Global hypomethylation of Alu repeats was used as a surrogate marker for DNA global hypomethylation, and was assessed using the Quantification of Unmethylated Alu (QUAlu) technique...
November 20, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29165653/transgenerational-effects-of-bisphenol-a-on-gene-expression-and-dna-methylation-of-imprinted-genes-in-brain
#7
Zuzana Drobná, Anne D Henriksen, Jennifer T Wolstenholme, Catalina Montiel, Philip S Lambeth, Stephen Shang, Erin P Harris, Changqing Zhou, Jodi A Flaws, Mazhar Adli, Emilie F Rissman
Bisphenol A (BPA) is a ubiquitous man-made endocrine disrupting compound (EDC). Developmental exposure to BPA changes behavioral and reproductive phenotypes and these effects can last for generations. We exposed embryos to BPA producing two lineages: controls and BPA-exposed. In the third generation (F3), brain tissues containing the preoptic area, the bed nucleus of the stria terminalis, and the anterior hypothalamus were collected. RNA sequencing (RNA-Seq) and subsequent data analyses revealed 50 differentially regulated genes in the brains of F3 juveniles from BPA- versus control-lineages...
November 17, 2017: Endocrinology
https://www.readbyqxmd.com/read/29165646/development-and-application-of-a-recombination-based-library-versus-library-high-throughput-yeast-two-hybrid-rll-y2h-screening-system
#8
Fang Yang, Yingying Lei, Meiling Zhou, Qili Yao, Yichao Han, Xiang Wu, Wanshun Zhong, Chenghang Zhu, Weize Xu, Ran Tao, Xi Chen, Da Lin, Khaista Rahman, Rohit Tyagi, Zeshan Habib, Shaobo Xiao, Dang Wang, Yang Yu, Huanchun Chen, Zhenfang Fu, Gang Cao
Protein-protein interaction (PPI) network maintains proper function of all organisms. Simple high-throughput technologies are desperately needed to delineate the landscape of PPI networks. While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still required. Here, we developed a recombination-based 'library vs library' Y2H system (RLL-Y2H), by which multi-library screening can be accomplished in a single pool without any individual treatment...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165643/expanding-the-repertoire-of-dna-shape-features-for-genome-scale-studies-of-transcription-factor-binding
#9
Jinsen Li, Jared M Sagendorf, Tsu-Pei Chiu, Marco Pasi, Alberto Perez, Remo Rohs
Uncovering the mechanisms that affect the binding specificity of transcription factors (TFs) is critical for understanding the principles of gene regulation. Although sequence-based models have been used successfully to predict TF binding specificities, we found that including DNA shape information in these models improved their accuracy and interpretability. Previously, we developed a method for modeling DNA binding specificities based on DNA shape features extracted from Monte Carlo (MC) simulations. Prediction accuracies of our models, however, have not yet been compared to accuracies of models incorporating DNA shape information extracted from X-ray crystallography (XRC) data or Molecular Dynamics (MD) simulations...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165638/feasibility-of-real-time-molecular-profiling-for-patients-with-newly-diagnosed-glioblastoma-without-mgmt-promoter-hypermethylation-the-nct-neuro-master-match-n2m2-pilot-study
#10
Elke Pfaff, Tobias Kessler, Gnana Prakash Balasubramanian, Anne Berberich, Daniel Schrimpf, Antje Wick, Jürgen Debus, Andreas Unterberg, Martin Bendszus, Christel Herold-Mende, David Capper, Irini Schenkel, Andreas Eisenmenger, Susan Dettmer, Benedikt Brors, Michael Platten, Stefan M Pfister, Andreas von Deimling, David T W Jones, Wolfgang Wick, Felix Sahm
Introduction: O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status is a predictive biomarker in glioblastoma patients. Glioblastoma without hypermethylated MGMT promoter are largely resistant to treatment with temozolomide. These patients are in particular need of new treatment approaches, which are offered by biomarker-driven clinical trials with targeted drugs based on molecular characterization of individual tumors. Methods: In preparation for an upcoming clinical study, a comprehensive molecular profiling approach was undertaken on tissues from 43 glioblastoma patients harboring an unmethylated MGMT promoter at diagnosis...
November 18, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29165368/human-protoparvoviruses
#11
REVIEW
Elina Väisänen, Yu Fu, Klaus Hedman, Maria Söderlund-Venermo
Next-generation sequencing and metagenomics have revolutionized the discovery of novel viruses. In recent years, three novel protoparvoviruses have been discovered in fecal samples of humans: bufavirus (BuV) in 2012, tusavirus (TuV) in 2014, and cutavirus (CuV) in 2016. BuV has since been studied the most, disclosing three genotypes that also represent serotypes. Besides one nasal sample, BuV DNA has been found exclusively in diarrheal feces, but not in non-diarrheal feces, suggesting a causal relationship...
November 22, 2017: Viruses
https://www.readbyqxmd.com/read/29165356/fast-detection-of-a-brca2-large-genomic-duplication-by-next-generation-sequencing-as-a-single-procedure-a-case-report
#12
Marcella Nunziato, Flavio Starnone, Barbara Lombardo, Matilde Pensabene, Caterina Condello, Francesco Verdesca, Chiara Carlomagno, Sabino De Placido, Lucio Pastore, Francesco Salvatore, Valeria D'Argenio
The aim of this study was to verify the reliability of a next generation sequencing (NGS)-based method as a strategy to detect all possible BRCA mutations, including large genomic rearrangements. Genomic DNA was obtained from a peripheral blood sample provided by a patient from Southern Italy with early onset breast cancer and a family history of diverse cancers. BRCA molecular analysis was performed by NGS, and sequence data were analyzed using two software packages. Comparative genomic hybridization (CGH) array was used as confirmatory method...
November 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29165300/foxi2-a-possible-gene-contributing-to-ectodermal-dysplasia
#13
Mazen Kurban, Savo Bou Zeineddine, Lamiaa Hamie, Remi Safi, Ossama Abbas, Abdul Ghani Kibbi, Fadi Bitar, Georges Nemer
Cardio-facio-cutaneous syndrome (CFC), Noonan syndrome (NS), and Costello syndrome are a group of diseases that belong to the RASopathies. The syndromes share clinical features making diagnosis a challenge. To investigate the phenotype and genotype of a 10-year-old Iraqi girl with overlapping features of CFC, NS, and Costello syndromes, with additional features of ectodermal dysplasia. DNA was examined by exome sequencing and protein expression by immunohistochemistry. Exome sequencing identified a mutation in the SOS1 gene and a de novo deletion in the FOXI2 gene which was neither present in the international databases, nor in 400 chromosomes from the same population...
November 22, 2017: European Journal of Dermatology: EJD
https://www.readbyqxmd.com/read/29165218/molecular-identification-of-trichuris-suis-and-trichuris-trichiura-eggs-in-human-populations-from-thailand-lao-pdr-and-myanmar
#14
Issarapong Phosuk, Oranuch Sanpool, Tongjit Thanchomnang, Lakkhana Sadaow, Rutchanee Rodpai, Witthaya Anamnart, Penchom Janwan, Adulsak Wijit, Sakhone Laymanivong, Win Pa Pa Aung, Pewpan M Intapan, Wanchai Maleewong
Trichuris trichiura is a soil-transmitted helminth infecting human populations globally. Human cases caused by Trichuris suis and Trichuris vulpis have also been reported. Molecular identifications of Trichuris species infecting human populations in Lao PDR and Myanmar are lacking. Here, we explored molecular data obtained from Trichuris eggs recovered from human fecal samples from these countries and compared these with new and existing data from Thailand. Nuclear ribosomal DNA (18S and ITS2) sequences were amplified from Trichuris eggs and sequenced...
November 20, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29165144/isolation-and-identification-of-acanthamoeba-strains-from-soil-and-tap-water-in-yanji-china
#15
Yinghua Xuan, Yanqin Shen, Yuxi Ge, Gen Yan, Shanzi Zheng
BACKGROUND: Members of the genus Acanthamoeba are widely distributed throughout the world, and some of them are considered pathogenic, as they are capable of causing corneal and central nervous system diseases. In this study, we isolated Acanthamoeba strains from soil and tap water in Yanji, China. METHODS: We identified four strains of Acanthamoeba (CJY/S1, CJY/S2, CJY/S3, and CJY/W1) using mitochondrial DNA restriction fragment length polymorphism (mtDNA RFLP) analysis...
June 30, 2017: Environmental Health and Preventive Medicine
https://www.readbyqxmd.com/read/29164808/a-universal-approach-to-correct-various-hbb-gene-mutations-in-human-stem-cells-for-gene-therapy-of-beta-thalassemia-and-sickle-cell-disease
#16
Liuhong Cai, Hao Bai, Vasiliki Mahairaki, Yongxing Gao, Chaoxia He, Yanfei Wen, You-Chuan Jin, You Wang, Rachel L Pan, Armaan Qasba, Zhaohui Ye, Linzhao Cheng
Beta-thalassemia is one of the most common recessive genetic diseases, caused by mutations in the HBB gene. Over 200 different types of mutations in the HBB gene containing three exons have been identified in patients with β-thalassemia (β-thal) whereas a homozygous mutation in exon 1 causes sickle cell disease (SCD). Novel therapeutic strategies to permanently correct the HBB mutation in stem cells that are able to expand and differentiate into erythrocytes producing corrected HBB proteins are highly desirable...
November 21, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/29164751/style-polymorphism-in-linum-linaceae-a-case-of-mediterranean-parallel-evolution
#17
J Ruiz-Martín, R Santos-Gally, M Escudero, J J Midgley, R Pérez-Barrales, J Arroyo
Heterostyly is a sex polymorphism which has challenged evolutionary biologists ever since Darwin. One of the lineages where heterostyly, and related stylar conditions, appears more frequently is the family Linaceae and its most diverse and widespread genus, Linum. Thus, this group is particularly suitable for testing competing hypotheses about ancestral and transitional stages on the evolutionary building up of heterostyly. We generated a well-resolved phylogeny of Linum based on extensive sampling and plastid and nuclear DNA sequences, and used it to trace the evolution of character states of style polymorphism and its association with traits related to pollination and breeding systems, obtained from our samples and the literature...
November 22, 2017: Plant Biology
https://www.readbyqxmd.com/read/29164616/protection-against-%C3%AE-amyloid-neurotoxicity-by-a-non-toxic-endogenous-n-terminal-%C3%AE-amyloid-fragment-and-its-active-hexapeptide-core-sequence
#18
Kelly H Forest, Naghum Alfulaij, Komal Arora, Ruth Taketa, Tessi Sherrin, Cedomir Todorovic, James L M Lawrence, Gene T Yoshikawa, Ho-Leung Ng, Victor J Hruby, Robert A Nichols
High levels (μM) of beta amyloid (Aβ) oligomers are known to trigger neurotoxic effects, leading to synaptic impairment, behavioral deficits and apoptotic cell death. The hydrophobic C-terminal domain of Aβ, together with sequences critical for oligomer formation, is essential for this neurotoxicity. However, Aβ at low levels (pM-nM) has been shown to function as a positive neuromodulator and this activity resides in the hydrophilic N-terminal domain of Aβ. An N-terminal Aβ fragment (1-15/16), found in cerebrospinal fluid, was also shown to be a highly active neuromodulator and to reverse Aβ-induced impairments of long-term potentiation...
November 21, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/29164518/reducing-production-of-fumonisin-mycotoxins-in-fusarium-verticillioides-by-rna-interference
#19
Eric T Johnson, Robert H Proctor, Christopher A Dunlap, Mark Busman
The fungus Fusarium verticillioides is a maize pathogen that can produce fumonisin mycotoxins in ears under certain environmental conditions. Because fumonisins pose health risks to humans and livestock, control strategies with minimal risk to the environment are needed to reduce fumonisin contamination. Host-induced gene silencing is a promising technique in which double-stranded RNA expressed in the plant host is absorbed by an invading fungus and down-regulates genes critical for pathogenicity or mycotoxin production in the fungus...
November 22, 2017: Mycotoxin Research
https://www.readbyqxmd.com/read/29164086/a-novel-missense-mutation-of-the-nsd1-gene-associated-with-overgrowth-in-three-generations-of-an-italian-family-case-report-differential-diagnosis-and-review-of-mutations-of-nsd1-gene-in-familial-sotos-syndrome
#20
Gianluigi Laccetta, Francesca Moscuzza, Angela Michelucci, Andrea Guzzetta, Sara Lunardi, Francesca Lorenzoni, Paolo Ghirri
Sotos syndrome (SoS) is characterized by overgrowth of prenatal onset, learning disability, and characteristic facial appearance; it is usually due to haploinsufficiency of NSD1 gene at chromosome 5q35. An Italian child was born at 37 weeks of gestation (weight 2,910 g, 25th-50th centiles; length 50 cm, 75th centile; head circumference 36 cm, 97th centile) showing cryptorchidism on the right side, hypertelorism, dolichocephaly, broad and prominent forehead, and narrow jaw; the pregnancy was worsened by maternal preeclampsia and gestational diabetes, and his mother had a previous history of four early miscarriages...
2017: Frontiers in Pediatrics
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