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https://www.readbyqxmd.com/read/28930642/microbial-complexes-and-caries-in-17-year-olds-with-and-without-streptococcus-mutans
#1
L Eriksson, P Lif Holgerson, A Esberg, I Johansson
Streptococcus mutans is a key bacterial species in the caries process, which affects >90% of the population worldwide. However, other acidogenic and aciduric/acidophilic species may contribute to disease development. In Sweden, a country with low prevalences of caries and S. mutans, a significant portion of caries-affected adolescents lack detectable levels of S. mutans. The objectives of the present study were 1) to characterize the tooth biofilm and saliva microbiota of adolescents with caries disease, with or without detectable S...
September 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28929968/c-state-an-interactive-web-app-for-simultaneous-multi-gene-visualization-and-comparative-epigenetic-pattern-search
#2
Divya Tej Sowpati, Surabhi Srivastava, Jyotsna Dhawan, Rakesh K Mishra
BACKGROUND: Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge. RESULTS: We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28928993/what-drives-embryo-development-chromosomal-normality-or-mitochondria
#3
A Bayram, I Elkhatib, A Arnanz, A Linan, F Ruiz, B Lawrenz, H M Fatemi
OBJECTIVE: To report the arrest of euploid embryos with high mtDNA content. DESIGN: A report of 2 cases. SETTING: Private fertility clinic. PATIENTS: 2 patients, 45 and 40 years old undergoing IVF treatment. INTERVENTIONS: Mature oocytes were collected and vitrified from two ovarian stimulations. Postthaw, survived mature oocytes underwent fertilization by intracytoplasmic sperm injection (ICSI)...
2017: Case Reports in Genetics
https://www.readbyqxmd.com/read/28927463/towards-precision-medicine-discovering-novel-gynecological-cancer-biomarkers-and-pathways-using-linked-data
#4
Alokkumar Jha, Yasar Khan, Muntazir Mehdi, Md Rezaul Karim, Qaiser Mehmood, Achille Zappa, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
BACKGROUND: Next Generation Sequencing (NGS) is playing a key role in therapeutic decision making for the cancer prognosis and treatment. The NGS technologies are producing a massive amount of sequencing datasets. Often, these datasets are published from the isolated and different sequencing facilities. Consequently, the process of sharing and aggregating multisite sequencing datasets are thwarted by issues such as the need to discover relevant data from different sources, built scalable repositories, the automation of data linkage, the volume of the data, efficient querying mechanism, and information rich intuitive visualisation...
September 19, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28927397/detection-of-bacterial-pathogens-from-clinical-specimens-using-conventional-microbial-culture-and-16s-metagenomics-a-comparative-study
#5
Lalanika M Abayasekara, Jennifer Perera, Vishvanath Chandrasekharan, Vaz S Gnanam, Nisala A Udunuwara, Dileepa S Liyanage, Nuwani E Bulathsinhala, Subhashanie Adikary, Janith V S Aluthmuhandiram, Chrishanthi S Thanaseelan, D Portia Tharmakulasingam, Tharaga Karunakaran, Janahan Ilango
BACKGROUND: Infectious disease is the leading cause of death worldwide, and diagnosis of polymicrobial and fungal infections is increasingly challenging in the clinical setting. Conventionally, molecular detection is still the best method of species identification in clinical samples. However, the limitations of Sanger sequencing make diagnosis of polymicrobial infections one of the biggest hurdles in treatment. The development of massively parallel sequencing or next generation sequencing (NGS) has revolutionized the field of metagenomics, with wide application of the technology in identification of microbial communities in environmental sources, human gut and others...
September 19, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28927254/integrated-analysis-of-microrna-and-mrna-expression-in-peripheral-blood-leukocytes-of-warmblood-horses-before-and-after-exercise
#6
Hang-Ah Kim, Myung-Chul Kim, Na-Yon Kim, Doug-Young Ryu, Hong-Seok Lee, Yongbaek Kim
Exercise capacity is a valuable trait in horses, and it has been used as one of their selection criteria. Although exercise affects molecular homeostasis and adaptation in horses, the mechanisms underlying these effects are not fully understood. This study was carried out to identify changes in the blood profiles of microRNAs (miRNAs) and mRNAs induced by exercise in horse leukocytes. Total RNAs isolated from the peripheral blood leukocytes of four Warmblood horses before and after exercise were subjected to next-generation sequencing (NGS) and microarray analyses to determine the miRNA and mRNA expression profiles, respectively...
September 20, 2017: Journal of Veterinary Science
https://www.readbyqxmd.com/read/28926993/satellite-dna-an-evolving-topic
#7
REVIEW
Manuel A Garrido-Ramos
Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes...
September 18, 2017: Genes
https://www.readbyqxmd.com/read/28926588/the-effects-of-storage-temperature-and-duration-of-blood-samples-on-dna-and-rna-qualities
#8
Lien-Hung Huang, Pei-Hsien Lin, Kuo-Wang Tsai, Liang-Jen Wang, Ying-Hsien Huang, Ho-Chang Kuo, Sung-Chou Li
DNA and RNA samples from blood are the common examination target for non-invasive physical tests and/or biomedical studies. Since high-quality DNA and RNA samples guarantee the correctness of these tests and/or studies, we investigated the effects of storage temperature and storage duration of whole blood on DNA and RNA qualities. Subjects were enrolled to donate blood samples which were stored for different durations and at different temperatures, followed by the examinations on RNA quality, qPCR, DNA quality and DNA methylation...
2017: PloS One
https://www.readbyqxmd.com/read/28926006/developing-a-framework-to-assess-the-costeffectiveness-of-compare-a-global-platform-for-the-exchange-of-sequence-based-pathogen-data
#9
F Alleweldt, S Kara, A Osinski, P Van Baal, K Kellerborg, F M Aarestrup, M Koopmans
Analysing the genomic data of pathogens with the help of next-generation sequencing (NGS) is an increasingly important part of disease outbreak investigations and helps guide responses. While this technology has already been successfully employed to elucidate and control disease outbreaks, wider implementation of NGS also depends on its cost-effectiveness. COMPARE - short for 'Collaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks' - is a major project, funded by the European Union, to develop a global platform for sharing and analysing NGS data and thereby improve the rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks...
April 2017: Revue Scientifique et Technique
https://www.readbyqxmd.com/read/28925935/technical-advances-in-the-measurement-of-residual-disease-in-acute-myeloid-leukemia
#10
REVIEW
Gregory W Roloff, Catherine Lai, Christopher S Hourigan, Laura W Dillon
Outcomes for those diagnosed with acute myeloid leukemia (AML) remain poor. It has been widely established that persistent residual leukemic burden, often referred to as measurable or minimal residual disease (MRD), after induction therapy or at the time of hematopoietic stem cell transplant (HSCT) is highly predictive for adverse clinical outcomes and can be used to identify patients likely to experience clinically evident relapse. As a result of inherent genetic and molecular heterogeneity in AML, there is no uniform method or protocol for MRD measurement to encompass all cases...
September 19, 2017: Journal of Clinical Medicine
https://www.readbyqxmd.com/read/28924587/colorectal-endoscopic-submucosal-dissection-predictors-and-neoplasm-related-gradients-of-difficulty
#11
Federico Iacopini, Yutaka Saito, Antonino Bella, Takuji Gotoda, Patrizia Rigato, Walter Elisei, Fabrizio Montagnese, Giampaolo Iacopini, Guido Costamagna
BACKGROUND AND STUDY AIM:  The role of colorectal endoscopic submucosal dissection (ESD) is standardized in Japan and East Asia, but technical difficulties hinder its diffusion. The aim was to identify predictors of difficulty for each neoplasm type. METHODS:  A competent operator performed all procedures. ESD difficulty was defined as: en bloc with a slow speed (< 0.07 cm (2) /min; 30 × 30 mm neoplasm in > 90 min), conversion to endoscopic mucosal resection, or resection abandonment...
September 2017: Endoscopy International Open
https://www.readbyqxmd.com/read/28924536/genetic-analyses-of-the-nf1-gene-in-turkish-neurofibromatosis-type-i-patients-and-definition-of-three-novel-variants
#12
S D Ulusal, H Gürkan, E Atlı, S A Özal, M Çiftdemir, H Tozkır, Y Karal, H Güçlü, D Eker, I Görker
Neurofibromatosis Type I (NF1) is a multi systemic autosomal dominant neurocutaneous disorder predisposing patients to have benign and/or malignant lesions predominantly of the skin, nervous system and bone. Loss of function mutations or deletions of the NF1 gene is responsible for NF1 disease. Involvement of various pathogenic variants, the size of the gene and presence of pseudogenes makes it difficult to analyze. We aimed to report the results of 2 years of multiplex ligation-dependent probe amplification (MLPA) and next generation sequencing (NGS) for genetic diagnosis of NF1 applied at our genetic diagnosis center...
June 30, 2017: Balkan Journal of Medical Genetics: BJMG
https://www.readbyqxmd.com/read/28923882/mutational-profiling-of-acute-myeloid-leukemia-with-normal-cytogenetics-in-brazilian-patients-the-value-of-next-generation-sequencing-for-genomic-classification
#13
Thiago Rodrigo de Noronha, Miguel Mitne-Neto, Maria de Lourdes Chauffaille
Karyotype (KT) aberrations are important prognostic factors for acute myeloid leukemia (AML); however, around 50% of cases present normal results. Single nucleotide polymorphism array can detect chromosomal gains, losses or uniparental disomy that are invisible to KT, thus improving patients' risk assessment. However, when both tests are normal, important driver mutations can be detected by the use of next-generation sequencing (NGS). Fourteen adult patients with AML with normal cytogenetics were investigated by NGS for 19 AML-related genes...
September 18, 2017: Journal of Investigative Medicine: the Official Publication of the American Federation for Clinical Research
https://www.readbyqxmd.com/read/28923025/intrafamilial-phenotypic-heterogeneity-in-a-taiwanese-family-with-a-mapt-p-r5h-mutation-a-case-report-and-literature-review
#14
Hui-Chi Lin, Chin-Hsien Lin, Pei-Lung Chen, Shih-Jung Cheng, Pei-Hao Chen
BACKGROUND: Frontotemporal degeneration (FTD) is a clinically and genetically heterogeneous neurodegenerative disorder characterized by deficits in executive function that frequently overlaps with parkinsonism and motor neuron disorders. Several genes have been identified to cause autosomal dominant forms of FTD, including the gene coding for the protein associated with microtubule tau (MAPT). While most reported pathogenic mutations in MAPT occur in exons 9-13, few families have been reported with mutations outside of this region...
September 18, 2017: BMC Neurology
https://www.readbyqxmd.com/read/28923014/scn8a-mutations-in-chinese-patients-with-early-onset-epileptic-encephalopathy-and-benign-infantile-seizures
#15
Jiaping Wang, Hua Gao, Xinhua Bao, Qingping Zhang, Jiarui Li, Liping Wei, Xiru Wu, Yan Chen, Shujie Yu
BACKGROUND: SCN8A mutations have recently been associated with epilepsy and neurodevelopmental disorders. This study aimed to broaden the phenotypic-spectrum of disease related with SCN8A mutations. METHODS: To identify the pathogenic gene of a Chinese family, in which six members suffered from epilepsy, whole-exome sequencing was performed. In addition, target next-generation sequencing (NGS) was performed on 178 sporadic patients, who had epilepsy of unknown etiology within 6 months after birth...
September 18, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28919550/improving-the-genotyping-resolution-of-cryptosporidium-hominis-subtype-iba10g2-using-one-step-pcr-based-amplicon-sequencing
#16
Jessica Beser, Björn M Hallström, Abdolreza Advani, Sofia Andersson, Gabriel Östlund, Jadwiga Winiecka-Krusnell, Marianne Lebbad, Erik Alm, Karin Troell, Romanico B G Arrighi
Cryptosporidium hominis gp60 subtype IbA10G2 is a common cause of cryptosporidiosis. This subtype is responsible for many waterborne outbreaks as well as sporadic cases and is considered virulent and highly important in the epidemiology of cryptosporidiosis. Due to low heterogeneity within the genome of C. hominis it has been difficult to identify epidemiological markers with higher resolution than gp60. However, new markers are required in order to improve outbreak investigations and studies of the transmission dynamics of this clinically important subtype...
September 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28919163/multiplex-pcr-and-ngs-based-identification-of-mrna-splicing-variants-analysis-of-brca1-splicing-pattern-as-a-model
#17
Jan Hojny, Petra Zemankova, Filip Lhota, Jan Sevcik, Viktor Stranecky, Hana Hartmannova, Katerina Hodanova, Ondrej Mestak, David Pavlista, Marketa Janatova, Jana Soukupova, Michal Vocka, Zdenek Kleibl, Petra Kleiblova
Alternative pre-mRNA splicing increases transcriptome plasticity by forming naturally-occurring alternative splicing variants (ASVs). Alterations of splicing processes, caused by DNA mutations, result in aberrant splicing and the formation of aberrant mRNA isoforms. Analyses of hereditary cancer predisposition genes reveal many DNA variants with unknown clinical significance (VUS) that potentially affect pre-mRNA splicing. Therefore, a comprehensive description of ASVs is an essential prerequisite for the interpretation of germline VUS in high-risk individuals...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28918274/distribution-comparison-and-risk-assessment-of-free-floating-and-particle-attached-bacterial-pathogens-in-urban-recreational-water-implications-for-water-quality-management
#18
Tingting Fang, Qijia Cui, Yong Huang, Peiyan Dong, Hui Wang, Wen-Tso Liu, Quanhui Ye
The risk of pathogen exposure in recreational water is a concern worldwide. Moreover, suspended particles, as ideal shelters for pathogens, in these waters also need attention. However, the risk caused by the pathogen-particle attachment is largely unknown. Accordingly, water samples in three recreational lakes in Beijing were collected and separated into free-floating (FL, 0.22-5μm) and particle-attached (PA, >5μm) fractions. Next-generation sequencing (NGS) was employed to determine the diversity of genera containing pathogens, and quantitative PCR (qPCR) was used to assess the presence of genes from Escherichia coli (uidA), Salmonella enterica (invA), Aeromonas spp...
September 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28917852/bio-responsive-alginate-keratin-composite-nanogels-with-enhanced-drug-loading-efficiency-for-cancer-therapy
#19
Zhe Sun, Zeng Yi, Huaiying Zhang, Xiaomin Ma, Wen Su, Xiaoyu Sun, Xudong Li
This article presents a novel dual-stimuli responsive nanogel prepared from human hair keratin and alginate through simple crosslinking method. Keratin offer the crosslinking structure and bio-responsive ability and alginate ameliorated properties of nanogels including particle size, stability and drug loading capacity. The resultant keratin-alginate nanogels (KSA-NGs) could function as promising vectors for doxorubicin hydrochloride (DOX) with a super-high drug-loading rate of 52.9% (w/w) and dual-stimuli responsive behavior to GSH and trypsin...
November 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28915855/massive-parallel-sequencing-as-a-new-diagnostic-approach-for-phenylketonuria-and-tetrahydrobiopterin-deficiency-in-thailand
#20
Pongsathorn Chaiyasap, Chupong Ittiwut, Chalurmpon Srichomthong, Apiruk Sangsin, Kanya Suphapeetiporn, Vorasuk Shotelersuk
BACKGROUND: Hyperphenylalaninemia (HPA) can be classified into phenylketonuria (PKU) which is caused by mutations in the phenylalanine hydroxylase (PAH) gene, and BH4 deficiency caused by alterations in genes involved in tetrahydrobiopterin (BH4) biosynthesis pathway. Dietary restriction of phenylalanine is considered to be the main treatment of PKU to prevent irreversible intellectual disability. However, the same dietary intervention in BH4 deficiency patients is not as effective, as BH4 is also a cofactor in many neurotransmitter syntheses...
September 16, 2017: BMC Medical Genetics
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