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https://www.readbyqxmd.com/read/29452580/measuring-integrated-hiv-dna-ex-vivo-and-in-vitro-provides-insights-about-how-reservoirs-are-formed-and-maintained
#1
REVIEW
Marilia Rita Pinzone, Una O'Doherty
The identification of the most appropriate marker to measure reservoir size has been a great challenge for the HIV field. Quantitative viral outgrowth assay (QVOA), the reference standard to quantify the amount of replication-competent virus, has several limitations, as it is laborious, expensive, and unable to robustly reactivate every single integrated provirus. PCR-based assays have been developed as an easier, cheaper and less error-prone alternative to QVOA, but also have limitations. Historically, measuring integrated HIV DNA has provided insights about how reservoirs are formed and maintained...
February 17, 2018: Retrovirology
https://www.readbyqxmd.com/read/29449793/clinical-proteomic-analysis-of-scrub-typhus-infection
#2
Edmond Changkyun Park, Sang-Yeop Lee, Sung Ho Yun, Chi-Won Choi, Hayoung Lee, Hyun Seok Song, Sangmi Jun, Gun-Hwa Kim, Chang-Seop Lee, Seung Il Kim
Background: Scrub typhus is an acute and febrile infectious disease caused by the Gram-negative α-proteobacterium Orientia tsutsugamushi from the family Rickettsiaceae that is widely distributed in Northern, Southern and Eastern Asia. In the present study, we analysed the serum proteome of scrub typhus patients to investigate specific clinical protein patterns in an attempt to explain pathophysiology and discover potential biomarkers of infection. Methods: Serum samples were collected from three patients (before and after treatment with antibiotics) and three healthy subjects...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29448188/genotype-phenotype-and-in-silico-pathogenicity-analysis-of-hexb-mutations-panel-based-sequencing-for-differential-diagnosis-of-gangliosidosis
#3
Nejat Mahdieh, Sahar Mikaeeli, Ali Reza Tavasoli, Zahra Rezaei, Majid Maleki, Bahareh Rabbani
OBJECTIVES: Gangliosidosis is an inherited metabolic disorder causing neurodegeneration and motor regression. Preventive diagnosis is the first choice for the affected families due to lack of straightforward therapy. Genetic studies could confirm the diagnosis and help families for carrier screening and prenatal diagnosis. An update of HEXB gene variants concerning genotype, phenotype and in silico analysis are presented. PATIENTS AND METHODS: Panel based next generation sequencing and direct sequencing of four cases were performed to confirm the clinical diagnosis and for reproductive planning...
February 8, 2018: Clinical Neurology and Neurosurgery
https://www.readbyqxmd.com/read/29447493/vitamin-d-and-ferritin-correlation-with-chronic-neck-pain-using-standard-statistics-and-a-novel-artificial-neural-network-prediction-model
#4
Haytham Eloqayli, Ali Al-Yousef, Raid Jaradat
AIM: Despite the high prevalence of chronic neck pain, there is limited consensus about the primary etiology, risk factors, diagnostic criteria and therapeutic outcome. Here, we aimed to determine if Ferritin and Vitamin D are modifiable risk factors with chronic neck pain using slandered statistics and artificial intelligence neural network (ANN). METHODS: Fifty-four patients with chronic neck pain treated between February 2016 and August 2016 in King Abdullah University Hospital and 54 patients age matched controls undergoing outpatient or minor procedures were enrolled...
February 15, 2018: British Journal of Neurosurgery
https://www.readbyqxmd.com/read/29447223/virome-and-bacteriome-characterization-of-children-with-pneumonia-and-asthma-in-mexico-city-during-winter-seasons-2014-and-2015
#5
Jose A Romero-Espinoza, Yazmin Moreno-Valencia, Rodrigo H Coronel-Tellez, Manuel Castillejos-Lopez, Andres Hernandez, Aaron Dominguez, Angel Miliar-Garcia, Arturo Barbachano-Guerrero, Rogelio Perez-Padilla, Alejandro Alejandre-Garcia, Joel A Vazquez-Perez
BACKGROUND: Acute asthma exacerbations and pneumonia are important causes of morbidity and mortality in children and may coexist in the same children, although symptom overlap may lead to difficulties in diagnosis. Microbial and viral diversity and differential abundance of either may play an important role in infection susceptibility and the development of acute and chronic respiratory diseases. OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively...
2018: PloS One
https://www.readbyqxmd.com/read/29444253/hiv-1-genotypic-resistance-testing-using-the-vela-automated-next-generation-sequencing-platform
#6
Stéphanie Raymond, Florence Nicot, Romain Carcenac, Caroline Lefebvre, Nicolas Jeanne, Karine Saune, Pierre Delobel, Jacques Izopet
Objectives: To evaluate the diagnostic performance of the Vela next-generation sequencing (NGS) system in conjunction with the Sentosa SQ HIV Genotyping Assay for genotyping HIV-1. Methods: Plasma RNA was extracted and templates prepared with the Sentosa SX instrument before sequencing the HIV-1 polymerase on the Sentosa SQ301 Sequencer (PGM IonTorrent). The Vela NGS System was compared with direct sequencing and the 454 GS-FLX (Roche) and MiSeq (Illumina) systems for genotypic resistance testing on clinical samples...
February 12, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29444232/hicaptools-a-software-suite-for-probe-design-and-proximity-detection-for-targeted-chromosome-conformation-capture-applications
#7
Anandashankar Anil, Rapolas Spalinskas, Örjan Åkerborg, Pelin Sahlén, Bonnie Berger
Summary: Folding of eukaryotic genomes within nuclear space enables physical and functional contacts between regions that are otherwise kilobases away in sequence space. Targeted chromosome conformation capture methods (T2C, chi-C and HiCap) are capable of informing genomic contacts for a subset of regions targeted by probes. We here present HiCapTools, a software package that can design sequence capture probes for targeted chromosome capture applications and analyse sequencing output to detect proximities involving targeted fragments...
February 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29443886/antibacterial-peptides-in-dermatology-strategies-for-evaluation-of-allergic-potential
#8
REVIEW
Milena Deptuła, Anna Wardowska, Maria Dzierżyńska, Sylwia Rodziewicz-Motowidło, Michał Pikuła
During recent decades, the market for peptide-based drugs, including antimicrobial peptides, has vastly extended and evolved. These drugs can be useful in treatment of various types of disorders, e.g., cancer, autoimmune diseases, infections, and non-healing wounds. Although peptides are less immunogenic than other biologic therapeutics, they can still induce immune responses and cause allergies. It is important to evaluate the immunogenic and allergic potential of peptides before they are forwarded to the expensive stages of clinical trials...
February 14, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29440449/impact-of-the-anti-cancer-drug-nt157-on-tyrosine-kinase-signalling-networks
#9
Shih-Ping Su, Efrat Flashner-Abramson, Shoshana Klein, Mor Gal, Rachel S Lee, Jianmin Wu, Alexander Levitzki, Roger J Daly
The small molecule drug NT157 has demonstrated promising efficacy in pre-clinical models of a number of different cancer types, reflecting activity against both cancer cells and the tumour microenvironment. Two known mechanisms of action are degradation of insulin-receptor substrates (IRS)-1/2, and reduced Stat3 activation, although it is possible that others exist. In order to interrogate the effects of this drug on cell signalling pathways in an unbiased manner, we have undertaken mass spectrometry-based global tyrosine phosphorylation profiling of NT157-treated A375 melanoma cells...
February 12, 2018: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/29438560/hiite-hiv-1-incidence-and-infection-time-estimator
#10
Sung Yong Park, Tanzy M T Love, Shivankur Kapoor, Ha Youn Lee, John Hancock
Motivation: Around 2.1 million new HIV-1 infections were reported in 2015, alerting that the HIV-1 epidemic remains a significant global health challenge. Precise incidence assessment strengthens epidemic monitoring efforts and guides strategy optimization for prevention programs. Estimating the onset time of HIV-1 infection can facilitate optimal clinical management and identify key populations largely responsible for epidemic spread and thereby infer HIV-1 transmission chains. Our goal is to develop a genomic assay estimating the incidence and infection time in a single cross-sectional survey setting...
February 9, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29435930/quantum-language-of-microrna-application-for-new-cancer-therapeutic-targets
#11
Yoichi Robertus Fujii
MicroRNA (miRNA) is the noncoding gene: therefore, the miRNA gene inheritably controls protein gene expression through transcriptional and post-transcriptional levels. Aberrant expression of miRNA genes causes various human diseases, especially cancers. Although cancer is a complex disease, cancer/miRNA implication has yet been grasped from the perspective of miRNA profile in bed side. Since miRNA is the mobile genetic element, the clinical verification of miRNA in microvesicle of blood is too much straggle to predict potential cancer/miRNA associations without bioinformatical computing...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29435569/interpreting-genetic-variants-in-titin-in-patients-with-muscle-disorders
#12
Marco Savarese, Lorenzo Maggi, Anna Vihola, Per Harald Jonson, Giorgio Tasca, Lucia Ruggiero, Luca Bello, Francesca Magri, Teresa Giugliano, Annalaura Torella, Anni Evilä, Giuseppina Di Fruscio, Olivier Vanakker, Sara Gibertini, Liliana Vercelli, Alessandra Ruggieri, Carlo Antozzi, Helena Luque, Sandra Janssens, Maria Barbara Pasanisi, Chiara Fiorillo, Monika Raimondi, Manuela Ergoli, Luisa Politano, Claudio Bruno, Anna Rubegni, Marika Pane, Filippo M Santorelli, Carlo Minetti, Corrado Angelini, Jan De Bleecker, Maurizio Moggio, Tiziana Mongini, Giacomo Pietro Comi, Lucio Santoro, Eugenio Mercuri, Elena Pegoraro, Marina Mora, Peter Hackman, Bjarne Udd, Vincenzo Nigro
Importance: Mutations in the titin gene (TTN) cause a wide spectrum of genetic diseases. The interpretation of the numerous rare variants identified in TTN is a difficult challenge given its large size. Objective: To identify genetic variants in titin in a cohort of patients with muscle disorders. Design, Setting, and Participants: In this case series, 9 patients with titinopathy and 4 other patients with possibly disease-causing variants in TTN were identified...
February 12, 2018: JAMA Neurology
https://www.readbyqxmd.com/read/29435032/bioinformatics-identification-of-dysregulated-micrornas-in-triple-negative-breast-cancer-based-on-microrna-expression-profiling
#13
Junqing Chen, Zhanhong Chen, Jian Huang, Feng Chen, Weiwu Ye, Guojun Ding, Xiaojia Wang
Triple negative breast cancer (TNBC) accounts for approximately 15-20% of all breast cancer cases and is usually more aggressive with a poorer clinical outcome compared with other breast cancer subtypes. Evidence of the involvement of microRNAs (miRNAs) in cancer has provided an opportunity for the development of novel effective therapeutic targets in TNBC. In the present study, the miRNA expression profiles of the human breast cancer cell line, MDA-MB-231, and MCF-7 cells, was evaluated by using miRNA microarray analysis...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29434326/culture-independent-discovery-of-the-malacidins-as-calcium-dependent-antibiotics-with-activity-against-multidrug-resistant-gram-positive-pathogens
#14
Bradley M Hover, Seong-Hwan Kim, Micah Katz, Zachary Charlop-Powers, Jeremy G Owen, Melinda A Ternei, Jeffrey Maniko, Andreia B Estrela, Henrik Molina, Steven Park, David S Perlin, Sean F Brady
Despite the wide availability of antibiotics, infectious diseases remain a leading cause of death worldwide 1 . In the absence of new therapies, mortality rates due to untreatable infections are predicted to rise more than tenfold by 2050. Natural products (NPs) made by cultured bacteria have been a major source of clinically useful antibiotics. In spite of decades of productivity, the use of bacteria in the search for new antibiotics was largely abandoned due to high rediscovery rates2,3. As only a fraction of bacterial diversity is regularly cultivated in the laboratory and just a fraction of the chemistries encoded by cultured bacteria are detected in fermentation experiments, most bacterial NPs remain hidden in the global microbiome...
February 12, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29432556/a-high-risk-haplotype-for-premature-menopause-in-childhood-cancer-survivors-exposed-to-gonadotoxic-therapy
#15
Russell J Brooke, Cindy Im, Carmen L Wilson, Matthew J Krasin, Qi Liu, Zhenghong Li, Yadav Sapkota, WonJong Moon, Lindsay M Morton, Gang Wu, Zhaoming Wang, Wenan Chen, Rebecca M Howell, Gregory T Armstrong, Smita Bhatia, Sogol Mostoufi-Moab, Kristy Seidel, Stephen J Chanock, Jinghui Zhang, Daniel M Green, Charles A Sklar, Melissa M Hudson, Leslie L Robison, Wassim Chemaitilly, Yutaka Yasui
Background: Childhood cancer survivors are at increased risk of therapy-related premature menopause (PM), with a cumulative incidence of 8.0%, but the contribution of genetic factors is unknown. Methods: Genome-wide association analyses were conducted to identify single nucleotide polymorphisms (SNPs) associated with clinically diagnosed PM (menopause < 40 years) among 799 female survivors of childhood cancer participating in the St. Jude Lifetime Cohort Study (SJLIFE)...
February 8, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29430186/identification-of-genomic-expression-differences-between-right-sided-and-left-sided-colon-cancer-based-on-bioinformatics-analysis
#16
Qiliang Peng, Kaisu Lin, Tao Chang, Li Zou, Pengfei Xing, Yuntian Shen, Yaqun Zhu
Introduction: More and more findings have demonstrated that right-sided colon cancers (RCC) and left-sided colon cancers (LCC) are distinct clinical and biological entities and suggest that they should be treated as different diseases. However, the reasons why RCC and LCC harbor different clinical and biological features remain unclear. Materials and methods: To identify the genomic expression differences between RCC and LCC and uncover the mechanisms underlying these differences, we chose the gene expression profiles of GSE14333 from the Gene Expression Omnibus (GEO) database as an object of study...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29426368/oxford-screening-csf-and-respiratory-samples-oscar-results-of-a-pilot-study-to-screen-clinical-samples-from-a-diagnostic-microbiology-laboratory-for-viruses-using-illumina-next-generation-sequencing
#17
Colin Sharp, Tanya Golubchik, William F Gregory, Anna L McNaughton, Nicholas Gow, Mathyruban Selvaratnam, Alina Mirea, Dona Foster, Monique Andersson, Paul Klenerman, Katie Jeffery, Philippa C Matthews
OBJECTIVES: There is increasing interest in the use of metagenomic (next generation sequencing, NGS) approaches for diagnosis of infection. We undertook a pilot study to screen samples submitted to a diagnostic microbiology laboratory in a UK teaching hospital using Illumina HiSeq. In the short-term, this small dataset provides insights into the virome of human respiratory and cerebrospinal fluid (CSF) samples. In the longer term, assimilating metagenomic data sets of this nature can inform optimization of laboratory and bioinformatic methods, and develop foundations for the interpretation of results in a clinical context...
February 9, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29426364/rhbdd1-promotes-colorectal-cancer-metastasis-through-the-wnt-signaling-pathway-and-its-downstream-target-zeb1
#18
Mengmeng Zhang, Fei Miao, Rong Huang, Wenjie Liu, Yuechao Zhao, Tao Jiao, Yalan Lu, Fan Wu, Xiaojuan Wang, Han Wang, Hong Zhao, Hongge Ju, Shiying Miao, Linfang Wang, Wei Song
BACKGROUND: 40-50% of colorectal cancer (CRC) patients develop metastatic disease; the presence of metastasis hinders the effective treatment of cancer through surgery, chemotherapy and radiotherapy, which makes 5-year survival rate extremely low; therefore, studying CRC metastasis is crucial for disease therapy. In the present study, we investigated the role of rhomboid domain containing 1 (RHBDD1) in tumor metastasis of CRC. METHODS: The expression of RHBDD1 was analyzed in 539 colorectal tumor tissues for its correlation with lymphatic metastasis and distal metastasis...
February 9, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29424918/highly-expressed-long-non-coding-rna-duxap10-promotes-proliferation-of-ovarian-cancer
#19
Q Zhang, W-W Wang, T-H Xu, Z-F Xu
OBJECTIVE: To investigate the expression of long non-coding RNA DUXAP10 in ovarian cancer and its effect on ovarian cancer cell lines HO8910 and A2780 cells. MATERIALS AND METHODS: Search the microarray dataset from the Gene Expression Omnibus (GEO) database using the keywords "ovarian cancer" and "GPL570". The differentially expressed genes in ovarian cancer tissues and normal ovarian tissues were analyzed by bioinformatics. Normal ovarian epithelial cells IOSE386, ovarian cancer HEY, HO8910 and A2780 cell lines were cultured...
January 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29423077/integrating-the-dysregulated-inflammasome-based-molecular-functionome-in-the-malignant-transformation-of-endometriosis-associated-ovarian-carcinoma
#20
Chia-Ming Chang, Mong-Lien Wang, Kai-Hsi Lu, Yi-Ping Yang, Chi-Mou Juang, Peng-Hui Wang, Ren-Jun Hsu, Mu-Hsien Yu, Cheng-Chang Chang
The coexistence of endometriosis (ES) with ovarian clear cell carcinoma (CCC) or endometrioid carcinoma (EC) suggested that malignant transformation of ES leads to endometriosis associated ovarian carcinoma (EAOC). However, there is still lack of an integrating data analysis of the accumulated experimental data to provide the evidence supporting the hypothesis of EAOC transformation. Herein we used a function-based analytic model with the publicly available microarray datasets to investigate the expression profiling between ES, CCC, and EC...
January 9, 2018: Oncotarget
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