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https://www.readbyqxmd.com/read/28324944/biclustering-strategies-for-genetic-marker-selection-in-gynecologic-tumor-cell-lines
#1
A Alevyzaki, S Sfakianakis, E S Bei, E Obermayr, R Zeillinger, D Fotiadis, M Zervakis
Over the past few decades great interest has been focused on cell lines derived from tumors, because of their usability as models to understand the biology of cancer. At the same time, advanced technologies such as DNA-microarrays have been broadly used to study the expression level of thousands of genes in primary tumors or cancer cell lines in a single experiment. Results from microarray analysis approaches have provided valuable insights into the underlying biology and proven useful for tumor classification, prognostication and prediction...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28324682/gene-expression-analysis-in-untreated-absence-epilepsy-demonstrates-an-inconsistent-pattern
#2
Markus von Deimling, Robert Häsler, Verena Steinbach, Paul-Martin Holterhus, Sarah von Spiczak, Ulrich Stephani, Ingo Helbig, Hiltrud Muhle
OBJECTIVE: Childhood and Juvenile Absence Epilepsy account for 30% of all genetic generalized epilepsies with a strong genetic contribution. At the current state the genetic background remains to be resolved. The aim of this study was to identify disease associated transcripts pinpointing potential underlying disease mechanisms in patients with CAE and JAE. METHODS: We performed gene expression analysis from peripheral blood mononuclear cells (PBMCs) in 30 patients with newly-diagnosed absence epilepsy prior to initiating treatment and 30 healthy age - and gender-matched pediatric controls...
February 28, 2017: Epilepsy Research
https://www.readbyqxmd.com/read/28324659/optimization-of-cell-based-cdna-microarray-conditions-for-gene-functional-studies-in-hek293-cells
#3
Hi Chul Kim, Jin Yeong Heo, Tae-Kyu Lee, Ssang-Goo Cho, Yong-Jun Kwon
Since the cell-based cDNA microarray (CBCM) technique has been a useful tool for gain-of-function studies, many investigators have used CBCMs to identify interesting genes. However, this method requires better-established conditions to ensure high reverse transfection efficiency without cross-contamination. Therefore, we optimized CBCM techniques through various means. We determined that Lipofectamine 2000 was the most appropriate transfection reagent by evaluating eight commercialized reagents, and we determined that the most effective concentrations for printing solution constituents were 0...
March 1, 2017: SLAS Discov
https://www.readbyqxmd.com/read/28324245/comparison-of-dna-microarray-loop-mediated-isothermal-amplification-lamp-and-real-time-pcr-with-dna-sequencing-for-identification-of-fusarium-spp-obtained-from-patients-with-hematologic-malignancies
#4
Marcela de Souza, Tetsuhiro Matsuzawa, Kanae Sakai, Yasunori Muraosa, Luzia Lyra, Ariane Fidelis Busso-Lopes, Anna Sara Shafferman Levin, Angélica Zaninelli Schreiber, Yuzuru Mikami, Tohoru Gonoi, Katsuhiko Kamei, Maria Luiza Moretti, Plínio Trabasso
The performance of three molecular biology techniques, i.e., DNA microarray, loop-mediated isothermal amplification (LAMP), and real-time PCR were compared with DNA sequencing for properly identification of 20 isolates of Fusarium spp. obtained from blood stream as etiologic agent of invasive infections in patients with hematologic malignancies. DNA microarray, LAMP and real-time PCR identified 16 (80%) out of 20 samples as Fusarium solani species complex (FSSC) and four (20%) as Fusarium spp. The agreement among the techniques was 100%...
March 21, 2017: Mycopathologia
https://www.readbyqxmd.com/read/28324114/novel-25-kb-deletion-of-mertk-causes-retinitis-pigmentosa-with-severe-progression
#5
Daniel R Evans, Jane S Green, Gordon J Johnson, Jeremy Schwartzentruber, Jacek Majewski, Chandree L Beaulieu, Wen Qin, Christian R Marshall, Tara A Paton, Nicole M Roslin, Andrew D Paterson, Somayyeh Fahiminiya, Justin French, Kym M Boycott, Michael O Woods
Purpose: Retinitis pigmentosa (RP) describes a complex group of inherited retinal dystrophies with almost 300 reported genes and loci. We investigated the genetic etiology of autosomal recessive RP (arRP) in a large kindred with 5 affected family members, who reside on the island of Newfoundland, Canada. Methods: Genetic linkage analysis was performed on 12 family members (Infinium HumanOmni2.5-8 BeadChip). Whole exome sequencing analysis (Illumina HiSeq) was performed on one affected individual...
March 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28324009/whole-exome-sequencing-for-diagnosis-of-turner-syndrome-towards-next-generation-sequencing-and-newborn-screening
#6
David R Murdock, Frank X Donovan, Settara C Chandrasekharappa, Nicole Banks, Carolyn Bondy, Maximilian Muenke, Paul Kruszka
Context, Objectives: Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in females and is not currently part of newborn screening. Diagnosis is often delayed resulting in missed crucial diagnostic and therapeutic opportunities. This study sought to determine if whole-exome sequencing (WES) as part of a potential newborn screening program could be used to diagnose TS. Design, Setting, Patients: Karyotype, chromosomal microarray, and WES were performed on women with TS (n=27) enrolled in the Personalized Genomic Research study at the National Institutes of Health...
January 24, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28323933/research-resource-transcriptional-dynamics-of-cultured-human-villous-cytotrophoblasts
#7
Joshua F Robinson, Mirhan Kapidzic, Matthew Gormley, Katherine Ona, Terrence Dent, Helia Seifikar, Emily G Hamilton, Susan J Fisher
During human pregnancy, cytotrophoblasts (CTBs) play key roles in uterine invasion, vascular remodeling, and anchoring of the feto-placental unit. Due to the challenges associated with studying human placentation in utero, cultured primary villous CTBs are used as a model of the differentiation pathway that leads to invasion of the uterine wall. In vitro, CTBs emulate in vivo cell behaviors, such as migration, aggregation and substrate penetration. While some of the molecular features related to these cell behaviors have been described, the underlying mechanisms, at a global level, remain undefined at mid-gestation...
March 8, 2017: Endocrinology
https://www.readbyqxmd.com/read/28323856/risk-factors-for-esbl-producing-escherichia-coli-on-pig-farms-a-longitudinal-study-in-the-context-of-reduced-use-of-antimicrobials
#8
Wietske Dohmen, Alejandro Dorado-García, Marc J M Bonten, Jaap A Wagenaar, Dik Mevius, Dick J J Heederik
The presence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) in food animals is a public health concern. This study aimed to determine prevalence of ESBL-E. coli on pig farms and to assess the effect of reducing veterinary antimicrobial use (AMU) and farm management practices on ESBL-E. coli occurrence on pig farms. During 2011-2013, 36 Dutch conventional pig farms participated in a longitudinal study (4 sampling times in 18 months). Rectal swabs were taken from 60 pigs per farm and pooled per 6 pigs within the same age category...
2017: PloS One
https://www.readbyqxmd.com/read/28323501/microarray-based-analysis-of-gene-expression-profiles-in-peripheral-blood-of-patients-with-acute-primary-angle-closure
#9
Jin Wook Jeoung, Jung Hwa Ko, Yu Jeong Kim, Yong Woo Kim, Ki Ho Park, Joo Youn Oh
BACKGROUND: We investigated the expression of molecules in peripheral blood mononuclear cells (PBMCs) and plasma of patients with acute primary angle closure (APAC). MATERIALS AND METHODS: Peripheral blood was collected from patients with APAC (n = 10) and age-matched controls (n = 5). The gene transcription profile was analyzed in PBMCs using microarrays and validated by real-time reverse transcription polymerase chain reaction (RT-PCR). The levels of secreted proteins were evaluated in plasma by ELISA...
March 21, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28319593/profiles-of-long-noncoding-rnas-in-hypertensive-rats-long-noncoding-rna-xr007793-regulates-cyclic-strain-induced-proliferation-and-migration-of-vascular-smooth-muscle-cells
#10
Qing-Ping Yao, Zhi-Wei Xie, Kai-Xuan Wang, Ping Zhang, Yue Han, Ying-Xin Qi, Zong-Lai Jiang
BACKGROUND: Long noncoding RNAs (lncRNAs) are being discovered in multiple diseases at a rapid pace. However, the contribution of lncRNAs to hypertension remains largely unknown. In hypertension, the vascular walls are exposed to abnormal mechanical cyclic strain, which leads to vascular remodelling. Here, we investigated the mechanobiological role of lncRNAs in hypertension. METHODS AND RESULTS: Differences in the lncRNAs and mRNAs between spontaneously hypertensive rats and Wistar-Kyoto rats were screened using a gene microarray...
March 17, 2017: Journal of Hypertension
https://www.readbyqxmd.com/read/28319137/the-h3k27-demethylase-utx-regulates-adipogenesis-in-a-differentiation-stage-dependent-manner
#11
Kazushige Ota, Kit I Tong, Kouichiro Goto, Shuta Tomida, Akiyoshi Komuro, Zhong Wang, Kazuto Nishio, Hitoshi Okada
Understanding the molecular mechanisms that drive adipogenesis is important in developing new treatments for obesity and diabetes. Epigenetic regulations determine the capacity of adipogenesis. In this study, we examined the role of a histone H3 lysine 27 demethylase, the ubiquitously transcribed tetratricopeptide repeat protein on the X chromosome (Utx), in the differentiation of mouse embryonic stem cells (mESCs) to adipocytes. Using gene trapping, we examined Utx-deficient male mESCs to determine whether loss of Utx would enhance or inhibit the differentiation of mESCs to adipocytes...
2017: PloS One
https://www.readbyqxmd.com/read/28319069/the-branched-chain-amino-acid-transaminase-1-sustains-growth-of-antiestrogen-resistant-and-er%C3%AE-negative-breast-cancer
#12
V Thewes, R Simon, M Hlevnjak, M Schlotter, P Schroeter, K Schmidt, Y Wu, T Anzeneder, W Wang, P Windisch, M Kirchgäßner, N Melling, N Kneisel, R Büttner, U Deuschle, H P Sinn, A Schneeweiss, S Heck, S Kaulfuss, H Hess-Stumpp, J G Okun, G Sauter, A E Lykkesfeldt, M Zapatka, B Radlwimmer, P Lichter, M Tönjes
Antiestrogen-resistant and triple-negative breast tumors pose a serious clinical challenge because of limited treatment options. We assessed global gene expression changes in antiestrogen-sensitive compared with antiestrogen-resistant (two tamoxifen resistant and two fulvestrant resistant) MCF-7 breast cancer cell lines. The branched-chain amino acid transaminase 1 (BCAT1), which catalyzes the first step in the breakdown of branched-chain amino acids, was among the most upregulated transcripts in antiestrogen-resistant cells...
March 20, 2017: Oncogene
https://www.readbyqxmd.com/read/28318799/transcriptome-analysis-of-il-10-stimulated-m2c-macrophages-by-next-generation-sequencing
#13
Emily B Lurier, Donald Dalton, Will Dampier, Pichai Raman, Sina Nassiri, Nicole M Ferraro, Ramakrishan Rajagopalan, Mahdi Sarmady, Kara L Spiller
Alternatively activated "M2" macrophages are believed to function during late stages of wound healing, behaving in an anti-inflammatory manner to mediate the resolution of the pro-inflammatory response caused by "M1" macrophages. However, the differences between two main subtypes of M2 macrophages, namely interleukin-4 (IL-4)-stimulated "M2a" macrophages and IL-10-stimulated "M2c" macrophages, are not well understood. M2a macrophages are characterized by their ability to inhibit inflammation and contribute to the stabilization of angiogenesis...
February 20, 2017: Immunobiology
https://www.readbyqxmd.com/read/28318079/design-and-synthesis-of-galactosylated-bifurcated-ligands-with-nanomolar-affinity-for-lectin-leca-from-pseudomonas-aeruginosa
#14
Anthony Angeli, Muchen Li, Lucie Dupin, Gerard Vergoten, Mathieu Noel, Mimouna Madaoui, Shuai Wang, Albert Meyer, Thomas Gehin, Sebastien Vidal, Jean-Jacques Vasseur, Yann Chevolot, Francois Morvan
Lectin LecA of Pseudomonas aeruginosa is established as a virulent factor. Glycoclusters targeting LecA able to compete with human glycoconjugates present on epithelial cells are promising candidates to treat P. aeruginosa infection. A family of 32 glycodendrimers of generation 0 and 1 displaying bifurcated bis-galactosides has been designed to interact with LecA. The influence of both the central multivalent core and the aglycon of these glycodendrimers on their affinity toward LecA has been evaluated using a microarray technology both qualitatively for a rapid screening of the binding properties but also quantitatively (Kd) leading to high affinity LecA ligands with Kd values in the low nanomolar range (Kd = 22 nM for the best one)...
March 20, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28317854/sets-of-serum-exosomal-micrornas-as-candidate-diagnostic-biomarkers-for-kawasaki-disease
#15
Hong-Ling Jia, Chao-Wu Liu, Li Zhang, Wei-Jun Xu, Xue-Juan Gao, Jun Bai, Yu-Fen Xu, Ming-Guo Xu, Gong Zhang
Although Kawasaki disease is the main cause of acquired heart disease in children, no diagnostic biomarkers are available. We aimed to identify candidate biomarkers for diagnosing Kawasaki disease using serum exosomal microRNAs (miRNAs). Using frozen serum samples from a biobank, high-throughput microarray technologies, two-stage real-time quantitative PCR, and a self-referencing strategy for data normalization, we narrowed down the list of biomarker candidates to a set of 4 miRNAs. We further validated the diagnostic capabilities of the identified miRNAs (namely, CT(miR-1246)-CT(miR-4436b-5p) and CT(miR-197-3p)-CT(miR-671-5p)) in 79 samples from two hospitals...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28316117/how-consistent-are-we-interlaboratory-comparison-study-in-fathead-minnows-using-the-model-estrogen-17%C3%AE-ethinylestradiol-to-develop-recommendations-for-environmental-transcriptomics
#16
April Feswick, Meghan Isaacs, Adam Biales, Robert W Flick, David C Bencic, Rong-Lin Wang, Chris Vulpe, Marianna Brown-Augustine, Alex Loguinov, Francesco Falciani, Philipp Antczak, John Herbert, Lorraine Brown, Nancy D Denslow, Kevin J Kroll, Candice Lavelle, Viet Dang, Lynn Escalon, Natàlia Garcia-Reyero, Christopher J Martyniuk, Kelly R Munkittrick
Fundamental questions remain about the application of omics in environmental risk assessments, such as the consistency of data across laboratories. The objective of this study was to determine the congruence of transcript data across six independent laboratories. Male fathead minnows (FHM) were exposed to a measured concentration of 15.8 ng /L EE2 for 96 h. Livers were divided equally and sent to the participating laboratories for transcriptomic analysis using the same FHM microarray. Each laboratory was free to apply bioinformatics pipelines of their choice...
March 18, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28316008/cytogenetic-analysis-of-metaplastic-squamous-cell-carcinoma-of-the-breast-inter-and-intratumoral-heterogeneity
#17
Masahiro Oikawa, Akiko Igawa, Kenichi Taguchi, Kimiko Baba, Mayumi Ishida, Sayuri Akiyoshi, Hiroshi Yano, Takeshi Nagayasu, Shinji Ohno, Eriko Tokunaga
BACKGROUND: Squamous cell carcinoma (SCC) of the breast is a rare and generally aggressive disease that accounts for less than 0.1% of all breast carcinomas. Although SCCs have distinct morphological features, their origin and cytogenetic profile are not well understood. METHODS: Five patients with SCC were studied. The tumor area that was predominantly composed of SCC components was macrodissected and DNA was extracted. In three cases, an invasive or noninvasive ductal carcinoma of no special type (NST) component was also present...
March 18, 2017: Breast Cancer: the Journal of the Japanese Breast Cancer Society
https://www.readbyqxmd.com/read/28315920/-unknown-title
#18
J S Schwartz, S Al-Mot, M F Endam, S Al-Romaih, J Madrenas, M Desrosiers
BACKGROUND: Staphylococcus aureus is a frequently implicated pathogen in chronic rhinosinusitis (CRS). S. aureus may promote commensalism by downregulating pro-inflammatory T cell host responses via an IL-10 mediated pathway. This finding, coupled with the observation that S. aureus and CD8+ T cell numbers are inversely correlated in CRS mucosa, suggests that S. aureus may evade immune destruction via IL-10 induction. To support this hypothesis, we evaluated i) whether IL-10 levels differ in CRS compared to controls (CTL) using microarray and immunohistochemistry and ii) whether IL-10 levels correlate with S...
March 19, 2017: Rhinology
https://www.readbyqxmd.com/read/28315863/circulating-mirnas-as-potential-biomarkers-of-age-related-macular-degeneration
#19
Chengda Ren, Qingyu Liu, Qingquan Wei, Wenting Cai, Mengmei He, Yaru Du, Ding Xu, Yan Wu, Jing Yu
Backgroud: Age-related macular degeneration (AMD) is one of the leading causes of irreversible blindness of the elder people. This research was intended to demonstrate the different expression of microRNAs (miRNA) in AMD patients and whether they can be used as biomarkers for AMD. METHODS: MiRNAs expression was measured by microarray of 6 AMD cases and 6 gender matched controls. In a larger-sample case-control study with 126 AMD cases and 140 controls, whole blood samples were detected for the differences of miRNA expression...
March 16, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28315673/chromosomal-microarray-detection-of-constitutional-copy-number-variation-using-saliva-dna
#20
Jennifer Reiner, Lisa Karger, Ninette Cohen, Lakshmi Mehta, Lisa Edelmann, Stuart A Scott
Chromosomal microarray (CMA) testing to detect copy number aberrations among individuals with multiple congenital anomalies and/or developmental delay is typically performed on peripheral blood DNA. However, the use of saliva DNA may be preferred for some patients, which prompted our validation study using six saliva DNA samples with a range of bacterial content (approximately 3% to 21%) and 20 paired blood and saliva specimens on the Agilent Technologies, Illumina, and Affymetrix CMA platforms. Ten of the 20 paired specimens were previously determined to carry clinically significant copy number aberrations by clinical CMA testing on blood DNA (100 kb to 2...
March 15, 2017: Journal of Molecular Diagnostics: JMD
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