keyword
MENU ▼
Read by QxMD icon Read
search

Genome analysis

keyword
https://www.readbyqxmd.com/read/29458166/statistical-approach-for-selection-of-biologically-informative-genes
#1
Samarendra Das, Anil Rai, D C Mishra, S N Rai
Selection of informative genes from high dimensional gene expression data has emerged as an important research area in genomics. Many gene selection techniques have been proposed so far are either based on relevancy or redundancy measure. Further, the performance of these techniques has been adjudged through post selection classification accuracy computed through a classifier using the selected genes. This performance metric may be statistically sound but may not be biologically relevant. A statistical approach, i...
February 16, 2018: Gene
https://www.readbyqxmd.com/read/29458134/antiviral-activity-of-pyrrole-imidazole-polyamides-against-sv40-and-bk-polyomaviruses
#2
Terri G Edwards, Chris Fisher
The ability of antiviral polyamides (AVP) to act upon polyomaviruses (PyV) was evaluated. Initial studies found that a single treatment of AVP protected SV40-infected BSC-1 cells from cytopathic effect (CPE) for as long as 11 days p.i.. AVP substantially suppressed SV40 genome copy numbers over the duration of the experiment. Immunofluorescence analysis of ataxia-telangiectasia mutated (ATM) activation and large T antigen (LTag) expression clearly demonstrated that AVP treatment at day 1 p.i. delayed the onset of productive SV40 replication by approximately 3 days, and substantially limited the infection relative to vehicle-treated controls...
February 16, 2018: Antiviral Research
https://www.readbyqxmd.com/read/29457967/dna-damage-and-genomic-instability-among-workers-formerly-and-currently-exposed-to-asbestos
#3
Mirta Milić, Monica Neri, Marcello Ceppi, Marco Bruzzone, Armelle Munnia, Donatella Ugolini, Alfonso Cristaudo, Alessandra Bonotti, Marco E Peluso, Stefano Bonassi
Objectives Despite an asbestos ban in the European Union, exposure to asbestos still represents an occupational risk. Biomarkers of DNA damage and genomic instability in groups exposed to asbestos may contribute to the identification of subgroups/subjects at higher risk. Methods A cross-sectional study was conducted on 468 male individuals (80 working in occupational settings with potential exposure to asbestos fibers, 202 retired workers with past exposure, and 186 non-exposed controls) to compare genomic instability, cell proliferation and differentiation level using the non-invasive micronucleus buccal cytome assay...
February 19, 2018: Scandinavian Journal of Work, Environment & Health
https://www.readbyqxmd.com/read/29457665/comparative-analysis-of-lipid-mediated-crispr-cas9-genome-editing-techniques
#4
Kelsey P Ringer, Mark G Roth, Mitchell S Garey, Ted B Piorczynski, Arminda Suli, Jason M Hansen, Jonathan K Alder
CRISPR-Cas technology has revolutionized genome engineering. While Cas9 was not the first programmable endonuclease identified, its simplicity of use has driven widespread adoption in a short period of time. While CRISPR-Cas genome editing holds enormous potential for clinical applications, its use in laboratory settings for genotype-phenotype studies and genome-wide screens has led to breakthroughs in the understanding of many molecular pathways. Numerous protocols have been described for introducing CRISPR-Cas components into cells, and here we sought to simplify and optimize a protocol for genome editing using readily available and inexpensive tools...
February 19, 2018: Cell Biology International
https://www.readbyqxmd.com/read/29457640/application-of-adaptive-laboratory-evolution-to-overcome-a-flux-limitation-in-an-escherichia-coli-production-strain
#5
Kento Tokuyama, Yoshihiro Toya, Takaaki Horinouchi, Chikara Furusawa, Fumio Matsuda, Hiroshi Shimizu
Gene deletion strategies using flux balance analysis (FBA) have improved the growth-coupled production of various compounds. However, the productivities were often below the expectation because the cells failed to adapt to these genetic perturbations. Here, we demonstrate the productivity of the succinate of the designed gene deletion strain was improved by adaptive laboratory evolution (ALE). Although FBA predicted deletions of adhE-pykAF-gldA-pflB lead to produce succinate from glycerol with a yield of 0...
February 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29456867/heterologous-and-endogenous-u6-snrna-promoters-enable-crispr-cas9-mediated-genome-editing-in-aspergillus-niger
#6
Xiaomei Zheng, Ping Zheng, Jibin Sun, Zhang Kun, Yanhe Ma
Background: U6 promoters have been used for single guide RNA (sgRNA) transcription in the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas9) genome editing system. However, no available U6 promoters have been identified in Aspergillus niger, which is an important industrial platform for organic acid and protein production. Two CRISPR/Cas9 systems established in A. niger have recourse to the RNA polymerase II promoter or in vitro transcription for sgRNA synthesis, but these approaches generally increase cloning efforts and genetic manipulation...
2018: Fungal Biology and Biotechnology
https://www.readbyqxmd.com/read/29456765/peripheral-blood-epi-signature-of-claes-jensen-syndrome-enables-sensitive-and-specific-identification-of-patients-and-healthy-carriers-with-pathogenic-mutations-in-kdm5c
#7
Laila C Schenkel, Erfan Aref-Eshghi, Cindy Skinner, Peter Ainsworth, Hanxin Lin, Guillaume Paré, David I Rodenhiser, Charles Schwartz, Bekim Sadikovic
Background: Claes-Jensen syndrome is an X-linked inherited intellectual disability caused by mutations in the KDM5C gene. Kdm5c is a histone lysine demethylase involved in histone modifications and chromatin remodeling. Males with hemizygous mutations in KDM5C present with intellectual disability and facial dysmorphism, while most heterozygous female carriers are asymptomatic. We hypothesized that loss of Kdm5c function may influence other components of the epigenomic machinery including DNA methylation in affected patients...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29456764/integrative-analysis-of-the-epigenetic-basis-of-muscle-invasive-urothelial-carcinoma
#8
Thomas Sanford, Maxwell V Meng, Reema Railkar, Piyush K Agarwal, Sima P Porten
Background: Elucidation of epigenetic alterations in bladder cancer will lead to further understanding of the biology of the disease and hopefully improved therapies. Our aim was to perform an integrative epigenetic analysis of invasive urothelial carcinoma of the bladder to identify the epigenetic abnormalities involved in the development and progression of this cancer. Methods: Pre-processed methylation data and RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) and processed using the R package TCGA-Assembler...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29456763/causal-effect-of-smoking-on-dna-methylation-in-peripheral-blood-a-twin-and-family-study
#9
Shuai Li, Ee Ming Wong, Minh Bui, Tuong L Nguyen, Ji-Hoon Eric Joo, Jennifer Stone, Gillian S Dite, Graham G Giles, Richard Saffery, Melissa C Southey, John L Hopper
Background: Smoking has been reported to be associated with peripheral blood DNA methylation, but the causal aspects of the association have rarely been investigated. We aimed to investigate the association and underlying causation between smoking and blood methylation. Methods: The methylation profile of DNA from the peripheral blood, collected as dried blood spots stored on Guthrie cards, was measured for 479 Australian women including 66 monozygotic twin pairs, 66 dizygotic twin pairs, and 215 sisters of twins from 130 twin families using the Infinium HumanMethylation450K BeadChip array...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29456732/two-protein-coding-genes-act-as-a-novel-clinical-signature-to-predict-prognosis-in-patients-with-ovarian-serous-cystadenocarcinoma
#10
Jue Zhang, Meng Xu, Han Gao, Jin-Chen Guo, Yu-Lin Guo, Miao Zou, Xu-Feng Wu
Ovarian cancer is the seventh most common type of cancer and the eighth most common cause of cancer-associated mortality among women. A number of studies have hypothesized that the expression status of certain genes may be used to predict prognosis in ovarian cancer. In the present study, the RNA expression data from next-generation sequencing and the clinical information of 413 patients from The Cancer Genome Atlas dataset was downloaded to identify the association between gene-expression level and the survival time of the patients with ovarian serous cystadenocarcinoma...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29456719/estrogen-receptor-%C3%AE-promoter-methylation-is-a-biomarker-for-outcome-prediction-of-cisplatin-resistance-in-triple-negative-breast-cancer
#11
Junnan Xu, Tao Sun, Xiangyu Guo, Yan Wang, Mingxi Jing
A number of previous studies have indicated the presence of a link between estrogen receptor-α (ERα) methylation and triple-negative breast cancer (TNBC). However, the association between ERα methylation and drug resistance during the treatment of TNBC remains unclear. Methylation-specific polymerase chain reaction was used to investigate the methylation of ERα in the genomic DNA of 35 patients with TNBC who were defined as cisplatin-based chemotherapy-resistant using chemosensitivity testing. Survival probabilities by covariates were assessed using Kaplan-Meier estimator survival analysis and Cox's proportional hazards models, adjusting for age, menopausal status, tumor size, lymph node metastasis and ERα promoter DNA methylation...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29456693/seminal-bacterial-composition-in-patients-with-obstructive-and-non-obstructive-azoospermia
#12
Houyang Chen, Tao Luo, Tingtao Chen, Gongxian Wang
A number of culture-dependent and -independent studies have reported that the number and significance of bacterial species in semen may have been underestimated. The aim of the present study was to profile the seminal microbiome in patients with obstructive or non-obstructive azoospermia. A high-throughput sequencing method was adopted to sequence genomic DNA extracted from the semen of healthy people (C group), patients with obstructive azoospermia (OA group) and patients with non-obstructive azoospermia (NOA group)...
March 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29456628/identification-of-influential-observations-in-high-dimensional-cancer-survival-data-through-the-rank-product-test
#13
Eunice Carrasquinha, André Veríssimo, Marta B Lopes, Susana Vinga
Background: Survival analysis is a statistical technique widely used in many fields of science, in particular in the medical area, and which studies the time until an event of interest occurs. Outlier detection in this context has gained great importance due to the fact that the identification of long or short-term survivors may lead to the detection of new prognostic factors. However, the results obtained using different outlier detection methods and residuals are seldom the same and are strongly dependent of the specific Cox proportional hazards model selected...
2018: BioData Mining
https://www.readbyqxmd.com/read/29456625/alignment-of-microbial-fitness-with-engineered-product-formation-obligatory-coupling-between-acetate-production-and-photoautotrophic-growth
#14
Wei Du, Joeri A Jongbloets, Coco van Boxtel, Hugo Pineda Hernández, David Lips, Brett G Oliver, Klaas J Hellingwerf, Filipe Branco Dos Santos
Background: Microbial bioengineering has the potential to become a key contributor to the future development of human society by providing sustainable, novel, and cost-effective production pipelines. However, the sustained productivity of genetically engineered strains is often a challenge, as spontaneous non-producing mutants tend to grow faster and take over the population. Novel strategies to prevent this issue of strain instability are urgently needed. Results: In this study, we propose a novel strategy applicable to all microbial production systems for which a genome-scale metabolic model is available that aligns the production of native metabolites to the formation of biomass...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29456553/silencing-of-iron-and-heme-related-genes-revealed-a-paramount-role-of-iron-in-the-physiology-of-the-hematophagous-vector-rhodnius-prolixus
#15
Ana B Walter-Nuno, Mabel L Taracena, Rafael D Mesquita, Pedro L Oliveira, Gabriela O Paiva-Silva
Iron is an essential element for most organisms However, free iron and heme, its complex with protoporphyrin IX, can be extremely cytotoxic, due to the production of reactive oxygen species, eventually leading to oxidative stress. Thus, eukaryotic cells control iron availability by regulating its transport, storage and excretion as well as the biosynthesis and degradation of heme. In the genome of Rhodnius prolixus , the vector of Chagas disease, we identified 36 genes related to iron and heme metabolism We performed a comprehensive analysis of these genes, including identification of homologous genes described in other insect genomes...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29456550/genomic-analysis-revealed-new-oncogenic-signatures-in-tp53-mutant-hepatocellular-carcinoma
#16
Venkatesh Kancherla, Samir Abdullazade, Matthias S Matter, Manuela Lanzafame, Luca Quagliata, Guglielmo Roma, Yujin Hoshida, Luigi M Terracciano, Charlotte K Y Ng, Salvatore Piscuoglio
The TP53 gene is the most commonly mutated gene in human cancers and mutations in TP53 have been shown to have either gain-of-function or loss-of-function effects. Using the data generated by The Cancer Genome Atlas, we sought to define the spectrum of TP53 mutations in hepatocellular carcinomas (HCCs) and their association with clinicopathologic features, and to determine the oncogenic and mutational signatures in TP53 -mutant HCCs. Compared to other cancer types, HCCs harbored distinctive mutation hotspots at V157 and R249, whereas common mutation hotspots in other cancer types, R175 and R273, were extremely rare in HCCs...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29456549/global-dna-methylation-in-the-chestnut-blight-fungus-cryphonectria-parasitica-and-genome-wide-changes-in-dna-methylation-accompanied-with-sectorization
#17
Kum-Kang So, Yo-Han Ko, Jeesun Chun, Jyotiranjan Bal, Junhyun Jeon, Jung-Mi Kim, Jaeyoung Choi, Yong-Hwan Lee, Jin Hoe Huh, Dae-Hyuk Kim
Mutation in CpBck1 , an ortholog of the cell wall integrity mitogen-activated protein kinase kinase kinase (MAPKKK) of Saccharomyces cerevisiae , in the chestnut blight fungus Cryphonectria parasitica resulted in a sporadic sectorization as culture proceeded. The progeny from the sectored area maintained the characteristics of the sector, showing a massive morphogenetic change, including robust mycelial growth without differentiation. Epigenetic changes were investigated as the genetic mechanism underlying this sectorization...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29456488/exploring-the-complexity-of-cortical-development-using-single-cell-transcriptomics
#18
REVIEW
Hyobin Jeong, Vijay K Tiwari
The developing neocortex in the mammalian brain is composed of multiple cell types including apical progenitors (AP), basal progenitors (BP), and neurons that populate three different layers, the ventricular zone (VZ), the subventricular zone (SVZ), and the cortical plate (CP). Despite recent advances, the diversity of the existing cell populations including those which are differentiating and mature, their biogenesis and the underlying gene regulatory mechanisms remain poorly known. Recent studies have taken advantage of the rapidly emerging single-cell technologies to decode the heterogeneity of cell populations at the transcriptome level during cortical development and their molecular details...
2018: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29456407/analysis-of-hepatitis-b-virus-pres1-variability-and-prevalence-of-the-rs2296651-polymorphism-in-a-spanish-population
#19
Rosario Casillas, David Tabernero, Josep Gregori, Irene Belmonte, Maria Francesca Cortese, Carolina González, Mar Riveiro-Barciela, Rosa Maria López, Josep Quer, Rafael Esteban, Maria Buti, Francisco Rodríguez-Frías
AIM: To determine the variability/conservation of the domain of hepatitis B virus (HBV) preS1 region that interacts with sodium-taurocholate cotransporting polypeptide (hereafter, NTCP-interacting domain) and the prevalence of the rs2296651 polymorphism (S267F, NTCP variant) in a Spanish population. METHODS: Serum samples from 246 individuals were included and divided into 3 groups: patients with chronic HBV infection (CHB) ( n = 41, 73% Caucasians), patients with resolved HBV infection ( n = 100, 100% Caucasians) and an HBV-uninfected control group ( n = 105, 100% Caucasians)...
February 14, 2018: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29456146/a-comprehensive-and-dated-phylogenomic-analysis-of-butterflies
#20
Marianne Espeland, Jesse Breinholt, Keith R Willmott, Andrew D Warren, Roger Vila, Emmanuel F A Toussaint, Sarah C Maunsell, Kwaku Aduse-Poku, Gerard Talavera, Rod Eastwood, Marta A Jarzyna, Robert Guralnick, David J Lohman, Naomi E Pierce, Akito Y Kawahara
Butterflies (Papilionoidea), with over 18,000 described species [1], have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species representing 98% of tribes, a 35-fold increase in gene sampling and 3-fold increase in taxon sampling over previous studies [4]...
February 14, 2018: Current Biology: CB
keyword
keyword
16873
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"