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https://www.readbyqxmd.com/read/29772837/conventional-pathology-versus-gene-signatures-for-assessing-luminal-a-and-b-type-breast-cancers-results-of-a-prospective-cohort-study
#1
Julia E C van Steenhoven, Anne Kuijer, Paul J van Diest, Joost M van Gorp, Marieke Straver, Sjoerd G Elias, Jelle Wesseling, Emiel Rutgers, Johanna N H Timmer-Bonte, Peter Nieboer, Tineke J Smilde, Alex Imholz, Charlotte F J M Blanken, Sabine Siesling, Thijs van Dalen
In this study, in estrogen receptor positive (ER+) early stage breast cancer patients who were considered candidates for 70-gene signature (70-GS, "MammaPrint") use, we compared molecular subtyping (MS) based on the previously validated 80-gene signature (80-GS, "BluePrint") versus surrogate pathological subtyping (PS). Between 1 January 2013 and 31 December 2015, 595 clinical intermediate risk ER+ early stage breast cancer patients were enrolled. Hormone receptor (HR) and HER2 receptor status were determined by conventional pathology using immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH)...
May 17, 2018: Genes
https://www.readbyqxmd.com/read/29772825/identification-and-characterization-of-the-wox-family-genes-in-five-solanaceae-species-reveal-their-conserved-roles-in-peptide-signaling
#2
Xiaoxu Li, Madiha Hamyat, Cheng Liu, Ahmad Salman, Xiaoming Gao, Cun Guo, Yuanying Wang, Yongfeng Guo
Members of the plant-specific WOX (WUSCHEL-related homeobox) transcription factor family have been reported to play important roles in peptide signaling that regulates stem cell maintenance and cell fate specification in various developmental processes. Even though remarkable advances have been made in studying WOX genes in Arabidopsis , little is known about this family in Solanaceae species. A total of 45 WOX members from five Solanaceae species were identified, including eight members from Solanum tuberosum , eight from Nicotiana tomentosiformis , 10 from Solanum lycopersicum , 10 from Nicotiana sylvestris and nine from Nicotiana tabacum ...
May 17, 2018: Genes
https://www.readbyqxmd.com/read/29772814/chronic-and-occult-hepatitis-b-virus-infection-in-pregnant-women-in-botswana
#3
Tshepiso Mbangiwa, Ishmael Kasvosve, Motswedi Anderson, Prisca K Thami, Wonderful T Choga, Austen Needleman, Bonolo B Phinius, Sikhulile Moyo, Melvin Leteane, Jean Leidner, Jason T Blackard, Gloria Mayondi, Betsy Kammerer, Rosemary M Musonda, Max Essex, Shahin Lockman, Simani Gaseitsiwe
The hepatitis B virus (HBV) is a global problem; however, the burden of HBV infection in pregnant women in Botswana is unknown. We sought to determine the prevalence of chronic and occult HBV infection in human immunodeficiency virus (HIV)-infected and -uninfected pregnant women in Botswana. Samples from 752 pregnant women were tested for hepatitis B surface antigen (HBsAg), and HBsAg-positive samples were tested for hepatitis B e antigen (HBeAg) and HBV DNA load. Samples that were HBsAg negative were screened for occult HBV infection by determining the HBV DNA load...
May 17, 2018: Genes
https://www.readbyqxmd.com/read/29772787/the-cross-entropy-based-multi-filter-ensemble-method-for-gene-selection
#4
Yingqiang Sun, Chengbo Lu, Xiaobo Li
The gene expression profile has the characteristics of a high dimension, low sample, and continuous type, and it is a great challenge to use gene expression profile data for the classification of tumor samples. This paper proposes a cross-entropy based multi-filter ensemble (CEMFE) method for microarray data classification. Firstly, multiple filters are used to select the microarray data in order to obtain a plurality of the pre-selected feature subsets with a different classification ability. The top N genes with the highest rank of each subset are integrated so as to form a new data set...
May 17, 2018: Genes
https://www.readbyqxmd.com/read/29772783/atpap2-a-unique-member-of-the-pap-family-functions-in-the-plasma-membrane
#5
Qingqing Sun, Jinyu Li, Wenzhen Cheng, Huihong Guo, Xiaomin Liu, Hongbo Gao
Purple acid phosphatases (PAPs) play various physiological roles in plants. AtPAP2 was previously shown to localize to both chloroplasts and mitochondria and to modulate carbon metabolism in Arabidopsis . Over-expression of AtPAP2 resulted in faster growth and increased biomass in several plant species, indicating its great potential for crop improvement of phosphate use and yield. Here, we studied the localization of AtPAP2 by transient expression in tobacco leaves. The results showed AtPAP2 was localized to the plasma membrane through the secretory pathway, which is different from previous studies...
May 17, 2018: Genes
https://www.readbyqxmd.com/read/29772742/characterization-of-antimicrobial-resistance-determinants-and-class-1-and-class-2-integrons-in-salmonella-enterica-spp-multidrug-resistant-isolates-from-pigs
#6
Héctor Argüello, Beatriz Guerra, Irene Rodríguez, Pedro Rubio, Ana Carvajal
Antimicrobial resistance (AMR) and Salmonella spp., are primary concerns in public health. The present study characterizes the AMR determinants of 62 multi-drug resistant (MDR) Salmonella enterica spp., isolates from swine, which were obtained between 2004⁻2006, a major source of human salmonellosis. The AMR determinants were investigated by PCR, checking the presence of class 1 and class 2 integrons and 29 resistance genes. Genes sul1 , blaTEM1 -like, aadA2 , tet (A), and dfrA12 were more prevalent ( p < 0...
May 16, 2018: Genes
https://www.readbyqxmd.com/read/29772684/the-changing-landscape-in-the-genetic-etiology-of-human-tooth-agenesis
#7
REVIEW
Meredith A Williams, Ariadne Letra
Despite much progress in understanding the genetics of syndromic tooth agenesis (TA), the causes of the most common, isolated TA remain elusive. Recent studies have identified novel genes and variants contributing to the etiology of TA, and revealed new pathways in which tooth development genes belong. Further, the use of new research approaches including next-generation sequencing has provided increased evidence supporting an oligogenic inheritance model for TA, and may explain the phenotypic variability of the condition...
May 16, 2018: Genes
https://www.readbyqxmd.com/read/29762547/the-role-of-transposable-elements-in-speciation
#8
REVIEW
Antonio Serrato-Capuchina, Daniel R Matute
Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition...
May 15, 2018: Genes
https://www.readbyqxmd.com/read/29762495/role-of-sdia-on-biofilm-formation-by-atypical-enteropathogenic-escherichia-coli
#9
Hebert F Culler, Samuel C F Couto, Juliana S Higa, Renato M Ruiz, Min J Yang, Vanessa Bueris, Marcia R Franzolin, Marcelo P Sircili
Atypical enteropathogenic Escherichia coli are capable to form biofilm on biotic and abiotic surfaces, regardless of the adherence pattern displayed. Several E. coli mechanisms are regulated by Quorum sensing (QS), including virulence factors and biofilm formation. Quorum sensing is a signaling system that confers bacteria with the ability to respond to chemical molecules known as autoinducers. Suppressor of division inhibitor (SdiA) is a QS receptor present in atypical enteropathogenic E. coli (aEPEC) that detects acyl homoserine lactone (AHL) type autoinducers...
May 15, 2018: Genes
https://www.readbyqxmd.com/read/29758014/investigating-the-epigenetic-discrimination-of-identical-twins-using-buccal-swabs-saliva-and-cigarette-butts-in-the-forensic-setting
#10
Athina Vidaki, Vivian Kalamara, Elena Carnero-Montoro, Timothy D Spector, Jordana T Bell, Manfred Kayser
Monozygotic (MZ) twins are typically indistinguishable via forensic DNA profiling. Recently, we demonstrated that epigenetic differentiation of MZ twins is feasible; however, proportions of twin differentially methylated CpG sites (tDMSs) identified in reference-type blood DNA were not replicated in trace-type blood DNA. Here we investigated buccal swabs as typical forensic reference material, and saliva and cigarette butts as commonly encountered forensic trace materials. As an analog to a forensic case, we analyzed one MZ twin pair...
May 14, 2018: Genes
https://www.readbyqxmd.com/read/29757968/erratum-dan-li-et-al-transcription-factor-and-lncrna-regulatory-networks-identify-key-elements-in-lung-adenocarcinoma-genes-2018-9-12
#11
Dan Li, William Yang, Jialing Zhang, Jack Y Yang, Renchu Guan, Mary Qu Yang
The authors wish to make the following change to their paper [...].
May 14, 2018: Genes
https://www.readbyqxmd.com/read/29751692/brain-mitochondria-aging-and-parkinson-s-disease
#12
REVIEW
Mario Rango, Nereo Bresolin
This paper reconsiders the role of mitochondria in aging and in Parkinson's Disease (PD). The most important risk factor for PD is aging. Alterations in mitochondrial activity are typical of aging. Mitochondrial aging is characterized by decreased oxidative phosphorylation, proteasome activity decrease, altered autophagy, and mitochondrial dysfunction. Beyond declined oxidative phosphorylation, mitochondrial dysfunction consists of a decline of beta-oxidation as well as of the Krebs cycle. Not inherited mitochondrial DNA (mtDNA) mutations are acquired over time and parallel the decrease in oxidative phosphorylation...
May 11, 2018: Genes
https://www.readbyqxmd.com/read/29751691/selecting-the-best-evolutionary-engineering-of-chemical-production-in-microbes
#13
REVIEW
Denis Shepelin, Anne Sofie Lærke Hansen, Rebecca Lennen, Hao Luo, Markus J Herrgård
Microbial cell factories have proven to be an economical means of production for many bulk, specialty, and fine chemical products. However, we still lack both a holistic understanding of organism physiology and the ability to predictively tune enzyme activities in vivo, thus slowing down rational engineering of industrially relevant strains. An alternative concept to rational engineering is to use evolution as the driving force to select for desired changes, an approach often described as evolutionary engineering...
May 11, 2018: Genes
https://www.readbyqxmd.com/read/29751669/mapping-grain-iron-and-zinc-content-quantitative-trait-loci-in-an-iniadi-derived-immortal-population-of-pearl-millet
#14
Sushil Kumar, Charles Tom Hash, Thirunavukkarasu Nepolean, Mahesh D Mahendrakar, Chellapilla Tara Satyavathi, Govind Singh, Abhishek Rathore, Rattan S Yadav, Rajeev Gupta, Rakesh K Srivastava
Pearl millet is a climate-resilient nutritious crop requiring low inputs and is capable of giving economic returns in marginal agro-ecologies. In this study, we report large-effect iron (Fe) and zinc (Zn) content quantitative trait loci ( QTLs) using diversity array technology (DArT) and simple sequence repeats (SSRs) markers to generate a genetic linkage map using 317 recombinant inbred line (RIL) population derived from the (ICMS 8511-S1-17-2-1-1-B-P03 × AIMP 92901-S1-183-2-2-B-08) cross. The base map [seven linkage groups (LGs)] of 196 loci was 964...
May 11, 2018: Genes
https://www.readbyqxmd.com/read/29748516/journey-into-bone-models-a-review
#15
REVIEW
Julia Scheinpflug, Moritz Pfeiffenberger, Alexandra Damerau, Franziska Schwarz, Martin Textor, Annemarie Lang, Frank Schulze
Bone is a complex tissue with a variety of functions, such as providing mechanical stability for locomotion, protection of the inner organs, mineral homeostasis and haematopoiesis. To fulfil these diverse roles in the human body, bone consists of a multitude of different cells and an extracellular matrix that is mechanically stable, yet flexible at the same time. Unlike most tissues, bone is under constant renewal facilitated by a coordinated interaction of bone-forming and bone-resorbing cells. It is thus challenging to recreate bone in its complexity in vitro and most current models rather focus on certain aspects of bone biology that are of relevance for the research question addressed...
May 10, 2018: Genes
https://www.readbyqxmd.com/read/29748504/trna-derived-small-rna-a-novel-regulatory-small-non-coding-rna
#16
REVIEW
Siqi Li, Zhengping Xu, Jinghao Sheng
Deep analysis of next-generation sequencing data unveils numerous small non-coding RNAs with distinct functions. Recently, fragments derived from tRNA, named as tRNA-derived small RNA (tsRNA), have attracted broad attention. There are mainly two types of tsRNAs, including tRNA-derived stress-induced RNA (tiRNA) and tRNA-derived fragment (tRF), which differ in the cleavage position of the precursor or mature tRNA transcript. Emerging evidence has shown that tsRNAs are not merely tRNA degradation debris but have been recognized to play regulatory roles in many specific physiological and pathological processes...
May 10, 2018: Genes
https://www.readbyqxmd.com/read/29748492/transcription-factor-binding-site-enrichment-analysis-in-co-expression-modules-in-celiac-disease
#17
Irati Romero-Garmendia, Koldo Garcia-Etxebarria, Hector Hernandez-Vargas, Izortze Santin, Amaia Jauregi-Miguel, Leticia Plaza-Izurieta, Marie-Pierre Cros, Maria Legarda, Iñaki Irastorza, Zdenko Herceg, Nora Fernandez-Jimenez, Jose Ramon Bilbao
The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD). Differential co-expression modules were identified in the acute and chronic responses to gliadin using expression data from a previous microarray study in duodenal biopsies. Transcription factor binding site (TFBS) and Gene Ontology (GO) annotation enrichment analyses were performed in differentially co-expressed genes (DCGs) and selection of candidate regulators was performed...
May 10, 2018: Genes
https://www.readbyqxmd.com/read/29747453/chitinase-mrna-levels-determined-by-qpcr-in-crab-eating-monkey-macaca-fascicularis-tissues-species-specific-expression-of-acidic-mammalian-chitinase-and-chitotriosidase
#18
Maiko Uehara, Eri Tabata, Kazuhiro Ishii, Akira Sawa, Misa Ohno, Masayoshi Sakaguchi, Vaclav Matoska, Peter O Bauer, Fumitaka Oyama
Mice and humans express two active chitinases: acidic mammalian chitinase (AMCase) and chitotriosidase (CHIT1). Both chitinases are thought to play important roles in specific pathophysiological conditions. The crab-eating monkey ( Macaca fascicularis ) is one of the most frequently used nonhuman primate models in basic and applied biomedical research. Here, we performed gene expression analysis of two chitinases in normal crab-eating monkey tissues by way of quantitative real-time polymerase chain reaction (qPCR) using a single standard DNA molecule...
May 9, 2018: Genes
https://www.readbyqxmd.com/read/29735924/the-oncojanus-paradigm-of-respiratory-complex-i
#19
REVIEW
Giulia Leone, Houda Abla, Giuseppe Gasparre, Anna Maria Porcelli, Luisa Iommarini
Mitochondrial respiratory function is now recognized as a pivotal player in all the aspects of cancer biology, from tumorigenesis to aggressiveness and chemotherapy resistance. Among the enzymes that compose the respiratory chain, by contributing to energy production, redox equilibrium and oxidative stress, complex I assumes a central role. Complex I defects may arise from mutations in mitochondrial or nuclear DNA, in both structural genes or assembly factors, from alteration of the expression levels of its subunits, or from drug exposure...
May 7, 2018: Genes
https://www.readbyqxmd.com/read/29734690/regulation-of-the-x-chromosome-in-the-germline-and-soma-of-drosophila-melanogaster-males
#20
Eliza Argyridou, John Parsch
During the evolution of heteromorphic sex chromosomes, the sex-specific Y chromosome degenerates, while the X chromosome evolves new mechanisms of regulation. Using bioinformatic and experimental approaches, we investigate the expression of the X chromosome in Drosophila melanogaster . We observe nearly complete X chromosome dosage compensation in male somatic tissues, but not in testis. The X chromosome contains disproportionately fewer genes with high expression in testis than the autosomes, even after accounting for the lack of dosage compensation, which suggests that another mechanism suppresses their expression in the male germline...
May 4, 2018: Genes
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