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https://www.readbyqxmd.com/read/29050306/the-hyaluronan-mediated-motility-receptor-rhamm-promotes-growth-invasiveness-and-dissemination-of-colorectal-cancer
#1
Valentina Mele, Lena Sokol, Viktor Hendrik Kölzer, Dennis Pfaff, Manuele Giuseppe Muraro, Irene Keller, Zahnd Stefan, Irene Centeno, Luigi Maria Terracciano, Heather Dawson, Inti Zlobec, Giandomenica Iezzi, Alessandro Lugli
In colorectal cancer (CRC), RHAMM is an independent adverse prognostic factor. The aim of the study was therefore to investigate on the role of RHAMM as a potential direct driver of cell proliferation and migration in CRC cell lines and to identify pathways dependent on RHAMM in human CRC. Proliferation, cell cycle alterations and invasive capacity were tested in two RHAMM- and control- knockdown CRC cell lines by flow cytometry and in vitro assays. Tumorigenicity and metastasis formation was assessed in immunodeficient mice...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050246/nrf2-regulated-metabolic-gene-signature-as-a-prognostic-biomarker-in-non-small-cell-lung-cancer
#2
Akhileshwar Namani, Qin Qin Cui, Yihe Wu, Hongyan Wang, Xiu Jun Wang, Xiuwen Tang
Mutations in Kelch-like ECH-associated protein 1 (KEAP1) cause the aberrant activation of nuclear factor erythroid-derived 2-like 2 (NRF2), which leads to oncogenesis and drug resistance in lung cancer cells. Our study was designed to identify the genes involved in lung cancer progression targeted by NRF2. A series of microarray experiments in normal and cancer cells, as well as in animal models, have revealed regulatory genes downstream of NRF2 that are involved in wide variety of pathways. Specifically, we carried out individual and combinatorial microarray analysis of KEAP1 overexpression and NRF2 siRNA-knockdown in a KEAP1 mutant-A549 non-small cell lung cancer (NSCLC) cell line...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049916/immune-cell-type-fingerprints-at-the-basis-of-outcome-diversity-of-human-infection
#3
REVIEW
Shelly Hen-Avivi, Roi Avraham
Despite the availability of antibiotics and immunization, infectious diseases remain a major cause of malignancy and death worldwide. Yet, it is well documented that for most infectious agents, clinical disease develops in only a small minority of infected individuals. There is, in fact, great heterogeneity in infection outcome, from complete clearance of the pathogen to severe illness. Understanding this variation remains elusive, despite its great potential to equip us with new tools for the treatment of infectious diseases...
October 16, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29049419/multi-time-series-rna-seq-analysis-of-enterobacter-lignolyticus-scf1-during-growth-in-lignin-amended-medium
#4
Roberto Orellana, Gina Chaput, Lye Meng Markillie, Hugh Mitchell, Matt Gaffrey, Galya Orr, Kristen M DeAngelis
The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth conditions with lignin as sole carbon source...
2017: PloS One
https://www.readbyqxmd.com/read/29048636/genome-wide-study-of-er-regulated-lncrnas-shows-ap000439-3-may-function-as-a-key-regulator-of-cell-cycle-in-breast-cancer
#5
Yin Zhang, Dan-Lan Wang, Hai-Yan Yan, Jian-You Liao, Jie-Hua He, Kai-Shun Hu, Wei-Xi Deng, Yan-Jie Wang, Hong-Tao Xing, H Phillip Koeffler, Dong Yin
Estrogen receptor (ER) plays important roles in cell growth, development and tumorigenesis. Although ER-regulated genes have been extensively investigated, little is known about roles of ER-regulated lncRNAs in breast cancer. Here, we conducted genome-wide study of ER-regulated lncRNAs by using RNA-seq, ChIP-seq and TCGA data. A total of identified 114 ER-regulated lncRNAs were identified, many of them were overexpressed in ER+ breast cancer and co-expressed with some key regulators. Silencing one of most prominent lncRNA, AP000439...
September 20, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29048528/pervasive-transcription-of-mitochondrial-plastid-and-nucleomorph-genomes-across-diverse-plastid-bearing-species
#6
Matheus Sanitá Lima, David Roy Smith
Organelle genomes exhibit remarkable diversity in content, structure, and size, and in their modes of gene expression, which are governed by both organelle- and nuclear-encoded machinery. Next generation sequencing (NGS) has generated unprecedented amounts of genomic and transcriptomic data, which can be used to investigate organelle genome transcription. However, most of the available eukaryotic RNA-sequencing (RNA-seq) data are used to study nuclear transcription only, even though large numbers of organelle-derived reads can typically be mined from these experiments...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29048434/common-microrna-mrna-interactions-exist-among-distinct-porcine-ipsc-lines-independent-of-their-metastable-pluripotent-states
#7
Shiqiang Zhang, Youlong Xie, Hongxia Cao, Huayan Wang
Previous evidences have proved that porcine-induced pluripotent stem cells (piPSCs) could be induced to distinctive metastable pluripotent states. This raises the issue of whether there is a common transcriptomic profile existing among the piPSC lines at distinctive state. In this study, we performed conjoint analysis of small RNA-seq and mRNA-seq for three piPSC lines which represent LIF dependence, FGF2 dependence and LFB2i dependence, respectively. Interestingly, we found there are 16 common microRNAs which potentially target 13 common mRNAs among the three piPSC lines...
August 31, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/29047334/a-support-vector-machine-based-method-to-distinguish-long-non-coding-rnas-from-protein-coding-transcripts
#8
Hugo W Schneider, Taina Raiol, Marcelo M Brigido, Maria Emilia M T Walter, Peter F Stadler
BACKGROUND: In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An important problem to be addressed when analyzing this data is distinguishing between long non-coding RNAs (lncRNAs) and protein coding transcripts (PCTs). Thus, we present a Support Vector Machine (SVM) based method to distinguish lncRNAs from PCTs, using features based on frequencies of nucleotide patterns and ORF lengths, in transcripts...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29047256/analysis-of-genes-with-alternatively-spliced-transcripts-in-the-leaf-root-panicle-and-seed-of-rice-using-a-long-oligomer-microarray-and-rna-seq
#9
Songhwa Chae, Joung Sug Kim, Kyong Mi Jun, Sang-Bok Lee, Myung Soon Kim, Baek Hie Nahm, Yeon-Ki Kim
Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes...
October 17, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/29046677/defining-genome-wide-expression-and-phenotypic-contextual-cues-in-macrophages-generated-by-granulocyte-macrophage-colony-stimulating-factor-macrophage-colony-stimulating-factor-and-heat-killed-mycobacteria
#10
Samer Bazzi, Emale El-Darzi, Tina McDowell, Helmout Modjtahedi, Satvinder Mudan, Marcel Achkar, Charles Akle, Humam Kadara, Georges M Bahr
Heat-killed (HK) Mycobacterium obuense (NCTC13365) is currently being evaluated in the clinic as an immunotherapeutic agent for cancer treatment. Yet, the molecular underpinnings underlying immunomodulatory properties of HK M. obuense are still largely undefined. To fill this void, we sought to perform immunophenotyping, chemokine/cytokine release analysis and genome-wide characterization of monocyte-derived macrophages (MDM) in which monocytes were originally isolated from healthy donors and differentiated by HK M...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29046501/characterization-of-amylolytic-enzyme-overproducing-mutant-of-aspergillus-luchuensis-obtained-by-ion-beam-mutagenesis
#11
Toshihiro Kojo, Chihiro Kadooka, Marisa Komohara, Shiori Onitsuka, Miya Tanimura, Yukiko Muroi, Shugo Kurazono, Yohei Shiraishi, Ken Oda, Kazuhiro Iwashita, Masahira Onoue, Kayu Okutsu, Yumiko Yoshizaki, Kazunori Takamine, Taiki Futagami, Kazuki Mori, Hisanori Tamaki
Aspergillus luchuensis is a kuro (black) koji fungus that has been used as a starch degrader for the awamori- and shochu-making industries in Japan. In this study, we investigated the effect of ion beam irradiation on A. luchuensis RIB2601 and obtained a high starch-degrading mutant strain U1. Strain U1 showed reduced growth rate, whereas it showed higher α-amylase, glucoamylase, and α-glucosidase activities on a mycelial mass basis than the wild type (wt) strain both on agar plates and in rice koji. In addition, strain U1 showed higher N-acetylglucosamine content in the cell wall and higher sensitivity to calcofluor white, suggesting a deficiency in cell wall composition...
October 17, 2017: Journal of General and Applied Microbiology
https://www.readbyqxmd.com/read/29046479/lipoprotein-lipase-reaches-the-capillary-lumen-in-chickens-despite-an-apparent-absence-of-gpihbp1
#12
Cuiwen He, Xuchen Hu, Rachel S Jung, Mikael Larsson, Yiping Tu, Sandra Duarte-Vogel, Paul Kim, Norma P Sandoval, Tara R Price, Christopher M Allan, Brian Raney, Haibo Jiang, André Bensadoun, Rosemary L Walzem, Richard I Kuo, Anne P Beigneux, Loren G Fong, Stephen G Young
In mammals, GPIHBP1 is absolutely essential for transporting lipoprotein lipase (LPL) to the lumen of capillaries, where it hydrolyzes the triglycerides in triglyceride-rich lipoproteins. In all lower vertebrate species (e.g., birds, amphibians, reptiles, fish), a gene for LPL can be found easily, but a gene for GPIHBP1 has never been found. The obvious question is whether the LPL in lower vertebrates is able to reach the capillary lumen. Using purified antibodies against chicken LPL, we showed that LPL is present on capillary endothelial cells of chicken heart and adipose tissue, colocalizing with von Willebrand factor...
October 19, 2017: JCI Insight
https://www.readbyqxmd.com/read/29046445/the-impacts-of-genome-wide-analyses-on-our-understanding-of-human-herpesvirus-diversity-and-evolution
#13
Daniel W Renner, Moriah L Szpara
Until fairly recently, genome-wide evolutionary dynamics and within-host diversity were more commonly examined in the context of small viruses, than large double-stranded DNA viruses such as herpesviruses. The high mutation rates and more compact genomes of RNA viruses have inspired the investigation of population dynamics for these species, and recent data now suggest that herpesviruses might also be considered candidates for population modeling. High-throughput sequencing (HTS) and bioinformatics have expanded our understanding of herpesviruses through genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures...
October 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29046389/the-antibody-repertoire-of-colorectal-cancer
#14
Seong Won Cha, Stefano Bonissone, Seungjin Na, Pavel A Pevzner, Vineet Bafna
Immunotherapy is becoming increasingly important in the fight against cancers, utilizing and manipulating the body's immune response to treat tumors. Understanding the immune repertoire - the collection of immunological proteins - of treated and untreated cells is possible at the genomic, but technically difficult at the protein level. Standard protein databases do not include the highly divergent sequences of somatic rearranged immunoglobulin genes, and may lead to missed identifications in a mass spectrometry search...
October 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29046340/nnt-is-a-key-regulator-of-adrenal-redox-homeostasis-and-steroidogenesis-in-male-mice
#15
Eirini Meimaridou, Michelle Goldsworthy, Vasileios Chortis, Ersi Fragouli, Paul A Foster, Wiebke Arlt, Roger Cox, Louise A Metherell
Nicotinamide nucleotide transhydrogenase, NNT, is a ubiquitous protein of the inner mitochondrial membrane with a key role in mitochondrial redox balance. NNT produces high concentrations of NADPH for detoxification of reactive oxygen species by glutathione and thioredoxin pathways. In humans, NNT dysfunction leads to an adrenal specific disorder, glucocorticoid deficiency. Certain sub-strains of C57BL/6 mice contain a spontaneously occurring inactivating Nnt mutation and display glucocorticoid deficiency along with glucose intolerance and reduced insulin secretion...
October 18, 2017: Journal of Endocrinology
https://www.readbyqxmd.com/read/29046014/tomato-cry1a-plays-a-critical-role-in-the-regulation-of-phytohormone-homeostasis-plant-development-and-carotenoid-metabolism-in-fruits
#16
Chao-Chao Liu, Golam Jalal Ahammed, Guo-Ting Wang, Chang-Jie Xu, Kun-Song Chen, Yan-Hong Zhou, Jing-Quan Yu
Blue light photoreceptors, cryptochromes (CRYs), regulate multiple aspects of plant growth and development. However, our knowledge of CRYs is predominantly based on model plant Arabidopsis at early growth stage. In this study, we elucidated functions of CRY1a gene in mature tomato (Solanum lycopersicum) plants by using cry1a mutants and CRY1a overexpressing lines (OE-CRY1a-1 and OE-CRY1a-2). In comparison with wild-type plants, cry1a mutants are relatively tall, accumulate low biomass and bear more fruits, whereas OE-CRY1a plants are short stature, and they not only flower lately but also bear less fruits...
October 18, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29045593/a-teleost-androgen-promotes-development-of-primary-ovarian-follicles-in-coho-salmon-and-rapidly-alters-the-ovarian-transcriptome
#17
Christopher Monson, Kristy Forsgren, Giles Goetz, Louisa Harding, Penny Swanson, Graham Young
Recent studies using several teleost models have revealed that androgens increase the size of previtellogenic (primary and/or early secondary) ovarian follicles. To explore our hypothesis that androgens drive the development of primary follicles into early secondary follicles, and to determine the mechanisms underlying these androgenic effects, we exposed juvenile coho salmon to near-physiological and relatively sustained levels of the non-aromatizable androgen 11-ketotestosterone (11-KT). This resulted in significant growth of primary ovarian follicles after 10 and 20 days, with follicles after 20 days displaying a morphological phenotype characteristic of early secondary follicles (presence of cortical alveoli)...
October 13, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29045536/the-warburg-effect-persistence-of-stem-cell-metabolism-in-cancers-as-a-failure-of-differentiation
#18
M Riester, Q Xu, A Moreira, J Zheng, F Michor, R J Downey
BACKGROUND: Two recent observations regarding the Warburg effect are that (i) the metabolism of stem cells is constitutive ('aerobic') glycolysis while normal cellular differentiation involves a transition to oxidative phosphorylation and (ii) the degree of glucose uptake of a malignancy as imaged by 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) is associated with histologic measures of tumor differentiation. Combining these observations, we hypothesized that the high levels of glucose uptake observed in poorly differentiated cancers may reflect persistence of the glycolytic metabolism of stem cells in malignant cells that fail to fully differentiate...
October 13, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29045406/microrna-profiling-of-human-primary-macrophages-exposed-to-dengue-virus-identifies-mirna-3614-5p-as-antiviral-and-regulator-of-adar1-expression
#19
Mayra Diosa-Toro, Liliana Echavarría-Consuegra, Jacky Flipse, Geysson Javier Fernández, Joost Kluiver, Anke van den Berg, Silvio Urcuqui-Inchima, Jolanda M Smit
BACKGROUND: Due to the high burden of dengue disease worldwide, a better understanding of the interactions between dengue virus (DENV) and its human host cells is of the outmost importance. Although microRNAs modulate the outcome of several viral infections, their contribution to DENV replication is poorly understood. METHODS AND PRINCIPAL FINDINGS: We investigated the microRNA expression profile of primary human macrophages challenged with DENV and deciphered the contribution of microRNAs to infection...
October 18, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29045404/transcriptomic-responses-of-biomphalaria-pfeifferi-to-schistosoma-mansoni-investigation-of-a-neglected-african-snail-that-supports-more-s-mansoni-transmission-than-any-other-snail-species
#20
Sarah K Buddenborg, Lijing Bu, Si-Ming Zhang, Faye D Schilkey, Gerald M Mkoji, Eric S Loker
BACKGROUND: Biomphalaria pfeifferi is highly compatible with the widespread human-infecting blood fluke Schistosoma mansoni and transmits more cases of this parasite to people than any other snail species. For these reasons, B. pfeifferi is the world's most important vector snail for S. mansoni, yet we know relatively little at the molecular level regarding the interactions between B. pfeifferi and S. mansoni from early-stage sporocyst transformation to the development of cercariae. METHODOLOGY/PRINCIPAL FINDINGS: We sought to capture a portrait of the response of B...
October 18, 2017: PLoS Neglected Tropical Diseases
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