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https://www.readbyqxmd.com/read/28110480/casubtype-an-r-package-to-identify-gene-sets-predictive-of-cancer-subtypes-and-clinical-outcomes
#1
Hualei Kong, Pan Tong, Xiaodong Zhao, Jielin Sun, Hua Li
In the past decade, molecular classification of cancer has gained high popularity owing to its high predictive power on clinical outcomes as compared with traditional methods commonly used in clinical practice. In particular, using gene expression profiles, recent studies have successfully identified a number of gene sets for the delineation of cancer subtypes that are associated with distinct prognosis. However, identification of such gene sets remains a laborious task due to the lack of tools with flexibility, integration and ease of use...
January 21, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28110275/traces-of-strong-selective-pressures-in-the-genomes-of-c4-grasses
#2
Pascal-Antoine Christin
C4 photosynthesis is nature's response to CO2 limitations, and evolved recurrently in several groups of plants. To identify genes related to C4 photosynthesis, Huang et al. looked for evidence of past episodes of adaptive evolution in the genomes of C4 grasses. They identified a large number of candidate genes that evolved under divergent selection, indicating that, besides alterations to expression patterns, the history of C4 involved strong selection on protein-coding sequences.
January 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28110220/hypoxia-inducing-factor-hif-1%C3%AE-derived-peptide-capable-of-inducing-cancer-reactive-cytotoxic-t-lymphocytes-from-hla-a24-patients-with-renal-cell-carcinoma
#3
Takafumi Minami, Naoki Matsumura, Koichi Sugimoto, Nobutaka Shimizu, Marco De Velasco, Masahiro Nozawa, Kazuhiro Yoshimura, Nanae Harashima, Mamoru Harada, Hirotsugu Uemura
Hypoxic tumor microenvironment makes cancer cells to be therapy-resistant and hypoxia-inducing factors (HIFs) play a central role in hypoxic adaptation. Especially, renal cell carcinoma (RCC) is often associated with von Hippel-Lindau (VHL) gene mutations, leading to up-regulation of HIFs. However, from a different point of view, this suggests the possibility that HIFs could be promising targets in anti-cancer therapy. In this study, we searched for HIF-1α-derived peptides that are able to induce RCC-reactive cytotoxic T lymphocytes (CTLs) from HLA-A24(+) RCC patients...
January 19, 2017: International Immunopharmacology
https://www.readbyqxmd.com/read/28110219/tgf-%C3%AE-engineered-mesenchymal-stem-cells-tgf-%C3%AE-mscs-for-treatment-of-type-1-diabetes-t1d-mice-model
#4
Saeed Daneshmandi, Mohammad Hossein Karimi, Ali Akbar Pourfathollah
OBJECTIVE: Mesenchymal stem cells (MSCs) are advantageous candidates for cell therapy of Type 1 diabetes (T1D). Considering immunomodulatory effect of MSC, in this study, we engineered MSCs with TGF-β gene to increase MSC potency for T1D therapy in mouse model. MATERIALS AND METHODS: Two plans were designed for prevention and treatment of diabetes, respectively. In both of them, MSCs were injected i.v. and then, the diabetes features including serum insulin, blood glucose, glucose tolerance, splenocytes proliferation, and IL-4/IFN-γ production were evaluated...
January 19, 2017: International Immunopharmacology
https://www.readbyqxmd.com/read/28110208/inflammatory-pathway-genes-associated-with-inter-individual-variability-in-the-trajectories-of-morning-and-evening-fatigue-in-patients-receiving-chemotherapy
#5
Fay Wright, Marilyn Hammer, Steven M Paul, Bradley E Aouizerat, Kord M Kober, Yvette P Conley, Bruce A Cooper, Laura B Dunn, Jon D Levine, Gail DEramo Melkus, Christine Miaskowski
Fatigue, a highly prevalent and distressing symptom during chemotherapy (CTX), demonstrates diurnal and interindividual variability in severity. Little is known about the associations between variations in genes involved in inflammatory processes and morning and evening fatigue severity during CTX. The purposes of this study, in a sample of oncology patients (N=543) with breast, gastrointestinal (GI), gynecological (GYN), or lung cancer who received two cycles of CTX, were to determine whether variations in genes involved in inflammatory processes were associated with inter-individual variability in initial levels as well as in the trajectories of morning and evening fatigue...
January 19, 2017: Cytokine
https://www.readbyqxmd.com/read/28110021/the-application-of-crispr-technology-to-high-content-screening-in-primary-neurons
#6
Ben L Callif, Brian Maunze, Nick L Krueger, Matthew T Simpson, Murray G Blackmore
Axon growth is coordinated by multiple interacting proteins that remain incompletely characterized. High content screening (HCS), in which manipulation of candidate genes is combined with rapid image analysis of phenotypic effects, has emerged as a powerful technique to identify key regulators of axon outgrowth. Here we explore the utility of a genome editing approach referred to as CRISPR (Clustered Regularly Interspersed Palindromic Repeats) for knockout screening in primary neurons. In the CRISPR approach a DNA-cleaving Cas enzyme is guided to genomic target sequences by user-created guide RNA (sgRNA), where it initiates a double-stranded break that ultimately results in frameshift mutation and loss of protein production...
January 18, 2017: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/28109907/circadian-gene-variants-and-breast-cancer
#7
Edyta Reszka, Monika Przybek, Olav Muurlink, Beata Peplonska
The endogenous and self-sustained circadian rhythm generated and maintained in suprachiasmatic nucleus and peripheral tissues can coordinate various molecular, biochemical and physiological processes in living organisms resulting in the adaptation to environmental cues, e.g. light. Multifactorial breast cancer etiology also involves circadian gene alterations, especially among individuals exposed to light at night. Indeed, shift work that causes circadian disruption has been classified by the International Agency for Research on Cancer as a probable human carcinogen, group 2A...
January 18, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28109636/management-of-non-variceal-upper-gastrointestinal-bleeding-position-statement-of-the-catalan-society-of-gastroenterology
#8
Pilar García-Iglesias, Josep-Maria Botargues, Faust Feu Caballé, Càndid Villanueva Sánchez, Xavier Calvet Calvo, Enric Brullet Benedi, Gabriel Cánovas Moreno, Esther Fort Martorell, Marta Gallach Montero, Emili Gené Tous, José-Manuel Hidalgo Rosas, Amelia Lago Macía, Ana Nieto Rodríguez, Michel Papo Berger, Montserrat Planella de Rubinat, Joan Saló Rich, Rafel Campo Fernández de Los Ríos
In recent years there have been advances in the management of non-variceal upper gastrointestinal bleeding that have helped reduce rebleeding and mortality. This document positioning of the Catalan Society of Digestologia is an update of evidence-based recommendations on management of gastrointestinal bleeding peptic ulcer.
January 18, 2017: Gastroenterología y Hepatología
https://www.readbyqxmd.com/read/28109622/genetics-for-the-identification-of-lipid-targets-beyond-pcsk9
#9
REVIEW
Linda R Wang, Robert A Hegele
From studies of rare families to genome-wide associations in populations, understanding of human genetics has accelerated the search for new drug targets for the prevention of atherosclerotic cardiovascular disease. DNA sequencing and genome-wide analyses of DNA markers have illuminated rare as well as common variants in genes that regulate lipids and ultimately atherosclerosis risk. A recent innovative approach called Mendelian randomization can endorse specific genes and variants as causative not just for lipid disturbances, but also for clinical cardiovascular end points...
November 11, 2016: Canadian Journal of Cardiology
https://www.readbyqxmd.com/read/28109190/qtl-mapping-and-candidate-genes-for-resistance-to-fusarium-ear-rot-and-fumonisin-contamination-in-maize
#10
Valentina Maschietto, Cinzia Colombi, Raul Pirona, Giorgio Pea, Francesco Strozzi, Adriano Marocco, Laura Rossini, Alessandra Lanubile
BACKGROUND: Fusarium verticillioides is a common maize pathogen causing ear rot (FER) and contamination of the grains with the fumonisin B1 (FB1) mycotoxin. Resistance to FER and FB1 contamination are quantitative traits, affected by environmental conditions, and completely resistant maize genotypes to the pathogen are so far unknown. In order to uncover genomic regions associated to reduced FER and FB1 contamination and identify molecular markers for assisted selection, an F2:3 population of 188 progenies was developed crossing CO441 (resistant) and CO354 (susceptible) genotypes...
January 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28108964/heme-oxygenase-1-defects-lead-to-reduced-chlorophyll-in-brassica-napus
#11
Lixia Zhu, Zonghui Yang, Xinhua Zeng, Jie Gao, Jie Liu, Bin Yi, Chaozhi Ma, Jinxiong Shen, Jinxing Tu, Tingdong Fu, Jing Wen
We previously described a Brassica napus chlorophyll-deficient mutant (ygl) with yellow-green seedling leaves and mapped the related gene, BnaC.YGL, to a 0.35 cM region. However, the molecular mechanisms involved in this chlorophyll defect are still unknown. In this study, the BnaC07.HO1 gene (equivalent to BnaC.YGL) was isolated by the candidate gene approach, and its function was confirmed by genetic complementation. Comparative sequencing analysis suggested that BnaC07.HO1 was lost in the mutant, while a long noncoding-RNA was inserted into the promoter of the homologous gene BnaA07...
January 20, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28108657/risearch2-suffix-array-based-large-scale-prediction-of-rna-rna-interactions-and-sirna-off-targets
#12
Ferhat Alkan, Anne Wenzel, Oana Palasca, Peter Kerpedjiev, Anders Frost Rudebeck, Peter F Stadler, Ivo L Hofacker, Jan Gorodkin
Intermolecular interactions of ncRNAs are at the core of gene regulation events, and identifying the full map of these interactions bears crucial importance for ncRNA functional studies. It is known that RNA-RNA interactions are built up by complementary base pairings between interacting RNAs and high level of complementarity between two RNA sequences is a powerful predictor of such interactions. Here, we present RIsearch2, a large-scale RNA-RNA interaction prediction tool that enables quick localization of potential near-complementary RNA-RNA interactions between given query and target sequences...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108401/constitutive-expression-and-characterization-of-a-surface-srs-ncsrs67-protein-of-neospora-caninum-with-no-orthologue-in-toxoplasma-gondii
#13
Marcos Alexandre Bezerra, Luiz Miguel Pereira, Aline Bononi, Carla Agostino Biella, Luciana Baroni, Leticia Pollo-Oliveira, Ana Patrícia Yatsuda
Neospora caninum is a parasite of the Apicomplexa phylum responsible for abortion and losses of fertility in cattle. As part of its intracellular cycle, the first interaction of the parasite with the target cell is performed with the surface proteins known as the SRS superfamily (Surface Antigen Glycoprotein - Related Sequences). SAG related or SRS proteins have been a target of intense research due to its immunodominant pattern, exhibiting potential as diagnostic and/or vaccine candidates. The aim of this study was the cloning, expression and characterization of the gene NcSRS67 of N...
January 17, 2017: Parasitology International
https://www.readbyqxmd.com/read/28108330/pleiotropic-responses-to-methionine-restriction
#14
Gene Ables, Jay Johnson
Methionine restriction (MR) extends lifespan across different species. The main responses of rodent models to MR are well-documented in adipose tissue (AT) and liver, which have reduced mass and improved insulin sensitivity, respectively. Recently, molecular mechanisms that improve healthspan have been identified in both organs during MR. In fat, MR induced a futile lipid cycle concomitant with beige AT accumulation, producing elevated energy expenditure. In liver, MR upregulated fibroblast growth factor 21 and improved glucose metabolism in aged mice and in response to a high-fat diet...
January 17, 2017: Experimental Gerontology
https://www.readbyqxmd.com/read/28108275/benzofuran-2-acetic-ester-derivatives-induce-apoptosis-in-breast-cancer-cells-by-upregulating-p21-cip-waf1-gene-expression-in-p53-independent-manner
#15
Cinzia Giordano, Daniela Rovito, Ines Barone, Raffaella Mancuso, Daniela Bonofiglio, Francesca Giordano, Stefania Catalano, Bartolo Gabriele, Sebastiano Andò
Breast cancer is the most common malignancy and the leading cause of cancer-related death in women worldwide. High toxicity of used chemotherapeutics and resistance of cancer cells to treatments are a driving force for searching the new drug candidates for breast cancer therapy. In this study, we tested the antiproliferative effects of a series of benzofuran-2-acetic methyl ester derivatives, synthesized by a palladium-catalyzed carbonylative heterocyclization approach, on breast cancer cells. We observed that benzofuran compounds bearing a phenyl or tert-butyl substituent α to the methoxycarbonyl group significantly inhibited anchorage-dependent and -independent cell growth, and induced G0/G1 cell cycle arrest in human estrogen receptor alpha positive (MCF-7 and T47D) and in triple negative MDA-MB-231 breast cancer cells, without affecting growth of MCF-10A normal breast epithelial cells...
January 15, 2017: DNA Repair
https://www.readbyqxmd.com/read/28108032/disruption-of-the-sheep-bmpr-ib-gene-by-crispr-cas9-in-in%C3%A2-vitro-produced-embryos
#16
Xuemei Zhang, Wenrong Li, Yangsheng Wu, Xinrong Peng, Bian Lou, Liqin Wang, Mingjun Liu
BMPR-IB (also known as FecB) is a key candidate gene for the genetic control of sheep reproductive performance. Loss-of-function mutations in the sheep BMPR-IB gene lead to an increase in ovulation rate and consequently larger litter size. However, the BMPR-IB gene has been identified in only a few sheep breeds. To improve sheep reproduction through modification of the BMPR-IB gene, we designed an sgRNA to target the sheep BMPR-IB gene by using the CRISPR/Cas9 system. First, we performed gene editing by injecting Cas9/sgRNA into the cytoplasm of one-cell fertilized eggs...
November 9, 2016: Theriogenology
https://www.readbyqxmd.com/read/28107812/tissue-resolved-gene-structure-refined-equine-transcriptome
#17
T A Mansour, E Y Scott, C J Finno, R R Bellone, M J Mienaltowski, M C Penedo, P J Ross, S J Valberg, J D Murray, C T Brown
BACKGROUND: Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome...
January 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28107663/antibacterial-anti-oxidant-electroactive-injectable-hydrogel-as-self-healing-wound-dressing-with-hemostasis-and-adhesiveness-for-cutaneous-wound-healing
#18
Xin Zhao, Hao Wu, Baolin Guo, Ruonan Dong, Yusheng Qiu, Peter X Ma
Injectable self-healing hydrogel dressing with multifunctional properties including anti-infection, anti-oxidative and conductivity promoting wound healing process will be highly desired in wound healing application and its design is still a challenge. We developed a series of injectable conductive self-healed hydrogels based on quaternized chitosan-g-polyaniline (QCSP) and benzaldehyde group functionalized poly(ethylene glycol)-co-poly(glycerol sebacate) (PEGS-FA) as antibacterial, anti-oxidant and electroactive dressing for cutaneous wound healing...
January 11, 2017: Biomaterials
https://www.readbyqxmd.com/read/28107443/identification-of-the-pla2g6-c-1579g-a-missense-mutation-in-papillon-dog-neuroaxonal-dystrophy-using-whole-exome-sequencing-analysis
#19
Masaya Tsuboi, Manabu Watanabe, Kazumi Nibe, Natsuko Yoshimi, Akihisa Kato, Masahiro Sakaguchi, Osamu Yamato, Miyuu Tanaka, Mitsuru Kuwamura, Kazuya Kushida, Takashi Ishikura, Tomoyuki Harada, James Kenn Chambers, Sumio Sugano, Kazuyuki Uchida, Hiroyuki Nakayama
Whole exome sequencing (WES) has become a common tool for identifying genetic causes of human inherited disorders, and it has also recently been applied to canine genome research. We conducted WES analysis of neuroaxonal dystrophy (NAD), a neurodegenerative disease that sporadically occurs worldwide in Papillon dogs. The disease is considered an autosomal recessive monogenic disease, which is histopathologically characterized by severe axonal swelling, known as "spheroids," throughout the nervous system. By sequencing all eleven DNA samples from one NAD-affected Papillon dog and her parents, two unrelated NAD-affected Papillon dogs, and six unaffected control Papillon dogs, we identified 10 candidate mutations...
2017: PloS One
https://www.readbyqxmd.com/read/28107441/fine-mapping-and-candidate-gene-analysis-of-the-tiller-suppression-gene-ts1-in-rice
#20
Lei Liu, Fen Meng, Yonggang He, Menghao Zhu, Yanhao Shen, Zhihong Zhang
Tiller number is one of the key factors that influences rice plant type and yield components. In this study, an EMS-induced rice tiller suppression mutant ts1 was characterized. Morphological and histological observations revealed that, in the ts1 plants, the tiller buds were abnormally formed and therefore cannot outgrow into tillers. With an F2 population derived from a cross between ts1 and an indica cultivar Wushansimiao, a major gene, tiller suppression 1 (ts1) was fine-mapped to a 108.5 kb genomic region between markers ID8378 and SSR6884 on the short arm of rice chromosome 2...
2017: PloS One
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