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https://www.readbyqxmd.com/read/28327601/bcip-a-gene-centered-platform-for-identifying-potential-regulatory-genes-in-breast-cancer
#1
Jiaqi Wu, Shuofeng Hu, Yaowen Chen, Zongcheng Li, Jian Zhang, Hanyu Yuan, Qiang Shi, Ningsheng Shao, Xiaomin Ying
Breast cancer is a disease with high heterogeneity. Many issues on tumorigenesis and progression are still elusive. It is critical to identify genes that play important roles in the progression of tumors, especially for tumors with poor prognosis such as basal-like breast cancer and tumors in very young women. To facilitate the identification of potential regulatory or driver genes, we present the Breast Cancer Integrative Platform (BCIP, http://omics.bmi.ac.cn/bcancer/). BCIP maintains multi-omics data selected with strict quality control and processed with uniform normalization methods, including gene expression profiles from 9,005 tumor and 376 normal tissue samples, copy number variation information from 3,035 tumor samples, microRNA-target interactions, co-expressed genes, KEGG pathways, and mammary tissue-specific gene functional networks...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325592/intersexuality-in-aquatic-invertebrates-prevalence-and-causes
#2
REVIEW
Tiago F Grilo, Rui Rosa
This review is the first assembling information on intersexuality in aquatic invertebrates, from freshwater to estuarine and marine environments. Intersex is a condition whereby an individual of a gonochorist (separate sexes) species has oocytes or distinct stages of spermatogonia, at varying degrees of development, within the normal gonad of the opposite gender (i.e. spermatocytes in the ovary or oocytes in the testis), often involving alterations in the gonadal structure, reproductive tract or external genitalia...
March 18, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28325553/metabolomics-through-the-lens-of-precision-cardiovascular-medicine
#3
REVIEW
Sin Man Lam, Yuan Wang, Bowen Li, Jie Du, Guanghou Shui
Metabolomics, which targets at the extensive characterization and quantitation of global metabolites from both endogenous and exogenous sources, has emerged as a novel technological avenue to advance the field of precision medicine principally driven by genomics-oriented approaches. In particular, metabolomics has revealed the cardinal roles that the environment exerts in driving the progression of major diseases threatening public health. Herein, the existent and potential applications of metabolomics in two key areas of precision cardiovascular medicine will be critically discussed: 1) the use of metabolomics in unveiling novel disease biomarkers and pathological pathways; 2) the contribution of metabolomics in cardiovascular drug development...
March 8, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28324583/revisiting-cdk-inhibitors-for-treatment-of-glioblastoma-multiforme
#4
REVIEW
Dorota Lubanska, Lisa Porter
Despite extensive efforts and continual progress in research and medicine, outcomes for patients with high-grade glioma remain exceptionally poor. Over the past decade, research has revealed a great deal about the complex biology behind glioma development, and has brought to light some of the major barriers preventing successful treatment. Glioblastoma multiforme (GBM) (stage 4 astrocytoma) is a highly dynamic tumour and one of the most extreme examples of intratumoural heterogeneity, making targeting with specific therapeutics an inefficient and highly unpredictable goal...
March 21, 2017: Drugs in R&D
https://www.readbyqxmd.com/read/28324299/fatal-familial-insomnia-clinical-aspects-and-molecular-alterations
#5
REVIEW
Franc Llorens, Juan-José Zarranz, Andre Fischer, Inga Zerr, Isidro Ferrer
PURPOSE OF REVIEW: Fatal familiar insomnia (FFI) is an autosomal dominant inherited prion disease caused by D178N mutation in the prion protein gene (PRNP D178N) accompanied by the presence of a methionine at the codon 129 polymorphic site on the mutated allele. FFI is characterized by severe sleep disorder, dysautonomia, motor signs and abnormal behaviour together with primary atrophy of selected thalamic nuclei and inferior olives, and expansion to other brain regions with disease progression...
April 2017: Current Neurology and Neuroscience Reports
https://www.readbyqxmd.com/read/28322544/graphene-oxide-quantum-dots-as-novel-nanozymes-for-alcohol-intoxication
#6
Anqi Sun, Li Mu, Xiangang Hu
Alcohol overconsumption as a worldwide issue results in alcoholic liver disease (ALD), such as steatosis, alcoholic hepatitis and cirrhosis. The treatment of ALD has been widely investigated but remains challenging. In this work, the protective effects of graphene oxide quantum dots (GOQDs) as novel nanozymes against alcohol overconsumption are discovered, and the specific mechanisms underlying these effects are elucidated via omics analysis. GOQDs dramatically alleviate the reduction of cell viability induced by ethanol and can act as nanozymes to accelerate ethanol metabolism and avoid the accumulation of toxic intermediates in cells...
March 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28321398/unveiling-the-metabolic-changes-on-muscle-cell-metabolism-underlying-p-phenylenediamine-toxicity
#7
Igor Marín de Mas, Silvia Marín, Gisela Pachón, Juan C Rodríguez-Prados, Pedro Vizán, Josep J Centelles, Romà Tauler, Amaya Azqueta, Vitaly Selivanov, Adela López de Ceraín, Marta Cascante
Rhabdomyolysis is a disorder characterized by acute damage of the sarcolemma of the skeletal muscle leading to release of potentially toxic muscle cell components into the circulation, most notably creatine phosphokinase (CK) and myoglobulin, and is frequently accompanied by myoglobinuria. In the present work, we evaluated the toxicity of p-phenylenediamine (PPD), a main component of hair dyes which is reported to induce rhabdomyolysis. We studied the metabolic effect of this compound in vivo with Wistar rats and in vitro with C2C12 muscle cells...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28321390/metabonomics-research-progress-on-liver-diseases
#8
REVIEW
Mengqian Yu, Ying Zhu, Qingwei Cong, Chunyan Wu
Metabolomics as the new omics technique develops after genomics, transcriptomics, and proteomics and has rapid development at present. Liver diseases are worldwide public health problems. In China, chronic hepatitis B and its secondary diseases are the common liver diseases. They can be diagnosed by the combination of history, virology, liver function, and medical imaging. However, some patients seldom have relevant physical examination, so the diagnosis may be delayed. Many other liver diseases, such as drug-induced liver injury (DILI), alcoholic liver disease (ALD) and nonalcoholic fatty liver disease (NAFLD), and autoimmune liver diseases, still do not have definite diagnostic markers; the diagnosis consists of history, medical imaging, and the relevant score...
2017: Canadian Journal of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28319856/systems-biology-solutions-for-biochemical-production-challenges
#9
REVIEW
Anne Sofie Lærke Hansen, Rebecca M Lennen, Nikolaus Sonnenschein, Markus J Herrgård
There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions...
March 16, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28319609/developmental-alterations-in-huntington-s-disease-neural-cells-and-pharmacological-rescue-in-cells-and-mice
#10
(no author information available yet)
Neural cultures derived from Huntington's disease (HD) patient-derived induced pluripotent stem cells were used for 'omics' analyses to identify mechanisms underlying neurodegeneration. RNA-seq analysis identified genes in glutamate and GABA signaling, axonal guidance and calcium influx whose expression was decreased in HD cultures. One-third of gene changes were in pathways regulating neuronal development and maturation. When mapped to stages of mouse striatal development, the profiles aligned with earlier embryonic stages of neuronal differentiation...
March 20, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28317029/listeriomics-an-interactive-web-platform-for-systems-biology-of-listeria
#11
Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i...
March 2017: MSystems
https://www.readbyqxmd.com/read/28316329/xerotolerant-bacteria-surviving-through-a-dry-spell
#12
REVIEW
Pedro H Lebre, Pieter De Maayer, Don A Cowan
Water is vital for many biological processes and is essential for all living organisms. However, numerous macroorganisms and microorganisms have adapted to survive in environments in which water is scarce; such organisms are collectively termed xerotolerant. With increasing global desertification due to climate change and human-driven desertification processes, it is becoming ever more important to understand how xerotolerant organisms cope with a lack of water. In this Review, we discuss the environmental, physiological and molecular adaptations that enable xerotolerant bacteria to survive in environments in which water is scarce and highlight insights from modern 'omics' technologies...
March 20, 2017: Nature Reviews. Microbiology
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
#13
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/28315793/highlighting-the-effects-of-coumarin-on-adult-plants-of-arabidopsis-thaliana-l-heynh-by-an-integrated-omic-approach
#14
Fabrizio Araniti, Monica Scognamiglio, Angela Chambery, Rosita Russo, Assunta Esposito, Brigida D'Abrosca, Antonio Fiorentino, Antonio Lupini, Francesco Sunseri, Maria Rosa Abenavoli
In this study, the effects of the allelochemical coumarin through a metabolomic, proteomic and morpho-physiological approach in Arabidopsis adult plants (25days old) were investigated. Metabolomic analysis evidenced an increment of amino acids and a high accumulation of soluble sugars, after 6days of coumarin treatment. This effect was accompanied by a strong decrease on plant fresh and dry weights, as well as on total protein content. On the contrary, coumarin did not affect leaf number but caused a reduction in leaf area...
March 1, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28314769/infrared-spectroscopic-characterization-of-monocytic-microvesicles-microparticles-released-upon-lipopolysaccharide-stimulation
#15
Joonsup Lee, Beryl Wen, Elizabeth A Carter, Valery Combes, Georges E R Grau, Peter A Lay
Microvesicles (MVs) are involved in cell-cell interactions, including disease pathogenesis. Nondestructive Fourier-transform infrared (FTIR) spectra from MVs were assessed as a technique to provide new biochemical insights into a LPS-induced monocyte model of septic shock. FTIR spectroscopy provided a quick method to investigate relative differences in biomolecular content of different MV populations that was complementary to traditional semiquantitative omics approaches, with which it is difficult to provide information on relative changes between classes (proteins, lipids, nucleic acids, carbohydrates) or protein conformations...
March 17, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28314298/multi-omics-profiling-of-patients-with-melanoma-treated-with-nivolumab-in-project-hope
#16
Shusuke Yoshikawa, Yoshio Kiyohara, Masaki Otsuka, Ryota Kondou, Chizu Nonomura, Haruo Miyata, Akira Iizuka, Keiichi Ohshima, Kenichi Urakami, Takeshi Nagashima, Masatoshi Kusuhara, Takashi Sugino, Tohru Mochizuki, Ken Yamaguchi, Yasuto Akiyama
BACKGROUND: Project HOPE (High-tech Omics-based Patient Evaluation) has been in progress since 2014 and uses whole-exome sequencing (WES) and gene expression profiling (GEP). Among a total of 1,685 patients with cancer, 13 with melanoma were registered and characterized using multi-omics analyses to investigate specific biomarkers in responders to programmed cell death-1 (PD-1) blockade. MATERIALS AND METHODS: The patients with melanoma comprised of six males and seven females, and their mean age was 68 years...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28303220/anemone-medicinal-plants-ethnopharmacology-phytochemistry-and-biology
#17
REVIEW
Da-Cheng Hao, Xiaojie Gu, Peigen Xiao
The Ranunculaceae genus Anemone (order Ranunculales), comprising more than 150 species, mostly herbs, has long been used in folk medicine and worldwide ethnomedicine. Various medicinal compounds have been found in Anemone plants, especially triterpenoid saponins, some of which have shown anti-cancer activities. Some Anemone compounds and extracts display immunomodulatory, anti-inflammatory, antioxidant, and antimicrobial activities. More than 50 species have ethnopharmacological uses, which provide clues for modern drug discovery...
March 2017: Acta Pharmaceutica Sinica. B
https://www.readbyqxmd.com/read/28302550/the-22q11-2-deletion-syndrome-in-congenital-heart-defects-prevalence-of-microdeletion-syndrome-in-cameroon
#18
Ambroise Wonkam, Ricardo Toko, David Chelo, Cedrik Tekendo-Ngongang, Samuel Kingue, Sophie Dahoun
BACKGROUND: The 22q11.2 deletion syndrome is amongst the most common microdeletion syndrome in humans. Its prevalence remains unknown in sub-Saharan Africa, and its clinical features are under-reported for people of African descent. OBJECTIVE: We have investigated the prevalence of the 22q11.2 deletion syndrome in patients with congenital heart defects in Cameroon. METHODS: A total of 70 of 100 cases of congenital cardiac malformation with echocardiographic evidence were examined prospectively and tested for the 22q11...
March 13, 2017: Global Heart
https://www.readbyqxmd.com/read/28302330/precision-surgery-for-colorectal-liver-metastases-opportunities-and-challenges-of-omics-based-decision-making
#19
REVIEW
R P Jones, K W Brudvik, J M Franklin, G J Poston
Precision surgery involves improving patient selection to ensure that surgical intervention that is proven to benefit on a population level is the optimal treatment for each individual patient. For patients with colorectal liver metastases (CRLM), existing prognostic scoring systems rely on well-recognised histopathological features such as size and number of lesions. Advances in preoperative imaging algorithms mean that increasingly low volume disease can be detected, improving assessment of these factors...
March 6, 2017: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28302035/translational-multimodality-neuroimaging
#20
Sushil K Sharma
Recently high-resolution, noninvasive, multimodality in-vivo molecular imaging with PET, SPECT, CT and MRI, employing fusion algorithms has revolutionized personalized medicine. However, specific radiopharmaceuticals (RPs) for the accurate diagnosis and effective treatment of progressive neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, drug addiction, and other cognitive impairments still remain in developmental phase. Currently, multimodality fusion neuroimaging is utilized for the determination of: pharmacokinetics and pre-clinical development of radiopharmaceuticals (RPs); in-vivo monitoring of stem cell transplantation therapy; nicotinic acetylcholine receptors (nAChRs) investigations; and regional cerebral blood flow and glucose metabolism in cognitively-impaired subjects employing noninvasive microPET and nano-SPECT imaging...
March 15, 2017: Current Drug Targets
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