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https://www.readbyqxmd.com/read/28641268/newgoa-predicting-new-go-annotations-of-proteins-by-bi-random-walks-on-a-hybrid-graph
#1
Guoxian Yu, Guangyuan Fu, Jun Wang, Yingwen Zhao
A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many of them are incomplete. We proposed a method called NewGOA to predict new Gene Ontology (GO) annotations for incompletely annotated proteins and for completely un-annotated ones. NewGOA employs a hybrid graph, composed of two types of nodes (proteins and GO terms), to encode interactions between proteins, hierarchical relationships between terms and available annotations of proteins...
June 15, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28641181/the-caveolae-dress-code-structure-and-signaling
#2
REVIEW
Christophe Lamaze, Nicolas Tardif, Melissa Dewulf, Stéphane Vassilopoulos, Cédric M Blouin
Over the past decade, interest in caveolae biology has peaked. These small bulb-shaped plasma membrane invaginations of 50-80nm diameter present in most cell types have been upgraded from simple membrane structures to a more complex bona fide organelle. However, although caveolae are involved in several essential cellular functions and pathologies, the underlying molecular mechanisms remain poorly defined. Following the identification of caveolins and cavins as the main caveolae constituents, recent studies have brought new insight into their structural organization as a coat...
June 19, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28641164/protective-effects-of-flavonoids-against-alzheimer-s-disease-related-neural-dysfunctions
#3
REVIEW
Mahsa Bakhtiari, Yunes Panahi, Javad Ameli, Behrad Darvishi
Senile ages of human life is mostly associated with developmental of several neurological complicated conditions including decreased cognition and reasoning, increased memory loss and impaired language performance. Alzheimer's disease (AD) is the most prevalent neural disorder associated with dementia, consisting of about 70% of dementia reported cases. Failure of currently approved chemical anti-AD therapeutic agents has once again brought up the idea of administering naturally occurring compounds as effective alternative and/or complementary regimens in AD treatment...
June 19, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28641158/determinants-of-cortisol-during-pregnancy-the-abcd-cohort
#4
Laura S Bleker, Tessa J Roseboom, Tanja G Vrijkotte, Rebecca M Reynolds, Susanne R de Rooij
BACKGROUND: Psychosocial stress during pregnancy has been proposed as a major contributor of glucocorticoid-mediated programming of the fetal hypothalamic-pituitary adrenal (HPA) axis, with later adverse health consequences. However, evidence linking maternal stress to maternal cortisol values during pregnancy is inconclusive. A possible explanation for this is that other maternal factors overshadow any potential effects of stress on cortisol levels. We studied a large cohort of pregnant women with extensive data on pregnancy characteristics to determine the respective contributions of biological, environmental and psychosocial stress factors to cortisol levels in pregnancy...
May 31, 2017: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28641126/dna-requirements-for-interaction-of-the-c-terminal-region-of-ku80-with-the-dna-dependent-protein-kinase-catalytic-subunit-dna-pkcs
#5
Sarvan Kumar Radhakrishnan, Susan P Lees-Miller
Non-homologous end joining (NHEJ) is the major pathway for the repair of ionizing radiation induced DNA double strand breaks (DSBs) in human cells. Critical to NHEJ is the DNA-dependent interaction of the Ku70/80 heterodimer with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form the DNA-PK holoenzyme. However, precisely how Ku recruits DNA-PKcs to DSBs ends to enhance its kinase activity has remained enigmatic, with contradictory findings reported in the literature. Here we address the role of the Ku80 C-terminal region (CTR) in the DNA-dependent interaction of Ku70/80 with DNA-PKcs using purified components and defined DNA structures...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28641117/structural-components-of-nuclear-integrity-with-gene-regulatory-potential
#6
REVIEW
Kelli D Fenelon, Sevan Hopyan
The nucleus is a mechanosensitive and load-bearing structure. Structural components of the nucleus interact to maintain nuclear integrity and have become subjects of exciting research that is relevant to cell and developmental biology. Here we outline the boundaries of what is known about key architectural elements within the nucleus and highlight their potential structural and transcriptional regulatory functions.
June 19, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28641056/the-odd-couple-using-biomedical-and-intersectional-approaches-to-address-health-inequities
#7
Olena Hankivsky, Lesley Doyal, Gillian Einstein, Ursula Kelly, Janet Shim, Lynn Weber, Robin Repta
BACKGROUND: Better understanding and addressing health inequities is a growing global priority. OBJECTIVE: In this paper, we contribute to the literature examining complex relationships between biological and social dimensions in the field of health inequalities. Specifically, we explore the potential of intersectionality to advance current approaches to socio-biological entwinements. DESIGN: We provide a brief overview of current approaches to combining both biological and social factors in a single study, and then investigate the contributions of an intersectional framework to such work...
January 2017: Global Health Action
https://www.readbyqxmd.com/read/28641051/beneficial-role-of-citrus-fruit-polyphenols-against-hepatic-dysfunctions-a-review
#8
Md Mohabbulla Mohib, Kazi Afnan, Tasfiq Zaman Paran, Salma Khan, Juthika Sarker, Nahid Hasan, Istiaque Hasan, Md Abu Taher Sagor
Alcoholic liver diseases and virus-induced hepatic dysfunctions are prevalent in western countries. Evidence also suggests that hyperglycemia and insulin resistance are key players in the development of hepatic diseases and their complications. Since the comorbid diseases like obesity, diabetes and vascular dysfunctions primarily affect liver, the modern therapies against other hepatic dysfunctions are becoming a major challenge to treat. In addition to these, polypharmacy and adverse drug reactions (ADRs) are further aggravating the phenomenon...
June 22, 2017: Journal of Dietary Supplements
https://www.readbyqxmd.com/read/28641048/updates-and-current-challenges-in-microrna-research-for-personalized-medicine-in-ovarian-cancer
#9
Victoria Mandilaras, Mégane Vernon, Matthieu Meryet-Figuière, Katherine Karakasis, Bernard Lambert, Laurent Poulain, Amit Oza, Christophe Denoyelle, Stephanie Lheureux
Ovarian cancer (OC) is the second most common and the most lethal of the gynecological malignancies. Currently, there exists no effective screening tool for OC. MicroRNAs (miRNAs) are endogenous 18-23 nucleotide non-coding RNAs that refine gene expression. MiRNAs have been found to be aberrantly expressed in OC tumor tissue as well as detectable in biological fluids such as the blood, urine, and ascites and have been proposed as biomarkers and therapeutic targets for OC. Areas covered: This review summarizes the current knowledge regarding the application of miRNAs as diagnostic, prognostic, and predictive biomarkers in OC...
June 22, 2017: Expert Opinion on Biological Therapy
https://www.readbyqxmd.com/read/28641043/radiogenomics-of-high-grade-serous-ovarian-cancer-multireader-multi-institutional-study-from-the-cancer-genome-atlas-ovarian-cancer-imaging-research-group
#10
Hebert Alberto Vargas, Erich P Huang, Yulia Lakhman, Joseph E Ippolito, Priya Bhosale, Vincent Mellnick, Atul B Shinagare, Maria Anello, Justin Kirby, Brenda Fevrier-Sullivan, John Freymann, C Carl Jaffe, Evis Sala
Purpose To evaluate interradiologist agreement on assessments of computed tomography (CT) imaging features of high-grade serous ovarian cancer (HGSOC), to assess their associations with time-to-disease progression (TTP) and HGSOC transcriptomic profiles (Classification of Ovarian Cancer [CLOVAR]), and to develop an imaging-based risk score system to predict TTP and CLOVAR profiles. Materials and Methods This study was a multireader, multi-institutional, institutional review board-approved, HIPAA-compliant retrospective analysis of 92 patients with HGSOC (median age, 61 years) with abdominopelvic CT before primary cytoreductive surgery available through the Cancer Imaging Archive...
June 22, 2017: Radiology
https://www.readbyqxmd.com/read/28641005/electron-crystallography-reveals-atomic-structures-of-metal-organic-nanoplates-with-m12-%C3%AE-3-o-8-%C3%AE-3-oh-8-%C3%AE-2-oh-6-m-zr-hf-secondary-building-units
#11
Ruihan Dai, Fei Peng, Pengfei Ji, Kuangda Lu, Cheng Wang, Junliang Sun, Wenbin Lin
Nanoscale metal-organic frameworks (nMOFs) have shown tremendous potential in cancer therapy and biomedical imaging. However, their small dimensions present a significant challenge in structure determination by single-crystal X-ray crystallography. We report here the structural determination of nMOFs by rotation electron diffraction (RED). Two isostructural Zr- and Hf-based nMOFs with linear biphenyldicarboxylate (BPDC) or bipyridinedicarboxylate (BPYDC) linkers are stable under intense electron beams to allow the collection of high-quality RED data, which reveal a MOF structure with M12(μ3-O)8(μ3-OH)8(μ2-OH)6 (M = Zr, Hf) secondary building units (SBUs)...
June 22, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28641003/synthesis-and-anti-inflammatory-evaluation-of-2-aminobenzaldehydes-via-ir-iii-catalyzed-c-h-amidation-of-aldimines-with-acyl-azides
#12
Saegun Kim, Prashant Chakrasali, Hyo Sun Suh, Neeraj Kumar Mishra, Taeyoung Kim, Sang Hoon Han, Hyung Sik Kim, Byung-Moo Lee, Soo Bong Han, In Su Kim
The aldimine-directed C-H amidation of various arenes with N-acyl azides as amidation surrogates under cationic iridium(III) catalysis is described. This transformation efficiently provides a range of 2-aminobenzaldehydes derivatives with excellent site-selectivity and functional group compatibility. The resulting 2-aminobenzaldehyde framework provides facile access to a range of biologically interesting heterocycles. In addition, all synthetic compounds were screened for anti-inflammatory activity against interleukin-1β (IL-1β) and tumor necrosis factor alpha (TNF-α) with lipopolysaccharide (LPS)-induced RAW264...
June 22, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28640998/oximes-and-hydrazones-in-bioconjugation-mechanism-and-catalysis
#13
Dominik K Kölmel, Eric T Kool
The formation of oximes and hydrazones is employed in numerous scientific fields as a simple and versatile conjugation strategy. This imine-forming reaction is applied in fields as diverse as polymer chemistry, biomaterials and hydrogels, dynamic combinatorial chemistry, organic synthesis, and chemical biology. Here we outline chemical developments in this field, with special focus on the past ∼10 years of developments. Recent strategies for installing reactive carbonyl groups and α-nucleophiles into biomolecules are described...
June 22, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28640995/colloidal-gold-nanoparticles-induce-changes-in-cellular-and-subcellular-morphology
#14
Xiaowei Ma, Raimo Hartmann, Dorleta Jimenez de Aberasturi, Fang Yang, Stefaan J H Soenen, Bella B Manshian, Jonas Franz, Daniel Valdeperez, Beatriz Pelaz, Neus Feliu, Norbert Hampp, Christoph Riethmüller, Henning Vieker, Natalie Frese, Armin Gölzhäuser, Michael Simonich, Robert L Tanguay, Xing-Jie Liang, Wolfgang J Parak
Exposure of cells to colloidal nanoparticles (NPs) can have concentration-dependent harmful effects. Mostly, such effects are monitored with biochemical assays or probes from molecular biology, i.e. viability assays, gene expression profiles, etc., neglecting that the presence of NPs can also drastically affect cellular morphology. In the case of polymer-coated Au NPs we demonstrate that upon NP internalization, cells undergo lysosomal swelling, alterations in mitochondrial morphology, disturbances in actin and tubulin cytoskeleton and associated signaling, and reduction of focal adhesion contact area and number of filopodia...
June 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28640972/understanding-adaptogenic-activity-specificity-of-the-pharmacological-action-of-adaptogens-and-other-phytochemicals
#15
REVIEW
Alexander Panossian
Adaptogens are stress-response modifiers that increase an organism's nonspecific resistance to stress by increasing its ability to adapt and survive. The classical reductionist model is insufficiently complex to explain the mechanistic aspects of the physiological notion of "adaptability" and the adaptogenic activity of adaptogens. Here, I demonstrate that (1) the mechanisms of action of adaptogens are impossible to rationally describe using the reductionist concept of pharmacology, whereas the network pharmacology approach is the most suitable method; and (2) the principles of systems biology and pharmacological networks appear to be more suitable for conceptualizing adaptogen function and are applicable to any phytochemical...
June 22, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28640952/label-free-dynamic-mass-redistribution-and-bio-impedance-methods-for-drug-discovery
#16
Manuel Grundmann
Label-free biosensors are increasingly employed in drug discovery. Cell-based biosensors provide valuable insights into the biological consequences of exposing cells and tissues to chemical agents and the underlying molecular mechanisms associated with these effects. Optical biosensors based on the detection of dynamic mass redistribution (DMR) and impedance biosensors using cellular dielectric spectroscopy (CDS) capture changes of the cytoskeleton of living cells in real time. Because signal transduction correlates with changes in cell morphology, DMR and CDS biosensors are exquisitely suited for recording integrated cell responses in an unbiased, yet pathway-specific manner without the use of labels that may interfere with cell function...
June 22, 2017: Current Protocols in Pharmacology
https://www.readbyqxmd.com/read/28640929/modulation-of-tumor-microenvironment-by-chemopreventive-natural-products
#17
REVIEW
Sin-Aye Park, Young-Joon Surh
The tumor microenvironment provides a niche in which cancer cells and their surrounding stromal cells reside and in which their interactions occur. The cross talk between cancer and stromal cells in the tumor microenvironment promotes many biological processes to support cancer cell growth, invasion, angiogenesis, and metastasis. Recently, not only cancer cells but also multiple types of surrounding stromal cells, including endothelial cells, immune cells, and fibroblasts in the tumor microenvironment, have been recognized to be attractive targets for reducing resistance to anticancer therapy and tumor recurrence...
June 22, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28640894/characterization-and-analysis-of-long-non-coding-rna-lncrna-in-in-vitro-and-ex-vivo-derived-cardiac-progenitor-cells
#18
Baron Arnone, Jake Y Chen, Gangjian Qin
Recent advancements in cell-based therapies for the treatment of cardiovascular disease (CVD) show continuing promise for the use of transplanted stem and cardiac progenitor cells (CPCs) to promote cardiac restitution. However, a detailed understanding of the molecular mechanisms that control the development of these cells remains incomplete and is critical for optimizing their use in such therapy. Long non-coding (lnc) RNA has recently emerged as a crucial class of regulatory molecules involved in directing a variety of critical biological processes including development, homeostasis and disease...
2017: PloS One
https://www.readbyqxmd.com/read/28640878/genetic-loci-associated-with-coronary-artery-disease-harbor-evidence-of-selection-and-antagonistic-pleiotropy
#19
Sean G Byars, Qin Qin Huang, Lesley-Ann Gray, Andrew Bakshi, Samuli Ripatti, Gad Abraham, Stephen C Stearns, Michael Inouye
Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28640862/a-biosystems-approach-to-identify-the-molecular-signaling-mechanisms-of-tmem30a-during-tumor-migration
#20
Jiao Wang, Qian Wang, Dongfang Lu, Fangfang Zhou, Dong Wang, Ruili Feng, Kai Wang, Robert Molday, Jiang Xie, Tieqiao Wen
Understanding the molecular mechanisms underlying cell migration, which plays an important role in tumor growth and progression, is critical for the development of novel tumor therapeutics. Overexpression of transmembrane protein 30A (TMEM30A) has been shown to initiate tumor cell migration, however, the molecular mechanisms through which this takes place have not yet been reported. Thus, we propose the integration of computational and experimental approaches by first predicting potential signaling networks regulated by TMEM30A using a) computational biology methods, b) our previous mass spectrometry results of the TMEM30A complex in mouse tissue, and c) a number of migration-related genes manually collected from the literature, and subsequently performing molecular biology experiments including the in vitro scratch assay and real-time quantitative polymerase chain reaction (qPCR) to validate the reliability of the predicted network...
2017: PloS One
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