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https://www.readbyqxmd.com/read/28636232/a-genetic-stochastic-process-model-for-genome-wide-joint-analysis-of-biomarker-dynamics-and-disease-susceptibility-with-longitudinal-data
#1
Liang He, Ilya Zhbannikov, Konstantin G Arbeev, Anatoliy I Yashin, Alexander M Kulminski
Unraveling the underlying biological mechanisms or pathways behind the effects of genetic variations on complex diseases remains one of the major challenges in the post-GWAS (where GWAS is genome-wide association study) era. To further explore the relationship between genetic variations, biomarkers, and diseases for elucidating underlying pathological mechanism, a huge effort has been placed on examining pleiotropic and gene-environmental interaction effects. We propose a novel genetic stochastic process model (GSPM) that can be applied to GWAS and jointly investigate the genetic effects on longitudinally measured biomarkers and risks of diseases...
June 21, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28635637/a-short-term-biological-indicator-for-long-term-kidney-damage-after-radionuclide-therapy-in-mice
#2
Giovanni Pellegrini, Klaudia Siwowska, Stephanie Haller, Daniel J Antoine, Roger Schibli, Anja Kipar, Cristina Müller
Folate receptor (FR)-targeted radionuclide therapy using folate radioconjugates is of interest due to the expression of the FR in a variety of tumor types. The high renal accumulation of radiofolates presents, however, a risk of radionephropathy. A potential option to address this challenge would be to use radioprotectants, such as amifostine. Methods for early detection of kidney damage that-in this case-cannot be predicted based on dose estimations, would facilitate the development of novel therapies. The aim of this study was, therefore, to assess potentially changing levels of plasma and urine biomarkers and to determine DNA damage at an early stage after radiofolate application...
June 21, 2017: Pharmaceuticals
https://www.readbyqxmd.com/read/28635396/microrna-34a-inhibits-tumor-invasion-and-metastasis-in-osteosarcoma-partly-by-effecting-c-iap2-and-bcl-2
#3
Jie Wen, Yan-Kun Zhao, Yan Liu, Jin-Feng Zhao
Osteosarcoma is a common primary malignant bone tumor that occurs mainly in children and adolescents. Recent evidence has demonstrated that miR-34a is involved in the invasion and metastasis of osteosarcoma. This study aims to explore the effect of biological behavior of miR-34a on osteosarcoma. First, we collect osteosarcoma and adjacent specimens, and the relative expression of miR-34a and C-IAP2 messenger RNA was quantitated by real-time polymerase chain reaction. Furthermore, miR-34a stimulant is synthesized and transfected onto osteosarcoma MG-63 cells...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28634120/highly-reproducible-improved-label-free-quantitative-analysis-of-cellular-phosphoproteome-by-optimization-of-lc-ms-ms-gradient-and-analytical-column-construction
#4
Nagib Ahsan, Judson Belmont, Zhuo Chen, James G Clifton, Arthur R Salomon
Expanding the sequencing depth of the peptides with a statistically significant quantitative change derived from a biological stimulation is critical. Here we demonstrate that optimization of LC gradient and analytical column construction can reveal over 30,000 unique peptides and 23,000 phosphopeptides at high confidence. The quantitative reproducibility of different analytical workflows was evaluated by comparing the phosphoproteome of CD3/4 stimulated and unstimulated T-cells as a model system. A fritless, 50cm-long column packed with 1...
June 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28634035/psoriasis-associated-late-cornified-envelope-lce-proteins-have-antibacterial-activity
#5
Hanna Niehues, Lam C Tsoi, Danique A van der Krieken, Patrick A M Jansen, Merel A W Oortveld, Diana Rodijk-Olthuis, Ivonne M J J van Vlijmen, Wiljan J A J Hendriks, Richard W Helder, Joke A Bouwstra, Ellen H van den Bogaard, Philip E Stuart, Rajan P Nair, James T Elder, Patrick L J M Zeeuwen, Joost Schalkwijk
Terminally differentiating epidermal keratinocytes express a large number of structural and antimicrobial proteins that are involved in the physical barrier function of the stratum corneum and provide innate cutaneous host defense. Late cornified envelope (LCE) genes, located in the epidermal differentiation complex on chromosome 1, encode a family of 18 proteins of unknown function, whose expression is largely restricted to epidermis. Deletion of two members, LCE3B and LCE3C (LCE3B/C-del), is a widely replicated psoriasis risk factor that interacts with the major psoriasis-psoriasis risk gene HLA-C*06...
June 17, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28633597/effect-of-t-2-toxin-injected-shrimp-muscle-extracts-on-mouse-macrophage-cells-raw264-7
#6
Zhanrui Huang, Yaling Wang, Mei Qiu, Lijun Sun, Jianmeng Liao, Rundong Wang, Xiaodong Sun, Siyuan Bi, Ravi Gooneratne
Following intramuscular injections of 0.1 mL, 3 mg kg(-1 )BW(-1)(1/10 LD50) T-2 toxin (T-2), the tissue concentration of T-2 in shrimp was quantitatively detected using LC-MS/MS. The biological half-time (t1/2) of T-2 in blood was 40.47 ± 0.24 min. The highest number of intramuscular T-2 shrimp could tolerate when given at blood t1/2 intervals was 4. The shrimps which were injected 5 T-2 died. The T-2 toxin highest accumulation was 0.471 ± 0.012 ng g(-1 )BW(-1). The effect of toxic shrimp muscle subjected to different processing conditions (high pressure, trifluoroacetic acid, acid and alkali digestions, artificial digestive juice [to simulate exposure to gastric and intestinal juices]) on mouse macrophage cells (RAW267...
February 10, 2017: Drug and Chemical Toxicology
https://www.readbyqxmd.com/read/28633108/bioactivity-and-quantitative-analysis-of-isohexenylnaphthazarins-in-root-periderm-of-two-echium-spp-e-%C3%A2-plantagineum-and-e-%C3%A2-gaditanum
#7
Alexandra G Durán, M Teresa Gutiérrez, Carlos Rial, Ascensión Torres, Rosa M Varela, Manuel M Valdivia, José M G Molinillo, Dominik Skoneczny, Leslie A Weston, Francisco A Macías
Isohexenylnaphthazarins are commonly found in the root periderm of several Boraginaceous plants and are known for their broad range of biological activities. The work described herein concerns the biological activity of compounds from the roots of Echium plantagineum L. and Echium gaditanum Boiss (Boraginaceae) collected from field sites in southern Spain and Australia. Bioactivity was assessed using etiolated wheat coleoptile bioassay and in vitro growth inhibitory activity in HeLa and IGROV-1 cells. The quantification of four isohexenylnaphthazarins (shikonin/alkannin, deoxyshikonin/deoxyalkannin, acetylshikonin/acetylalkannin and dimethylacrylshikonin/dimethylacrylalkannin) was performed by LC-MS/MS using juglone as internal standard...
June 17, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28631900/-experimental-development-and-rationale-for-a-renal-decellularization-protocol-with-subsequent-comprehensive-assessment-of-the-biological-scaffold
#8
P V Glybochko, S N Alekseenko, E A Gubareva, E V Kuevda, A A Basov, A S Sotnichenko, S S Dzhimak, I S Gumenyuk, I Kh Egiev, V N Chechelyan, R Z Nakokhov, O M Lyasota, Yu V Teterin
Chronic renal failure (CRF) is one of the most challenging problems of contemporary medicine. Patients with chronic renal failure usually need renal replacement therapy as either hemodialysis, peritoneal dialysis or a kidney transplant. The latter is the most promising option for end-stage kidney disease. However, the shortage of donor organs, the complexity of their delivery, the difficulty in finding an immunologically compatible donor and the need for lifelong immunosuppression triggered advances in modern tissue engineering...
June 2017: Urologii︠a︡
https://www.readbyqxmd.com/read/28631574/microrna-125a-5p-plays-a-role-as-a-tumor-suppressor-in-lung-carcinoma-cells-by-directly-targeting-stat3
#9
Lou Zhong, Siyuan Sun, Jiahai Shi, Fei Cao, Xiao Han, Zhong Chen
Increasing evidence supports that the dysregulation of microRNA expression plays an important role in the process of tumor occurrence and development. Studies have found that mir-125a-5p expression was downregulated in a variety of tumors, but the effects and mechanism of mir-125a-5p in lung cancer are still unclear. The aim of this study is to detect the expression of mir-125a-5p in lung cancer tissues and lung cancer cell lines and to explore the effects of mir-125a-5p on the biological characteristics of lung cancer cells; thus, this study aims to provide new methods and new strategies for the treatment of lung cancer...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28631568/mir-183-overexpression-inhibits-tumorigenesis-and-enhances-ddp-induced-cytotoxicity-by-targeting-mta1-in-nasopharyngeal-carcinoma
#10
Guanghui Wang, Shujing Wang, Congying Li
MicroRNA 183 (miR-183) was identified to be downregulated in nasopharyngeal carcinoma spheroids and served as a tumor suppressor in nasopharyngeal carcinoma. However, the regulatory mechanism of miR-183 and its role in cisplatin (DDP) resistance in nasopharyngeal carcinoma cells are still unclear. The expression of miR-183 and metastasis-associated protein 1 at messenger RNA and protein levels in nasopharyngeal carcinoma tissues and cells was evaluated using quantitative reverse transcription real-time polymerase chain reaction and western blotting, respectively...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28630930/real-time-quantitative-analysis-of-metabolic-flux-in-live-cells-using-a-hyperpolarized-micromagnetic-resonance-spectrometer
#11
Sangmoo Jeong, Roozbeh Eskandari, Sun Mi Park, Julio Alvarez, Sui Seng Tee, Ralph Weissleder, Michael G Kharas, Hakho Lee, Kayvan R Keshari
Metabolic reprogramming is widely considered a hallmark of cancer, and understanding metabolic dynamics described by the conversion rates or "fluxes" of metabolites can shed light onto biological processes of tumorigenesis and response to therapy. For real-time analysis of metabolic flux in intact cells or organisms, magnetic resonance (MR) spectroscopy and imaging methods have been developed in conjunction with hyperpolarization of nuclear spins. These approaches enable noninvasive monitoring of tumor progression and treatment efficacy and are being tested in multiple clinical trials...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28630783/highly-sensitive-colorimetric-assay-for-determining-fe-3-based-on-gold-nanoparticles-conjugated-with-glycol-chitosan
#12
Kyungmin Kim, Yun-Sik Nam, Yeonhee Lee, Kang-Bong Lee
A highly sensitive and simple colorimetric assay for the detection of Fe(3+) ions was developed using gold nanoparticles (AuNPs) conjugated with glycol chitosan (GC). The Fe(3+) ion coordinates with the oxygen atoms of GC in a hexadentate manner (O-Fe(3+)-O), decreasing the interparticle distance and inducing aggregation. Time-of-flight secondary ion mass spectrometry showed that the bound Fe(3+) was coordinated to the oxygen atoms of the ethylene glycol in GC, which resulted in a significant color change from light red to dark midnight blue due to aggregation...
2017: Journal of Analytical Methods in Chemistry
https://www.readbyqxmd.com/read/28629618/conditioning-and-robustness-of-rna-boltzmann-sampling-under-thermodynamic-parameter-perturbations
#13
Emily Rogers, David Murrugarra, Christine Heitsch
Understanding how RNA secondary structure prediction methods depend on the underlying nearest-neighbor thermodynamic model remains a fundamental challenge in the field. Minimum free energy (MFE) predictions are known to be "ill conditioned" in that small changes to the thermodynamic model can result in significantly different optimal structures. Hence, the best practice is now to sample from the Boltzmann distribution, which generates a set of suboptimal structures. Although the structural signal of this Boltzmann sample is known to be robust to stochastic noise, the conditioning and robustness under thermodynamic perturbations have yet to be addressed...
June 16, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28629450/interaction-with-adipocyte-stromal-cells-induces-breast-cancer-malignancy-via-s100a7-upregulation-in-breast-cancer-microenvironment
#14
Minako Sakurai, Yasuhiro Miki, Kiyoshi Takagi, Takashi Suzuki, Takanori Ishida, Noriaki Ohuchi, Hironobu Sasano
BACKGROUND: Breast adipocytes play important roles in both the development and function of mammary epithelial cells. Therefore, carcinoma-adipose stromal cell (ASC) interactions have been considered pivotal in supporting tumor growth in breast cancer. In addition, it has been demonstrated that the biological features of cancer-associated adipocytes differ from those of normal ASCs. Therefore, we investigated an interaction between ASCs and carcinoma cell lines to identify genes associated with ASC invasion of carcinoma cells...
June 19, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28629431/microrna-330-3p-promotes-cell-invasion-and-metastasis-in-non-small-cell-lung-cancer-through-gria3-by-activating-mapk-erk-signaling-pathway
#15
Chun-Hua Wei, Gang Wu, Qian Cai, Xi-Can Gao, Fan Tong, Rui Zhou, Rui-Guang Zhang, Ji-Hua Dong, Yu Hu, Xiao-Rong Dong
BACKGROUND: Brain metastasis (BM) is associated with poor prognosis in patients with non-small cell lung cancer (NSCLC). Recent studies demonstrated that microRNA-330-3p (miR-330-3p) was involved in NSCLC brain metastasis (BM). However, the exact parts played by miR-330-3p in BM of NSCLC remain unknown. Discovery and development of biomarkers and elucidation of the mechanism underlying BM in NSCLC is critical for effective prophylactic interventions. Here, we evaluated the expression and biological effects of miR-330-3p in NSCLC cells and explored the underlying mechanism of miR-330-3p in promoting cell migration and invasion in NSCLC...
June 19, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28629368/identification-and-characterization-of-long-intergenic-noncoding-rnas-in-bovine-mammary-glands
#16
Chao Tong, Qiaoling Chen, Lili Zhao, Junfei Ma, Eveline M Ibeagha-Awemu, Xin Zhao
BACKGROUND: Mammary glands of dairy cattle produce milk for the newborn offspring and for human consumption. Long intergenic noncoding RNAs (lincRNAs) play various functions in eukaryotic cells. However, types and roles of lincRNAs in bovine mammary glands are still poorly understood. RESULTS: Using computational methods, 886 unknown intergenic transcripts (UITs) were identified from five RNA-seq datasets from bovine mammary glands. Their non-coding potentials were predicted by using the combination of four software programs (CPAT, CNCI, CPC and hmmscan), with 184 lincRNAs identified...
June 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28629117/alpha-and-gamma-tocopherol-and-telomere-length-in-5768-us-men-and-women-a-nhanes-study
#17
Larry A Tucker
Antioxidants have a number of potential health benefits. The present investigation was designed to determine the relationship between serum alpha- and gamma-tocopherol levels (powerful antioxidants), and leukocyte telomere length (a biomarker of biological aging). A cross-sectional design was employed to study 5768 adults from the National Health and Nutrition Examination Survey (NHANES). DNA was obtained via blood samples. Telomere length was assessed using the quantitative polymerase chain reaction method...
June 13, 2017: Nutrients
https://www.readbyqxmd.com/read/28628219/application-of-swath-proteomics-to-mouse-biology
#18
Yibo Wu, Evan G Williams, Ruedi Aebersold
The quantitative measurement of the proteome has been shown to yield new insights into physiology and cell biology that cannot be determined from the genome and transcriptome because the quantitative relationship between transcriptome and proteome is complex. MS-based proteomics techniques, such as SWATH-MS, have recently advanced to the point at which they may be reliably applied by biologists who are not specialists in mass spectrometry. Here we provide standard protocols for preparation of tissue samples for input into the SWATH-MS analytical pipeline...
June 19, 2017: Current Protocols in Mouse Biology
https://www.readbyqxmd.com/read/28627686/hypoxia-and-acidosis-driven-aberrations-of-secreted-micrornas-in-endometrial-cancer-in-vitro
#19
Julia Eismann, Marc Hirschfeld, Thalia Erbes, Gerta Rücker, Markus Jäger, Andrea Ritter, Daniela Weiss, Gerald Gitsch, Sebastian Mayer
Due to their post-transcriptional regulatory impact on gene expression, microRNAs (miRNA, miRs) influence decisively cellular processes of differentiation, proliferation and apoptosis. In oncogenic pathways various miRNAs exert either oncogenic or tumor suppressor activities in a stage-specific manner. Dysregulation of miRNA expression pattern has been associated with several human cancers including endometrial cancer (EC). In the present study, expression profile alterations of EC associated secreted miRNAs were determined under the microenvironmental stress situations hypoxia and acidosis occurring in tumor progression and metastasis...
June 13, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28627619/expression-of-dicer-in-rheumatoid-arthritis-is-associated-with-disease-activity-and-balances-the-production-of-tnf%C3%A2-%C3%AE
#20
Shujun Wang, Min Yuan, Lijun Song, Xiuying Zhang, Qin Geng, Hongju Zhang, Xingfu Li
Gene expression can be altered through RNA interference (RNAi), including microRNA (miRNA) or small interfering RNA. Alterations of miRNAs in rheumatoid arthritis (RA) have been reported, however, the components of the RNAi machinery in RA remain to be fully elucidated. The aim of the present study was to detect the levels of Dicer, Argonaute2 and Drosha, components of the RNAi machinery, in the peripheral blood mononuclear cells of patients with RAusingreverse transcription‑quantitative polymerase chain reaction, and to compare the results with disease activity and clinical features...
June 9, 2017: Molecular Medicine Reports
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