ALBERT

Description: Glands are vital structures found throughout the human body and their structure and function are affected by many diseases. The ability to segment and detect glands among other types of tissues is important fo...

Description: Background: Physic nut (Jatropha curcas L.) is a small perennial tree or large shrub, which is well-adapted to semi-arid regions and is considered to have potential as a crop for biofuel production. It is now regarded as an excellent model for studying biofuel plants. However, our knowledge about the molecular responses of this species to drought stress is currently limited. Results: In this study, genome-wide transcriptional profiles of roots and leaves of 8-week old physic nut seedlings were analyzed 1, 4 and 7?days after withholding irrigation. We observed a total of 1533 and 2900 differentially expressed genes (DEGs) in roots and leaves, respectively. Gene Ontology analysis showed that the biological processes enriched in droughted plants relative to unstressed plants were related to biosynthesis, transport, nucleobase-containing compounds, and cellular protein modification. The genes found to be up-regulated in roots were related to abscisic acid (ABA) synthesis and ABA signal transduction, and to the synthesis of raffinose. Genes related to ABA signal transduction, and to trehalose and raffinose synthesis, were up-regulated in leaves. Endoplasmic reticulum (ER) stress response genes were significantly up-regulated in leaves under drought stress, while a number of genes related to wax biosynthesis were also up-regulated in leaves. Genes related to unsaturated fatty acid biosynthesis were down-regulated and polyunsaturated fatty acids were significantly reduced in leaves 7?days after withholding irrigation. As drought stress increased, genes related to ethylene synthesis, ethylene signal transduction and chlorophyll degradation were up-regulated, and the chlorophyll content of leaves was significantly reduced by 7?days after withholding irrigation. Conclusions: This study provides us with new insights to increase our understanding of the response mechanisms deployed by physic nut seedlings under drought stress. The genes and pathways identified in this study also provide much information of potential value for germplasm improvement and breeding for drought resistance.

Description: Background: SKIP is a transcription cofactor in many eukaryotes. It can regulate plant stress tolerance in rice and Arabidopsis. But the homolog of SKIP protein in soybean has been not reported up to now. Results: In this study, the expression patterns of soybean GAMYB binding protein gene (GmGBP1) encoding a homolog of SKIP protein were analyzed in soybean under abiotic stresses and different day lengths. The expression of GmGBP1 was induced by polyethyleneglycol 6000, NaCl, gibberellin, abscisic acid and heat stress. GmGBP1 had transcriptional activity in C-terminal. GmGBP1 could interact with R2R3 domain of GmGAMYB1 in SKIP domain to take part in gibberellin flowering pathway. In long-day (16 h-light) condition, transgenic Arabidopsis with the ectopic overexpression of GmGBP1 exhibited earlier flowering and less number of rosette leaves; Suppression of AtSKIP in Arabidopsis resulted in growth arrest, flowering delay and down-regulation of many flowering-related genes (CONSTANS, FLOWERING LOCUS T, LEAFY); Arabidopsis myb33 mutant plants with ectopic overexpression of GmGBP1 showed the same flowering phenotype with wild type. In short-day (8 h-light) condition, transgenic Arabidopsis plants with GmGBP1 flowered later and showed a higher level of FLOWERING LOCUS C compared with wild type. When treated with abiotic stresses, transgenic Arabidopsis with the ectopic overexpression of GmGBP1 enhanced the tolerances to heat and drought stresses but reduced the tolerance to high salinity, and affected the expressions of several stress-related genes. Conclusions: In Arabidopsis, GmGBP1 might positively regulate the flowering time by affecting CONSTANS, FLOWERING LOCUS T, LEAFY and GAMYB directly or indirectly in photoperiodic and gibberellin pathways in LDs, but GmGBP1 might represse flowering by affecting FLOWERING LOCUS C and SHORT VEGETATIVE PHASE in autonomous pathway in SDs. GmGBP1 might regulate the activity of ROS-eliminating to improve the resistance to heat and drought but reduce the high-salinity tolerance.

Description: Background: Accurate modeling of electrostatic potential and corresponding energies becomesincreasingly important for understanding properties of biological macromolecules and theircomplexes. However, this is not an easy task due to the irregular shape of biological entitiesand the presence of water and mobile ions. Results: Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi,enriched with additional features to facilitate DelPhi usage. The suite allows for easydownload of both DelPhi executable files and source code along with a makefile for localinstallations. The users can obtain the DelPhi manual and parameter files required for thecorresponding investigation. Non-experienced researchers can download examples containingall necessary data to carry out DelPhi runs on a set of selected examples illustrating variousDelPhi features and demonstrating DelPhi's accuracy against analytical solutions. Conclusions: DelPhi suite offers not only the DelPhi executable and sources files, examples and parameterfiles, but also provides links to third party developed resources either utilizing DelPhi orproviding plugins for DelPhi. In addition, the users and developers are offered a forum toshare ideas, resolve issues, report bugs and seek help with respect to the DelPhi package. Theresource is available free of charge for academic users from URL:http://compbio.clemson.edu/delphi.php

Description: Background: Identifying diagnosis and prognosis biomarkers from expression profiling data is of great significance for achieving personalized medicine and designing therapeutic strategy in complex diseases. However, the reproducibility of identified biomarkers across tissues and experiments is still a challenge for this issue. Results: We propose a strategy based on discriminative area of module activities to identify gene biomarkers which interconnect as a subnetwork or module by integrating gene expression data and protein-protein interactions. Then, we implement the procedure in T2DM as a case study and identify a module biomarker with 32 genes from mRNA expression data in skeletal muscle for T2DM. This module biomarker is enriched with known causal genes and related functions of T2DM. Further analysis shows that the module biomarker is of superior performance in classification, and has consistently high accuracies across tissues and experiments. Conclusion: The proposed approach can efficiently identify robust and functionally meaningful module biomarkers in T2DM, and could be employed in biomarker discovery of other complex diseases characterized by expression profiles.

Description: Background: Dyslipidemia and activation of renin-angiotensin system (RAS) contribute to the progression of chronic kidney disease (CKD). This study investigated possible synergistic effects of intrarenal RAS activation with hyperlipidemia in renal injuries. Methods: Apolipoprotein knockout mice were fed with normal chow diet (control) or high fat diet (HF group) for eight weeks. Human proximal tubular epithelial cell line (HK-2) was treated without (control) or with cholesterol (30 mug/ml) plus 25-hydroxycholesterol (1 mug/ml) (lipid group) for 24 hours. The plasma lipid profile and RAS components were determined by clinical biochemistry assay and radiommunoassay, respectively. Collagen deposition in kidneys was evaluated by Masson-staining. The gene and protein expressions of molecules involved in RAS components and biomarkers of epithelial mesenchymal transition (EMT) were examined by real-time PCR, immunochemical staining, and Western blot. Results: The mice fed with high-fat diet showed significant hyperlipidemia with collagen deposition in renal tubular interstitium compared to controls. The plasma levels of renin, angiotensin I, and angiotensin II were no difference in two groups. However, the kidneys of HF group showed up-regulated RAS components, which were positively associated with increased plasma levels of triglyceride, total cholesterol, and LDL. These effects were further confirmed by in vitro studies. Lipid loading induced HK-2 cells underwent EMT, which was closely associated with the increased expressions of intracellular RAS components. Conclusions: Local RAS activation was involved in hyperlipidemia-mediated renal injuries, suggesting that there are synergistic effects resulting from RAS activation with hyperlipidemia that accelerates the progression of CKD.

Description: Background: The objective of this study was to evaluate the feasibility and diagnostic value of 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) and 99mTc-methylenediphosphonate (MDP) whole-body bone scanning (BS) for the detection of osteolytic bone metastases. Methods: Thirty-four patients with pathologically confirmed malignancies and suspected osteolytic bone metastases underwent 18F-FDG PET/CT and 99mTc-MDP whole-body BS within 30 days. The sensitivity, specificity, and accuracy with respect to the diagnosis of osteolytic bone metastases and bone lesions were compared between the two imaging methods. Results: The sensitivity, specificity, and accuracy of 18F-FDG PET/CT for the diagnosis of osteolytic bone metastases were 94.3% (95% confidence interval [CI], 91.6–96.2%), 83.3% (95% CI, 43.6–96.9%), and 94.2% (95% CI, 91.5–96.1%), respectively. It was found that 99mTc-MDP whole-body BS could discriminate between patients with 50.2% (95% CI, 45.4–55.1%) sensitivity, 50.0% (95% CI, 18.8–81.2%) specificity, and 50.2% (95% CI, 45.5–55.1%) accuracy. 18F-FDG PET/CT achieved higher sensitivity, specificity, and accuracy in detecting osteolytic bone metastases than 99mTc-MDP whole-body BS (p

Description: Background: Obesity-induced chronic inflammation plays a fundamental role in the pathogenesis of metabolic syndrome (MS). Recently, a growing body of evidence supports that miRNAs are largely dysregulated in obesity and that specific miRNAs regulate obesity-associated inflammation. We applied an approach aiming to identify active miRNA-TF-gene regulatory pathways in obesity. Firstly, we detected differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) from mRNA and miRNA expression profiles, respectively. Secondly, by mapping the DEGs and DEmiRs to the curated miRNA-TF-gene regulatory network as active seed nodes and connect them with their immediate neighbors, we obtained the potential active miRNA-TF-gene regulatory subnetwork in obesity. Thirdly, using a Breadth-First-Search (BFS) algorithm, we identified potential active miRNA-TF-gene regulatory pathways in obesity. Finally, through the hypergeometric test, we identified the active miRNA-TF-gene regulatory pathways that were significantly related to obesity. Results: The potential active pathways with FDR