Expression of ob gene coding the production of the hormone leptin in hepatocytes of liver with steatosis

Leptin is a circulating pleiotropic hormone that play an important role in appetite control, fat metabolism, regulation of body weight, fetus growth, growth and aging of adults and hematopoiesis. It is expressed abundantly and specifically in the adipose tissue. A liver cell with developed steatosis represents a cell metabolism similar to metabolism of cells of adipose tissue. Analyses of serum leptin and free leptin receptor in the serum of patients with steatosis showed significant variations from reference limits of normal values. However in liver tissue with verified steatosis detection of mRNA gene for leptin was not proven. Such expression of ob gene for leptin was not found even in the liver tissue without steatosis. With respect to the absence of ob gene expression, the direct effect of ob gene expression on other parameters of leptin metabolism could not be evaluated. The RT-PCR method with verified specificity and satisfying sensitivity was developed. The results obtained from analysis of serum leptin and free leptin receptor in the serum are presented and evaluated. The used methods were verified and reference limits for Czech population were defined in dependence on age and other clinical parameters.     

circRNA-associated ceRNA network construction reveals the circRNAs involved in the progression and prognosis of breast cancer

Recently, increasing evidences show that circular RNAs (circRNAs) are important regulators of various diseases, especially cancer. However, the regulatory role and the potential mechanism of action of circRNAs in breast cancer remain largely unknown. In this study, weighted gene co-expression network analysis was conducted with the differentially expressed miRNAs and mRNAs in breast cancer from The Cancer Genome Atlas database to identify the key modules associated with the carcinogenesis of breast cancer. In the significant turquoise and brown modules, 22 miRNAs and 1877 mRNAs were identified, respectively. Then, We compared and predicted the target genes and performed survival analysis to identify the miRNAs and mRNAs related to the prognosis of breast cancer. A circRNA-related competitive endogenous RNA network was identified by database co-screening, and deleted in liver cancer 1 (DLC1) was identified as a key gene. Finally, to assess how genes in key modules and key genes contribute to the development of breast cancer, relevant pathway information was obtained through DAVID and Gene Set Enrichment Analysis. These data demonstrated that three circRNAs (hsa-circ-0083373, hsa-circ-0083374, and hsa-circ-0083375) that regulate DLC1 expression via hsa-mir-511 and are involved in the pathogenesis and development of breast cancer.     

Genetic and biochemical characterization of a Cat2 catalase null mutant of zea mays

Summary In all maize inbred lines examined to date, the Cat2 gene which codes for the CAT-2 catalase is expressed primarily in the scutellum upon seed imbibition. The activity of CAT-2 increases dramatically during the initial four days after germination and subsequently declines. In contrast, we have recently identified and inbred strain (A16) of maize which does not express the Cat2 gene (i.e., the CAT-2 catalase is undetectable). Electrophoretic and immunological analyses indicate that the CAT-2 protein is not present in either an active or inactive form in line A16. Genetic analysis suggests that the absence of CAT-2 expression in line A16 is due to a null allele at the Cat2 gene locus although the possibility of a mutation at a regulatory locus, closely linked to the structural gene has not been excluded. Two other enzymes involved in H₂O₂ metabolism (superoxide dismutase and peroxidase) were also compared in W64A and A16 with no significant differences being observed. Aminotriazole (AT), a known inhibitor of catalase, has been used to simulate the A16 phenomenon by inhibiting catalase activity in line W64A (which has normal expression of CAT-2). AT, in very low concentrations, effectively inhibits the expression of CAT-2 in the scutellum. This inhibition of catalase by AT does not result in changes of the developmental time-course of superoxide dismutase and peroxidase.Research supported by National Institutes of Health Grant No. GM 22733-05 to J.G.S.Paper No. 6601 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, NC     

Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR

The work presented here is a first step toward a long term goal of systems biology, the complete elucidation of the gene regulatory networks of a living organism. To this end, we have employed DNA microarray technology to identify genes involved in the regulatory networks that facilitate the transition of Escherichia coli cells from an aerobic to an anaerobic growth state. We also report the identification of a subset of these genes that are regulated by a global regulatory protein for anaerobic metabolism, FNR. Analysis of these data demonstrated that the expression of over one-third of the genes expressed during growth under aerobic conditions are altered when E. coli cells transition to an anaerobic growth state, and that the expression of 712 (49%) of these genes are either directly or indirectly modulated by FNR. The results presented here also suggest interactions between the FNR and the leucine-responsive regulatory protein (Lrp) regulatory networks. Because computational methods to analyze and interpret high dimensional DNA microarray data are still at an early stage, and because basic issues of data analysis are still being sorted out, much of the emphasis of this work is directed toward the development of methods to identify differentially expressed genes with a high level of confidence. In particular, we describe an approach for identifying gene expression patterns (clusters) obtained from multiple perturbation experiments based on a subset of genes that exhibit high probability for differential expression values.     

cDNA macroarray analysis of gene expression in ineffective nodules induced on the Lotus japonicus sen1 mutant

The Lotus japonicus sen1 mutant forms ineffective nodules in which development is arrested at the stage of bacterial differentiation into nitrogen-fixing bacteroids. Here, we used cDNA macroarray systems to compare gene expression in ineffective nodules induced on the sen1 mutant with gene expression in wild-type nodules, in order to identify the host plant genes that are involved in nitrogen fixation. Macroarray analysis coupled with Northern blot analysis revealed that the expression of 18 genes was significantly enhanced in ineffective sen1 nodules, whereas the expression of 30 genes was repressed. Many of the enhanced genes encoded hydrolase enzymes, such as cysteine proteinase and asparaginase, that might function in the early senescence of sen1 nodules. By contrast, the repressed genes encoded nodulins, enzymes that are involved in carbon and nitrogen metabolism, membrane transporters, enzymes involved in phytohormone metabolism and secondary metabolism, and regulatory proteins. These proteins might have a role in the establishment of nitrogen fixation. In addition, we discovered two novel genes that encoded glutamate-rich proteins and were localized in the vascular bundles of the nodules. The expression of these genes was repressed in the ineffective nodules, which had lower levels of nitrogenase activity.     

Comparison of age-dependent expression of aggrecan and ADAMTSs in mandibular condylar cartilage, tibial growth plate, and articular cartilage in rats

A disintegrin and metalloproteinase with thrombospondin motif (adamalysin–thrombospondins, ADAMTS) degrades aggrecan, one of the major extracellular matrix (ECM) components in cartilage. Mandibular condylar cartilage differs from primary cartilage, such as articular and growth plate cartilage, in its metabolism of ECM, proliferation, and differentiation. Mandibular condylar cartilage acts as both articular and growth plate cartilage in the growing period, while it remains as articular cartilage after growth. We hypothesized that functional and ECM differences between condylar and primary cartilages give rise to differences in gene expression patterns and levels of aggrecan and ADAMTS-1, -4, and -5 during growth and aging. We employed in situ hybridization and semiquantitative RT-PCR to identify mRNA expression for these molecules in condylar cartilage and primary cartilages during growth and aging. All of the ADAMTSs presented characteristic, age-dependent expression patterns and levels among the cartilages tested in this study. ADAMTS-5 mainly contributed to ECM metabolism in growth plate and condylar cartilage during growth. ADAMTS-1 and ADAMTS-4 may be involved in ECM turn over in articular cartilage. The results of the present study reveal that ECM metabolism and expression of related proteolytic enzymes in primary and secondary cartilages may be differentially regulated during growth and aging.     

Feedback regulation of an Agrobacterium catalase gene katA involved in Agrobacterium–plant interaction

Catalases are known to detoxify H2O2, a major component of oxidative stress imposed on a cell. An Agrobacterium tumefaciens catalase encoded by a chromosomal gene katA has been implicated as an important virulence factor as it is involved in detoxification of H2O2 released during Agrobacterium-plant interaction. In this paper, we report a feedback regulation pathway that controls the expression of katA in A. tumefaciens cells. We observed that katA could be induced by plant tissue sections and by acidic pH on a minimal medium, which resembles the plant environment that the bacteria encounter during the course of infection. This represents a new regulatory factor for catalase induction in bacteria. More importantly, a feedback regulation was observed when the katA-gfp expression was studied in different genetic backgrounds. We found that introduction of a wild-type katA gene encoding a functional catalase into A. tumefaciens cells could repress the katA-gfp expression over 60-fold. The katA gene could be induced by H2O2 and the encoded catalase could detoxify H2O2. In addition, the katA-gfp expression of one bacterial cell could be repressed by other surrounding catalase-proficient bacterial cells. Furthermore, mutation at katA caused a 10-fold increase of the intracellular H2O2 concentration in the bacteria grown on an acidic pH medium. These results suggest that the endogenous H2O2 generated during A. tumefaciens cell growth could serve as the intracellular and intercellular inducer for the katA gene expression and that the acidic pH could pose an oxidative stress on the bacteria. Surprisingly, one mutated KatA protein, exhibiting no significant catalase activity as a result of the alteration of two important residues at the putative active site, could partially repress the katA-gfp expression. The feedback regulation of the katA gene by both catalase activity and KatA protein could presumably maintain an appropriated level of catalase activity and H2O2 inside A. tumefaciens cells.