Allele diversity of the H-ras-1 variable number of tandem repeats in Norwegian lung cancer patients

We have examined restriction fragment length polymorphisms of the H-ras-1 gene in germ-line DNA from 214 lung cancer patients and 309 unaffected controls. When DNA samples were digested with MspI/HpaII, Southern blot analysis revealed at least 22 different alleles, grouped according to their frequencies as common, intermediate, and rare. The frequency of rare alleles in lung cancer patients (16/428) is significantly different (p = 0.002) from that in the control group (5/618). Individuals with rare alleles were found to be at 4.7-fold greater risk of lung cancer than those with no rare alleles.publishedVersio

Muscarinic receptor subtypes and signalling involved in the attenuation of isoprenaline-induced rat urinary bladder relaxation

β-Adrenoceptors are important mediators of smooth muscle relaxation in the urinary bladder, but the concomitant presence of a muscarinic agonist, e.g., carbachol, can attenuate relaxation responses by reducing potency and/or efficacy of β-adrenoceptor agonists such as isoprenaline. Therefore, the present study was designed to explore the subtypes and signalling pathways of muscarinic receptors involved in the attenuation of isoprenaline-induced isolated rat detrusor preparations using novel subtype-selective receptor ligands. In radioligand binding studies, we characterized BZI to be a M3-sparing muscarinic agonist, providing selective M2 stimulation in rat bladder, and THRX-182087 as a highly M2-selective antagonist. The use of BZI and of THRX-182087 in the presence of carbachol enabled experimental conditions with a selective stimulation of only M2 or M3 receptors, respectively. Confirming previous findings, carbachol attenuated isoprenaline-induced detrusor relaxation. M2-selective stimulation partly mimicked this attenuation, indicating that both M2 and M3 receptors are involved. During M3-selective stimulation, the attenuation of isoprenaline responses was reduced by the phospholipase C inhibitor U 73,122 but not by the protein kinase C inhibitor chelerythrine. We conclude that both M2 and M3 receptors contribute to attenuation of β-adrenoceptor-mediated relaxation of rat urinary bladder; the signal transduction pathway involved in the M3 component of this attenuation differs from that mediating direct contractile effects of M3 receptors

AGO6 Functions in RNA-Mediated Transcriptional Gene Silencing in Shoot and Root Meristems in Arabidopsis thaliana

RNA-directed DNA methylation (RdDM) is a small interfering RNA (siRNA)-mediated epigenetic modification that contributes to transposon silencing in plants. RdDM requires a complex transcriptional machinery that includes specialized RNA polymerases, named Pol IV and Pol V, as well as chromatin remodelling proteins, transcription factors, RNA binding proteins, and other plant-specific proteins whose functions are not yet clarified. In Arabidopsis thaliana, DICER-LIKE3 and members of the ARGONAUTE4 group of ARGONAUTE (AGO) proteins are involved, respectively, in generating and using 24-nt siRNAs that trigger methylation and transcriptional gene silencing of homologous promoter sequences. AGO4 is the main AGO protein implicated in the RdDM pathway. Here we report the identification of the related AGO6 in a forward genetic screen for mutants defective in RdDM and transcriptional gene silencing in shoot and root apical meristems in Arabidopsis thaliana. The identification of AGO6, and not AGO4, in our screen is consistent with the primary expression of AGO6 in shoot and root growing points

Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice

Functional redundancy limits detailed analysis of genes in many organisms. Here, we report a method to efficiently overcome this obstacle by combining gene expression data with analysis of gene-indexed mutants. Using a rice NSF45K oligo-microarray to compare 2-week-old light- and dark-grown rice leaf tissue, we identified 365 genes that showed significant 8-fold or greater induction in the light relative to dark conditions. We then screened collections of rice T-DNA insertional mutants to identify rice lines with mutations in the strongly light-induced genes. From this analysis, we identified 74 different lines comprising two independent mutant lines for each of 37 light-induced genes. This list was further refined by mining gene expression data to exclude genes that had potential functional redundancy due to co-expressed family members (12 genes) and genes that had inconsistent light responses across other publicly available microarray datasets (five genes). We next characterized the phenotypes of rice lines carrying mutations in ten of the remaining candidate genes and then carried out co-expression analysis associated with these genes. This analysis effectively provided candidate functions for two genes of previously unknown function and for one gene not directly linked to the tested biochemical pathways. These data demonstrate the efficiency of combining gene family-based expression profiles with analyses of insertional mutants to identify novel genes and their functions, even among members of multi-gene families

Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy

Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics

ANTIOXIDANT CAPACITY IN SOME TRADITIONAL UGANDAN DIETS

Several studies indicate that a plant-based diet protects against the development of both infectious and non-communicable diseases (NCD) like cancer, diabetes and cardiovascular diseases. It is assumed that the antioxidant content in food is an important reason for this protection. Dietary plants contain several hundred antioxidants, many of which are believed to act in a synergistic way to protect the body against oxidative stress. Sub-Saharan Africa is under a double burden of disease, with the classical malnutrition-related and infectious diseases coexisting with the NCD caused by western influenced diet and lifestyle. The objective of this work was to analyse antioxidant activity (AA) in fruits and vegetables from Uganda and investigate whether AA in traditional food is sufficiently high to prevent oxidative stress and thus combat diseases. We used the FRAP (ferric reducing ability of plasma) procedure. The results showed a great variation in AA ranging from 72.3 ± 13.5 (Syzygium cuminii seed) to 0.09 ± 0.05 (Cucurbita maxima fruit) mmol /100g fresh weight (FW). We estimate serving sizes and determine the total antioxidant capacity (TDAC) per day of three traditional Ugandan diets. The dietary plants with highest AA per serving size are pomegranate (Punica granatum), Canarium schweinfurthii, guava (Psidium guajava), mango (Mangifera indica) and tree tomato (Cyphomandra betacea) with values ranging from 8.91 to 3.00 mmol/serving. Of the traditional diets the central/eastern (C/E) and the western (W) diets had almost the same AA (9.31-9.78 and 9.75 mmol/day), while the northern (N) diet had an AA of 7.50-8.02 mmol/day

DOMESTICATION OF SOME MEDICINAL TREES IN UGANDA

Most rural communities in developing countries rely on medicinal plants for their health care. Unfortunately, important medicinal trees are threatened by overexploitation and landuse changes. Important trees need to be conserved. This requires a good understanding of their seed and germination ecology. In this study we investigated the influence of temperature and light on germination and seedling growth of two locally threatened medicinal trees, Hallea rubrostipulata and Sarcocephalus latifolius, in order to facilitate their establishment. Both species needed light to germinate. H. rubrostipulata had a temperature optimum of 25oC with 79 % germination, while for S. latifolius the total germination after 28 days was close to 60 % at temperatures from 20 to 35oC. Seedlings of S. latifolius survived well at 35oC, while those of H. rubrostipulata died at this high temperature. Conversely seedling of S. latifolius died at the low temperature of 15oC. We have chosen the Framework species method for reforestation. We raised seedlings of 38 different, mostly indigenous, trees in nursery for 6 to 12 months. The trees are a mixture of medicinal, firewood, fruit trees and trees useful for soil conservation. In the early rainy season in April 2008 we planted the same mixture of trees in three plots, each 40 x 40 m big. The trees were monitored two weeks after planting for height, crown width, root collar diameter and health. The plots are weeded three times during the rainy season, and growth is monitored once a month for one year

Allele diversity of the H-ras-1 variable number of tandem repeats in Norwegian lung cancer patients

We have examined restriction fragment length polymorphisms of the H-ras-1 gene in germ-line DNA from 214 lung cancer patients and 309 unaffected controls. When DNA samples were digested with MspI/HpaII, Southern blot analysis revealed at least 22 different alleles, grouped according to their frequencies as common, intermediate, and rare. The frequency of rare alleles in lung cancer patients (16/428) is significantly different (p = 0.002) from that in the control group (5/618). Individuals with rare alleles were found to be at 4.7-fold greater risk of lung cancer than those with no rare alleles