Small GTPase ‘Rop’: molecular switch for plant defense responses

AbstractThe conserved Rho family of GTPases (Rho, Rac, and Cdc42) in fungi and mammals has emerged as a key regulator of diverse cellular activities, such as cytoskeletal rearrangements, programmed cell death, stress-induced signaling, and cell growth and differentiation. In plants, a unique class of Rho-like proteins, most closely related to mammalian Rac, has only been found and termed ‘Rop’ (Rho-related GTPase from plant [Li et al. (1998) Plant Physiol. 118, 407–417; Yang (2002) Plant Cell 14, S375–S388]). ROPs have been implicated in regulating various plant cellular responses including defense against pathogens. It has been shown that ROPs, like mammalian Rac, trigger hydrogen peroxide production and hence the ‘oxidative burst’, a crucial component associated with the cell death, most likely via activation of nicotinamide adenine dinucleotide phosphate oxidase in both monocotyledonous and dicotyledonous species. Recent studies have established that ROPs also function as a molecular switch for defense signaling pathway(s) linked with disease resistance. As discerning the defense pathway remains one of the priority research areas in the field of plant biology, this review is therefore particularly focused on recent progresses that have been made towards understanding the plant defense responses mediated by ROPs

Evaluation of toxicity of the mycotoxin citrinin using yeast ORF DNA microarray and Oligo DNA microarray

BACKGROUND: Mycotoxins are fungal secondary metabolites commonly present in feed and food, and are widely regarded as hazardous contaminants. Citrinin, one of the very well known mycotoxins that was first isolated from Penicillium citrinum, is produced by more than 10 kinds of fungi, and is possibly spread all over the world. However, the information on the action mechanism of the toxin is limited. Thus, we investigated the citrinin-induced genomic response for evaluating its toxicity. RESULTS: Citrinin inhibited growth of yeast cells at a concentration higher than 100 ppm. We monitored the citrinin-induced mRNA expression profiles in yeast using the ORF DNA microarray and Oligo DNA microarray, and the expression profiles were compared with those of the other stress-inducing agents. Results obtained from both microarray experiments clustered together, but were different from those of the mycotoxin patulin. The oxidative stress response genes – AADs, FLR1, OYE3, GRE2, and MET17 – were significantly induced. In the functional category, expression of genes involved in "metabolism", "cell rescue, defense and virulence", and "energy" were significantly activated. In the category of "metabolism", genes involved in the glutathione synthesis pathway were activated, and in the category of "cell rescue, defense and virulence", the ABC transporter genes were induced. To alleviate the induced stress, these cells might pump out the citrinin after modification with glutathione. While, the citrinin treatment did not induce the genes involved in the DNA repair. CONCLUSION: Results from both microarray studies suggest that citrinin treatment induced oxidative stress in yeast cells. The genotoxicity was less severe than the patulin, suggesting that citrinin is less toxic than patulin. The reproducibility of the expression profiles was much better with the Oligo DNA microarray. However, the Oligo DNA microarray did not completely overcome cross hybridization

The stress response against denatured proteins in the deletion of cytosolic chaperones SSA1/2 is different from heat-shock response in Saccharomyces cerevisiae

BACKGROUND: A yeast strain lacking the two genes SSA1 and SSA2, which encode cytosolic molecular chaperones, acquires thermotolerance as well as the mild heat-shocked wild-type yeast strain. We investigated the genomic response at the level of mRNA expression to the deletion of SSA1/2 in comparison with the mild heat-shocked wild-type using cDNA microarray. RESULTS: Yeast cDNA microarray analysis revealed that genes involved in the stress response, including molecular chaperones, were up-regulated in a similar manner in both the ssa1/2 deletion mutant and the mild heat-shocked wild-type. Genes involved in protein synthesis were up-regulated in the ssa1/2 deletion mutant, but were markedly suppressed in the mild heat-shocked wild-type. The genes involved in ubiquitin-proteasome protein degradation were also up-regulated in the ssa1/2 deletion mutant, whereas the unfolded protein response (UPR) genes were highly expressed in the mild heat-shocked wild-type. RT-PCR confirmed that the genes regulating protein synthesis and cytosolic protein degradation were up-regulated in the ssa1/2 deletion mutant. At the translational level, more ubiquitinated proteins and proteasomes were detected in the ssa1/2 deletion mutant, than in the wild-type, confirming that ubiquitin-proteasome protein degradation was up-regulated by the deletion of SSA1/2. CONCLUSION: These results suggest that the mechanism for rescue of denatured proteins in the ssa1/2 deletion mutant is different from that in the mild heat-shocked wild-type: Activated protein synthesis in the ssa1/2 deletion mutant supplies a deficiency of proteins by their degradation, whereas mild heat-shock induces UPR

RNA Quality Control Using External Standard RNA

In this paper, we propose a new evaluation method using external standard RNA for quality control of the extracted RNA. RNA Integrity Number and UV absorption are generally used as a basis for RNA quality control; however, these methods do not always reflect the quality of mRNA. While standard RNA is supposedly designed on the basis of mRNA, it has the potential to be used to evaluate the quality of the mRNA. In this study, we took into consideration the three essential factors, viz., yield of mRNA, inhibition to DNA polymerase, and degradation of mRNA for determining the RNA quality using standard RNA. It would be possible to know yield of mRNA and inhibition of the enzyme reaction by adding standard RNA before RNA extraction and looking at standard RNA loss. Degradation was evaluated by comparing the differences in the 3’ and 5’ regions of the RNA. In our study, it was demonstrated that in the crude extract of Saccharomyces cerevisiae, degradation was comparatively higher at the 3’ end of RNA than at the 5’ end. Hence, the degree of RNA degradation can be evaluated by comparing the ratio of degradation from the 3’ and 5’ end

STRONG ANTIMICROBIAL OF LACTIC ACID BACTERIA AND SPECIES IDENTIFICATION OF VIRGIN COCONUT OIL PRODUCTS IN PADANG WEST SUMATERA, INDONESIA

Virgin Coconut Oil (VCO) products are available in the market of Padang west Sumatra Indonesia, Produced by lokal Home Industry. Coconut, Cocos nucifera, is an important member of the family Arecaceae, have been traditional used for food and medicine in peoples of West Sumatra. Differently with coconut itself, the oil of coconut , VCO not all accepted to use as food supplement because of the image of the oil will increase blood cholesterol. Recently several reports proved that VCO contain Medium Chain Fatty Acids, as Lauric Acids is metabolize quickly to produce high energy and has antimicrobial activities. Lactic Acids Bacteria, known as antimicrobial also, have been isolated from 7 VCO samples, and 4 samples have strong lactic acid bacteria as antimicrobial. All of isolates VCO in MRS medium are gram positive, catalase negative and homofermentative. All isolates are able to inhibit pathogen bacteria such as Escherichia coli, Bacillus subtilis and Staphylococcus aureus. Antimicrobial test was obtained, the largest inhibition zones from pathogen bacteria are by sample codes 1A (12 mm), 6C (13.5 mm), and 3A (15 mm), respectively. Ampicillin Sodium 100 μg/mL is used as a positive control. All isolates can inhibit pathogenic bacteria in pH range of 3-9, but gave negative results on pH 3 against S. aureus. All of Lactic Acid Bacteria was obtained to sequence analysis using 16 S rRNA showed that Lactobacillus plantarum strain PON100536, Lactobacillus plantarum strain C410L1, Lactobacillus plantarum strain MF1298, Lactobacillus plantarum strain LY-78, Lactobacillus plantarum strain NM22-22, Lactobacillus plantarum strain DS2 KCTC12992BP, and Lactobacillus plantarum strain L41 with concentration Lactic acid 0.2725, 0.2775, 0.2950, 0.3050, 0.31, 0.2925, 0.3050 M, respectively

Analysis of Mechanisms of T-2 Toxin Toxicity Using Yeast DNA Microarrays

T-2 toxin is a mycotoxin that belongs to a group of type A tricothecenes found in agricultural products. The cytotoxicity of T-2 toxin was characterized by analysis of the yeast transcriptome upon challenge with T-2 toxin. Interestingly, T-2 toxin-induced yeast gene expression profiles were found to be similar to profiles obtained following cycloheximide treatment. Moreover, T-2 toxin treatment was found to activate facilitators, gluconeogenesis and cell arrest related genes such as mitogen-activated protein kinase genes (FUS3). T-2 toxin attacks the membrane and as a result the membrane transport system was disturbed. A large number of genes are induced to restore the toxicity caused by T-2 toxin. However, the data did not suggest that DNA damage by alkylation (Mag1, a gene 3-methyl-adenine DNA glycosylase, 0.46-fold down regulated), no induction of DNA repair mechanisms such as recombination (RAD26, RAD52 and etc.) and excision repair (RAD7, RAD14, RAD16, RAD23 and etc.). These results suggested that the toxicity of the T-2 toxin was due to the disturbance of the cell membrane of the yeast cell and that T-2 toxin caused mild mutagenesis

AN INTEGER TONE MAPPING OPERATION FOR HDR IMAGES IN OPENEXR WITH DENORMALIZED NUMBERS

ABSTRACT We propose an integer tone mapping operator (TMO) for high dynamic range (HDR) images expressed in a floating-point data format. Two purposes are achieved by the proposed TMO. The first purpose is to implement a TMO with less memory space. The second purpose is to give an important step to realize a fixed-point TMO. The proposed TMO is available for HDR images in the OpenEXR format. The OpenEXR format has two numerical representations (the normalized number and the denormalized number) which are not in other HDR formats such as RGBE. These two numerical representations cause a problem in applying an integer TMO. The proposed method enables us to avoid the problem by using the intermediate format. Moreover, the exponent part and the mantissa part are processed separately as two integer numbers. As a result, an integer TMO with less numerical range is achieved by our method. The experimental results show that the proposed method can generate high-quality low dynamic range (LDR) images with less memory space. Index Terms-high dynamic range, tone mapping, OpenEXR, denormalized number, integer operatio