Identification of differential gene expression for <Emphasis Type="Italic">Kr1</Emphasis> gene in bread wheat using annealing control primer system

Intergeneric hybridization is an important strategy to introgress alien genes into common wheat for its improvement. But presence of cross ability barrier mechanism regulated by Kr1 gene played a major destructive role for hybridization than other reported genes. In order to know the underlying molecular mechanism and to dissect out this barrier, a new annealing system, ACP (anneling control primer) system was used in chromosome 5B (containing Kr1 gene) specific Recombinant Inbred Line (RIL) population. Two differentially expressed fragments for Kr1 gene was identified, cloned and sequenced. Further the expression was confirmed by northern blotting analysis. Sequence analysis of the resulted clones revealed classes of putative genes, including stress responsive and signal transduction.     

NCYM,a Cis-Antisense Gene of MYCN,Encodes a De Novo Evolved Protein That Inhibits GSK3β Resulting in the Stabilization of MYCN in Human Neuroblastomas

The rearrangement of pre-existing genes has long been thought of as the major mode of new gene generation. Recently, de novo gene birth from non-genic DNA was found to be an alternative mechanism to generate novel protein-coding genes. However, its functional role in human disease remains largely unknown. Here we show that NCYM, a cis-antisense gene of the MYCN oncogene, initially thought to be a large non-coding RNA, encodes a de novo evolved protein regulating the pathogenesis of human cancers, particularly neuroblastoma. The NCYM gene is evolutionally conserved only in the taxonomic group containing humans and chimpanzees. In primary human neuroblastomas, NCYM is 100% co-amplified and co-expressed with MYCN, and NCYM mRNA expression is associated with poor clinical outcome. MYCN directly transactivates both NCYM and MYCN mRNA, whereas NCYM stabilizes MYCN protein by inhibiting the activity of GSK3β, a kinase that promotes MYCN degradation. In contrast to MYCN transgenic mice, neuroblastomas in MYCN/NCYM double transgenic mice were frequently accompanied by distant metastases, behavior reminiscent of human neuroblastomas with MYCN amplification. The NCYM protein also interacts with GSK3β, thereby stabilizing the MYCN protein in the tumors of the MYCN/NCYM double transgenic mice. Thus, these results suggest that GSK3β inhibition by NCYM stabilizes the MYCN protein both in vitro and in vivo. Furthermore, the survival of MYCN transgenic mice bearing neuroblastoma was improved by treatment with NVP-BEZ235, a dual PI3K/mTOR inhibitor shown to destabilize MYCN via GSK3β activation. In contrast, tumors caused in MYCN/NCYM double transgenic mice showed chemo-resistance to the drug. Collectively, our results show that NCYM is the first de novo evolved protein known to act as an oncopromoting factor in human cancer, and suggest that de novo evolved proteins may functionally characterize human disease.     

Changes in carbohydrate metabolism by triazole growth regulators in cassava (Manihot esculenta Crantz); effects on tuber production and quality

We have evaluated the ability of two triazole growth regulators, viz. triadimefon (TDM) and hexaconazole (HEX), in the enhancement of tuber production and quality in cassava (Manihot esculenta Crantz) through their effects on carbohydrate metabolism. One litre of 20 mg(-1) TDM and 15 mg(-1) HEX solution per plant were used for the treatments and groundwater was given to control plants. Triazole treatments reduced plant height and leaf area, but increased fresh and dry weights. Plants treated with TDM showed an increased net assimilation rate, which is followed by HEX and control plants. Triazole compounds increased the relative growth rate of cassava after 200 DAP, i.e. in the phase of tuber enlargement. Triazole compounds increased the starch and other carbohydrate contents and carbohydrate metabolising enzyme activities. From the results of this study, it can be concluded that these triazoles can significantly enhance the tuber production and quality by affecting the starch metabolism, apart from their fungicidal properties.     

Comparative Gene Expression Analysis of Susceptible and Resistant Near-Isogenic Lines in Common Wheat Infected by Puccinia triticina

Gene expression after leaf rust infection was compared in near-isogenic wheat lines differing in the Lr10 leaf rust resistance gene. RNA from susceptible and resistant plants was used for cDNA library construction. In total, 55 008 ESTs were sequenced from the two libraries, then combined and assembled into 14 268 unigenes for further analysis. Of these ESTs, 89% encoded proteins similar to (E value of ≤10⁻⁵) characterized or annotated proteins from the NCBI non-redundant database representing diverse molecular functions, cellular localization and biological processes based on gene ontology classification. Further, the unigenes were classified into susceptible and resistant classes based on the EST members assembled from the respective libraries. Several genes from the resistant sample (14-3-3 protein, wali5 protein, actin-depolymerization factor and ADP-ribosylation factor) and the susceptible sample (brown plant hopper resistance protein, caffeic acid O-methyltransferase, pathogenesis-related protein and senescence-associated protein) were selected and their differential expression in the resistant and susceptible samples collected at different time points after leaf rust infection was confirmed by RT–PCR analysis. The molecular pathogenicity of leaf rust in wheat was studied and the EST data generated made a foundation for future studies.     

TRIM28 Is an E3 Ligase for ARF-Mediated NPM1/B23 SUMOylation That Represses Centrosome Amplification

The tumor suppressor ARF enhances the SUMOylation of target proteins; however, the physiological function of ARF-mediated SUMOylation has been unclear due to the lack of a known, associated E3 SUMO ligase. Here we uncover TRIM28/KAP1 as a novel ARF-binding protein and SUMO E3 ligase for NPM1/B23. ARF and TRIM28 cooperate to SUMOylate NPM1, a nucleolar protein that regulates centrosome duplication and genomic stability. ARF-mediated SUMOylation of NPM1 was attenuated by TRIM28 depletion and enhanced by TRIM28 overexpression. Coexpression of ARF and TRIM28 promoted NPM1 centrosomal localization by enhancing its SUMOylation and suppressed centrosome amplification; these functions required the E3 ligase activity of TRIM28. Conversely, depletion of ARF or TRIM28 increased centrosome amplification. ARF also counteracted oncogenic Ras-induced centrosome amplification. Centrosome amplification is often induced by oncogenic insults, leading to genomic instability. However, the mechanisms employed by tumor suppressors to protect the genome are poorly understood. Our findings suggest a novel role for ARF in maintaining genome integrity by facilitating TRIM28-mediated SUMOylation of NPM1, thus preventing centrosome amplification.     

Drought tolerance in rice: morphological and molecular genetic consideration

Rice is one of the most important food crop drastically affected by drought in lowland rice ecosystem. Dissecting out the traits of importance and genomic regions influencing the response of drought tolerance and yield traits on grain yield will aid the breeders to know the genetic mechanism of drought tolerance of rice leads to the development of drought tolerant varieties. Grain yield and its components on drought situation of recombinant inbred population (IR 58821/IR 52561) were investigated under lowland managed stress situation in 2003 and 2004 by given importance to the relative water content. Water deficit resulted in significant effect on phenology and grain yield. Best lines were selected for further varietal development programme. Variability studies showed the traits viz., days to 70% relative water content, leaf rolling, leaf drying, harvest index, biomass yield and grain yield offer high scope for improvement for drought tolerance by way of simple selection technique. Correlation and path analysis indicated that, to harness high yielding combined with drought tolerance breeders should give selection pressure on relative water content, panicle length, grains per panicle, harvest index, biomass yield, root/shoot ratio and root length in positive direction, and low scores of leaf rolling, leaf drying and drought recovery rate. Analysis of quantitative trait loci for drought tolerance, yield and its components allowed the identification of 38 regions associated with both drought tolerant and yield traits. Out of these, 18 were closely linked with DNA markers could be used for marker assisted selection in breeding for drought tolerance in rice. Pleiotropism and G × E effects interaction were noticed in some of the traits. Parent IR 58821 contributed favorable alleles for the entire drought related and most of the yield component traits. Identification of traits of importance and their nature of relationship by morphological and molecular level under lowland condition will be useful to improve drought tolerance of rice.     

Genome- wide structural and functional variant discovery of rice landraces using genotyping by sequencing

Molecular Biology Reports - Rice landraces are vital genetic resources for agronomic and quality traits but the undeniable collection of Kerala landraces remains poorly delineated. To effectively...     

NaCl as a physiological modulator of proline metabolism and antioxidant potential in Phyllanthus amarus

Some medicinal plants need to be cultivated commercially in order to meet the ever-increasing demand for medicinal plants for the indigenous systems of medicine as well as for the pharmaceutical industry; in this regard, it seems significant to test the important medicinal plants for their salt-tolerance capacity, with a view to exploiting the saline lands for medicinal plant cultivation. Phyllanthus amarus plants were grown in the presence of NaCl in order to study the effect of NaCl (80 mM NaCl) in the induction of oxidative stress in terms of lipid peroxidation (TBARS content), H2O2 content, osmolyte concentration, proline(PRO)-metabolizing enzymes, and antioxidant enzyme activities. Groundwater was used for irrigation of control plants. Plants were uprooted randomly on 90 days after sowing (DAS). NaCl-stressed plants showed increased TBARS, H2O2, glycine betaine (GB), and PRO contents, whereas NaCl uptake decreased proline oxidase (PROX) activity and increased gamma-glutamyl kinase (gamma-GK) activity when compared to control. The antioxidant enzymes superoxide dismutase (SOD), peroxidase (POX) and catalase (CAT) were increased under salinity.     

Changes in antioxidant potential and sink-organ dry matter with pigment accumulation induced by hexaconazole in Plectranthus forskholii Briq

An investigation was conducted in Plectranthus forskholii by giving it different concentrations (10, 15, 20, 25, and 30 mg L(-1)) of hexaconazole, a fungicide cum plant-growth regulator, in order to find out its effects on growth, pigment composition, and antioxidant potential. The treatments were given as soil drenching on different growth stages. All the concentrations of hexaconazole used significantly decreased the stem length and leaf area, whereas side branches, fresh and dry matter content, photosynthetic pigments, and antioxidant potential were increased. The number of tubers, length and girth of tubers, fresh and dry weight of tubers and tuber pigments were found to be the highest at a 25 mg L(-1) concentration of hexaconazole. Hexaconazole application at 25 mg L(-1) concentration was found to be more effective than 10, 15, 20, 25, and 30 mg L(-1) in promoting fresh and dry weight of root tuber over 165 days after planting. The pigments like chlorophyll, carotenoid; anthocyanins, xanthophylls and antioxidants such as ascorbic acid, reduced glutathione and total phenol were significantly increased under hexaconazole treatment when compared to untreated control plants.