Productivity of important crop rice is greatly affected by salinity. The plant hormone jasmonate plays a vital role in salt stress adaptation, but also evokes detrimental side effects if not timely shut down again. As novel strategy to avoid such side effects, OsJAZ8, a negative regulator of jasmonate signalling, is expressed under control of the salt-inducible promoter of the transcription factor ZOS3–11, to obtain a transient jasmonate signature in response to salt stress. To modulate the time course of jasmonate signalling, either a full-length or a dominant negative C-terminally truncated version of OsJAZ8 driven by the ZOS3–11 promoter were expressed in a stable manner either in tobacco BY-2 cells, or in japonica rice. The transgenic tobacco cells showed reduced mortality and efficient cycling under salt stress adaptation. This was accompanied by reduced sensitivity to Methyl jasmonate and increased responsiveness to auxin. In the case of transgenic rice, the steady-state levels of OsJAZ8 transcripts were more efficiently induced under salt stress compared to the wild type, this induction was more pronounced in the dominant-negative OsJAZ8 variant. The result concluded that, more efficient activation of OsJAZ8 was accompanied by improved salt tolerance of the transgenic seedlings and demonstrates the impact of temporal signatures of jasmonate signalling for stress tolerance.

Application of chemical substances as stress pre-treatment factors may positively influence androgenetic responses in cereal and other crops. AgNO3 is an anti-ethylene compounds that played a significant role in combination with other chemicals for anther culture responses in cereal and other crop plants. For this study two local wheat cultivars viz. Kheri and Akbar were considered to evaluate the effect of AgNO3 and to optimize the suitable doses of plant growth regulators, amino acids and sucrose that supplemented in MS medium. Data were recorded on the basis of embryoids induction, regenerated green and albino plants. The results clearly stated that anther culture responses and its major outcomes on regeneration significantly increased with suitable dosages of chemicals. The most noteworthy increases embryo like structures and regenerated green plants accomplished by utilizing the combined effect of AgNO3 (50 mg/l) and as plant growth regulators IAA (1.0 mg/l) + kinetin (0.5 mg/l). Best embryo like structures (79.17%) and green plants (33.33%) were recorded in Kheri. The results clearly stated that reducing albinism and increasing embryos induction and green plants 50–75 mg/l silver nitrate along with optimum doses of IAA and kinetin showed very effective results in wheat.

Enhancement of callus induction and its regeneration efficiency through in vitro techniques has been optimized for two abiotic stresses (salt and air desiccation) using three rice genotypes viz. BR10, BRRI dhan32 and BRRI dhan47. The highest frequency of callus induction was obtained for BRRI dhan32 (64.44%) in MS medium supplemented with 2, 4-D (2.5 mgL−1) and Kin (1.0 mgL−1). Different concentrations of NaCl (2.9, 5.9, 8.8 and 11.7 gL−1) were used and its effect was recorded on the basis of viability of calli (VC), relative growth rate (RGR), tolerance index (TI) and relative water content (RWC). It was observed that in all cases BRRI dhan47 showed highest performance on tolerance to VC (45.33%), RGR (1.03%), TI (0.20%) and RWC (10.23%) with 11.7 gL−1 NaCl. Plant regeneration capability was recorded after partial air desiccation pretreatment to calli for 15, 30, 45 and 60 h. In this case BRRI dhan32 gave maximum number of regeneration (76.19%) when four weeks old calli were desiccated for 45 h. ...

Background and objectives: Identification of cancer biomarkers that are differentially expressed (DE) between two biological conditions is an important task in many microarray studies. There exist several methods in the literature in this regards and most of these methods designed especially for unpaired samples, those are not suitable for paired samples. Furthermore, the traditional methods use p-values or fold change (FC) values to detect the DE genes. However, sometimes, p-value based results do not comply with FC based results due to the smaller pooled variance of gene expressions, which occurs when variance of each individual condition becomes smaller. There are some methods that combine both p-values and FC values to solve this problem. But, those methods also show weak performance for small sample cases in the presence of outlying expressions. To overcome this problem, in this paper, an attempt is made to propose a hybrid robust SAM-FC approach by combining rank of FC values and rank of p-values computed by SAM statistic using minimum β-divergence method, which is designed for paired samples. Materials and Methods: The proposed method introduces a weight function known as β-weight function. This weight function produces larger weights corresponding to usual and smaller weights for unusual expressions. The β-weight function plays the significant role on the performance of the proposed method. The proposed method uses β-weight function as a measure of outlier detection by setting β = 0.2. We unify both classical and robust estimates using β-weight function, such that maximum likelihood estimators (MLEs) are used in absence of outliers and minimum β-divergence estimators are used in presence of outliers to obtain reasonable p-values and FC values in the proposed method. Results: We examined the performance of proposed method in a comparison of some popular methods (t-test, SAM, LIMMA, Wilcoxon, WAD, RP, and FCROS) using both simulated and real gene expression profiles for both small and large sample cases. From the simulation and a real spike in data analysis results, we observed that the proposed method outperforms other methods for small sample cases in the presence of outliers and it keeps almost equal performance with other robust methods (Wilcoxon, RP, and FCROS) otherwise. From the head and neck cancer (HNC) gene expression dataset, the proposed method identified two additional genes (CYP3A4 and NOVA1) that are significantly enriched in linoleic acid metabolism, drug metabolism, steroid hormone biosynthesis and metabolic pathways. The survival analysis through Kaplan–Meier curve revealed that combined effect of these two genes has prognostic capability and they might be promising biomarker of HNC. Moreover, we retrieved the 12 candidate drugs based on gene interaction from glad4u and drug bank literature based gene associations. Conclusions: Using pathway analysis, disease association study, protein–protein interactions and survival analysis we found that our proposed two additional genes might be involved in the critical pathways of cancer. Furthermore, the identified drugs showed statistical significance which indicates that proteins associated with these genes might be therapeutic target in cancer.

Three Bangladeshi barley genotypes viz. BARI barley?1, 3 and 6 were selected for this study to evaluate the efficiency of callus induction and plant regeneration. The effect of five doses of AgNO3 singly, and combined with amino acids (Lproline, L?glutamine) on callus induction and plant regeneration efficiency was evaluated using BARI barley?3 and 6. The maximum values of callus induction were recorded at 49.20 and 32.66% for BARI barley?6 and 3, respectively when 2.0 mg/l AgNO3 and 200 mg/l L?glutamine were added to the callus induction medium. Moreover, plant regeneration remarkably increased on MS + 1.0 mg/l BAP + 1.5 mg/l AgNO3 + 150 mg/l L?glutamine as 37.20% in BARI barley?6 and 16.13% in BARI barley?3. For rooting AgNO3 singly affect positively, whereas negative influence was observed in combinations with any amino acids. However, by using AgNO3 and amino acids, around < 4, < 27 and < 5 fold increase in callus induction were obtained. Regeneration and rooting were also found to increase considerably.Plant Tissue Cult. & Biotech. 25(1): 37-50, 2015 (June)