Molecular dissection of QTL governing grain size traits employing association and linkage mapping in Basmati rice

Grain size is one of the key traits that determines the quality of Basmati rice from the consumers’ as well as the traders’ point of view. Though many genes governing grain size have been identified in indica and japonica, little work has been done in Basmati rice. The present study aims at dissection of a QTL region governing grain size traits in Basmati employing association and linkage mapping approaches. Association mapping revealed that three markers, i.e., RM 6024 (grain breadth), RM1237 and RM18582 (grain length-breadth ratio), which cover 889 kb in the targeted QTL region have been significantly associated with grain size traits. Using linkage mapping, the targeted QTL region has been further delimited to a physical distance of 268 kb that comprises 24 annotated genes. The gene expression analysis of parents, revealed 19 genes differentially expressing within the QTL. Of them, 15 genes showed high expression in Basmati370, while four were expressed in Jaya, and whereas five genes did not show any differential expression between parents. Among differentially expressed genes, a highly expressed gene in Basmati370, Os05g0374200 (Cytokinin dehydrogenase 1 precursor) seems to be involved in accumulation of cytokinins, thus affecting the grain size. Therefore, our findings demonstrated that by complimenting association and linkage mapping, it is likely to dissect a QTL governing grain size traits in Basmati rice and also the QTL could be a potential target for marker-assisted breeding and map-based cloning studies.     

Modulation of ROS production and hormone levels by AHK5 during abiotic and biotic stress signaling

Histidine kinases have been shown to mediate responses to endogenous and exogenous stimuli in organisms such as yeast, bacteria and plants. In the model plant Arabidopsis, histidine kinases have been shown to function in hormone signaling, and abiotic and biotic stress responses. More recently, the least characterized of the Arabidopsis histidine kinases, AHK5, was demonstrated to function in resistance toward the virulent bacterium Pseudomonas syringae pv tomato DC3000 (PstDC3000) and the necrotrophic fungus Botrytis cinerea, and as a negative regulator of tolerance toward salinity. Here, we present data which indicate that AHK5 also impacts on drought stress resistance and on the outcome of an incompatible interaction with avrRpm1-expressing PstDC3000 (PstDC3000 (avrRpm1)). We present a model which proposes a role for reactive oxygen species (ROS) and hormones in integrating abiotic and biotic stress responses via AHK5.     

Arrhythmogenic risks of stem cell replacement therapy for cardiovascular diseases

Ischemic heart disease and congestive heart failure are major contributors to high morbidity and mortality. Approximately 1.5 million cases of myocardial infarction occur annually in the United States; the yearly incidence rate is approximately 600 cases per 100,000 people. Although significant progress to improve the survival rate has been made by medications and implantable medical devices, damaged cardiomyocytes are unable to be recovered by current treatment strategies. After almost two decades of research, stem cell therapy has become a very promising approach to generate new cardiomyocytes and enhance the function of the heart. Along with clinical trials with stem cells conducted in cardiac regeneration, concerns regarding safety and potential risks have emerged. One of the contentious issues is the electrical dysfunctions of cardiomyocytes and cardiac arrhythmia after stem cell therapy. In this review, we focus on the cell sources currently used for stem cell therapy and discuss related arrhythmogenic risk.     

Sonic hedgehog pathway activation regulates cervical cancer stem cell characteristics during epithelial to mesenchymal transition

Resistance to therapy and metastasis remains one of the leading causes of mortality due to cervical cancer despite advances in detection and treatment. The mechanism of epithelial to mesenchymal transition (EMT) provides conceptual explanation to the invasiveness and metastatic spread of cancer but it has not been fully understood in cervical cancer. This study aims to investigate the mechanism by which silencing of E-cadherin gene regulates EMT leading to proliferation, invasion, and chemoresistance of cervical cancer cells through the Hedgehog (Hh) signaling pathway. We developed an in vitro EMT model by the knockdown of E-cadherin expression in cervical cancer cell lines. To understand the role of developmental pathway like Hh in the progression of cervical cancer, we investigated the expression of Hh pathway mediators by array in E-cadherin low cervical cancer cells and observed upregulation of Hh pathway. This was further validated on low passage patient-derived cell lines and cervical carcinoma tissue sections from cervical cancer patients. Further, we evaluated the role of two inhibitors (cyclopamine and GANT58) of the Hh pathway on invasiveness and apoptosis in E-cadherin low cervical cancer cells. In conclusion, we observed that inhibition of Hh pathway with GANT58 along with current therapeutic procedures could be more effective in targeting drug-resistant EMT cells and bulk tumor cells in cervical cancer.     

The role of stigma peroxidases in flowering plants: insights from further characterization of a stigma-specific peroxidase (SSP) from Senecio squalidus (Asteraceae)

Angiosperm stigmas have long been known to exhibit high levels of peroxidase activity when they are mature and most receptive to pollen but the biological function of stigma peroxidases is not known. A novel stigma-specific class III peroxidase gene, SSP (stigma-specific peroxidase) expressed exclusively in the stigmas of Senecio squalidus L. (Asteraceae) has recently been identified. Expression of SSP is confined to the specialized secretory cells (papillae) that compose the stigma epidermis. The literature on stigma peroxidases and hypotheses on their function(s) is reviewed here before further characterization of SSP and an attempt to determine its function are described. It is shown that SSP is localized to cytoplasmic regions of stigmatic papillae and also to the surface of these cells, possibly as a component of the pellicle, a thin layer of condensed protein typical of "dry" stigmas. Enzyme assays on recombinant SSP showed it to be a peroxidase with a preference for diphenolic substrates (ABTS and TMB) and a pH optimum of approximately 4.5. In such assays the peroxidase activity of SSP was low when compared with horseradish peroxidase. To explore the function of SSP and other stigmatic peroxidases, levels of reactive oxygen species (ROS) in stigmas of S. squalidus were investigated. Relatively large amounts of ROS, principally H(2)O(2), were detected in S. squalidus stigmas where most ROS/H(2)O(2) was localized to the stigmatic papillae, the location of SSP. These observations are discussed in the context of possible functions for SSP, other peroxidases, and ROS in the stigmas of angiosperms.     

Bounded search for de novo identification of degenerate cis-regulatory elements

Background  

The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-counting strategy for their identification. While numerous methods exist for inferring base distributions using a position weight matrix, recent studies suggest that the independence assumptions inherent in the model, as well as the inability to reach a global optimum, limit this approach.