Signal transduction-related responses to phytohormones and environmental challenges in sugarcane

BACKGROUND: Sugarcane is an increasingly economically and environmentally important C4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. Sugarcane originated from crosses of Saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. Environmental stresses limit enormously sugarcane productivity worldwide. To investigate transcriptome changes in response to environmental inputs that alter yield we used cDNA microarrays to profile expression of 1,545 genes in plants submitted to drought, phosphate starvation, herbivory and N(2)-fixing endophytic bacteria. We also investigated the response to phytohormones (abscisic acid and methyl jasmonate). The arrayed elements correspond mostly to genes involved in signal transduction, hormone biosynthesis, transcription factors, novel genes and genes corresponding to unknown proteins. RESULTS: Adopting an outliers searching method 179 genes with strikingly different expression levels were identified as differentially expressed in at least one of the treatments analysed. Self Organizing Maps were used to cluster the expression profiles of 695 genes that showed a highly correlated expression pattern among replicates. The expression data for 22 genes was evaluated for 36 experimental data points by quantitative RT-PCR indicating a validation rate of 80.5% using three biological experimental replicates. The SUCAST Database was created that provides public access to the data described in this work, linked to tissue expression profiling and the SUCAST gene category and sequence analysis. The SUCAST database also includes a categorization of the sugarcane kinome based on a phylogenetic grouping that included 182 undefined kinases. CONCLUSION: An extensive study on the sugarcane transcriptome was performed. Sugarcane genes responsive to phytohormones and to challenges sugarcane commonly deals with in the field were identified. Additionally, the protein kinases were annotated based on a phylogenetic approach. The experimental design and statistical analysis applied proved robust to unravel genes associated with a diverse array of conditions attributing novel functions to previously unknown or undefined genes. The data consolidated in the SUCAST database resource can guide further studies and be useful for the development of improved sugarcane varieties

Characterization of a DNA Fragment from Streptococcus Pyogenes with Nucleotide Homology to Gyrase A Active Site

The concept of a topologically active DNA molecule, as opposed to a static Watson and Crick double helix, emerged in the mid 1960\u27s and since then researchers have attempted to elucidate the function that topological changes might have for DNA. An essential enzyme in this topological activity is deoxyribonucleic acid topoisomerase II or gyrase as it is referred to in eubacteria and archaebacteria. Gyrase has been focused on not only because of its genetic regulation, but also because of its interaction with several groups of antibiotics, one of these being the quinolone family of antibiotics. The newer fluoroquinolones, such as ciprofloxacin, norfloxacin, and enoxacin, exhibit improved antimicrobial activity, however activity against gram-positive bacteria such as streptococci is still considerably less than that observed for gram-negative bacteria. Streptococcal strains, and Streptococcus pyogenes in particular, consistently have been shown to exhibit the highest MICs to these drugs. For these reasons I feel that S. pyogenes would make an appropriate choice of gram-positive eubacteria from which to find a functional gyrase A subunit gene whose gene product interacts differently with quinolones, and hence may possess additional or different functional domains. With functionally different gyrase subunit A genes available for analysis, it will be possible to analyze function-to domain relationships of the A subunit and its interactions with the B subunit

Pim3 negatively regulates glucose-stimulated insulin secretion

Pancreatic β-cell response to glucose stimulation is governed by tightly regulated signaling pathways which have not been fully characterized. A screen for novel signaling intermediates identified Pim3 as a glucose-responsive gene in the β-cell, and here, we characterize its role in the regulation of β-cell function. Pim3 expression in the β-cell was first observed through microarray analysis on glucose-stimulated murine insulinoma (MIN6) cells where expression was strongly and transiently induced. In the pancreas, Pim3 expression exhibited similar dynamics and was restricted to the β-cell. Perturbation of Pim3 function resulted in enhanced glucose-stimulated insulin secretion, both in MIN6 cells and in isolated islets from Pim3-/- mice, where the augmentation was specifically seen in the second phase of secretion. Consequently, Pim3-/- mice displayed an increased glucose tolerance in vivo. Interestingly, Pim3-/- mice also exhibited increased insulin sensitivity. Glucose stimulation of isolated Pim3-/- islets resulted in increased phosphorylation of ERK1/2, a kinase involved in regulating β-cell response to glucose. Pim3 was also found to physically interact with SOCS6 and SOCS6 levels were strongly reduced in Pim3-/- islets. Overexpression of SOCS6 inhibited glucose-induced ERK1/2 activation, strongly suggesting that Pim3 regulates ERK1/2 activity through SOCS6. These data reveal that Pim3 is a novel glucose-responsive gene in the β-cell that negatively regulates insulin secretion by inhibiting the activation of ERK1/2, and through its effect on insulin sensitivity, has potentially a more global function in glucose homeostasis

Dealing with High Background Rates in the STAR Heavy Flavor Tracker in Simulation: Embedding Simulation into Real Events

The STAR Heavy Flavor Tracker (HFT) has enabled a rich physics program, providing important insights into heavy quark behavior in heavy ion collisions. Acquiring data during the 2014 through 2016 runs at the Relativistic Heavy Ion Collider (RHIC), the HFT consisted of four layers of precision silicon sensors. Used in concert with the Time Projection Chamber (TPC), the HFT enables the reconstruction and topological identification of tracks arising from charmed hadron decays. The ultimate understanding of the detector efficiency and resolution demands large quantities of high quality simulations, accounting for the precise alignment of sensors, and the detailed response of the detectors and electronics to the incident tracks. The background environment presented additional challenges, as simulating the significant rates from pileup events accumulated during the long integration times of the tracking detectors could have quickly exceeded the available computational resources, and the relative contributions from different sources was unknown. STAR has long addressed these issues by embedding simulations into background events directly sampled during data taking at the experiment. This technique has the advantage of providing a completely realistic picture of the dynamic background environment while introducing minimal additional computational overhead compared to simulation of the primary collision alone, thus scaling to any luminosity. We will discuss how STAR has applied this technique to the simulation of the HFT, and will show how the careful consideration of misalignment of precision detectors and calibration uncertainties results in the detailed reproduction of basic observables, such as track projection to the primary vertex. We will further summarize the experience and lessons learned in applying these techniques to heavy-flavor simulations and discuss recent results

Dealing with High Background Rates in the STAR Heavy Flavor Tracker in Simulation: Embedding Simulation into Real Events

The STAR Heavy Flavor Tracker (HFT) has enabled a rich physics program, providing important insights into heavy quark behavior in heavy ion collisions. Acquiring data during the 2014 through 2016 runs at the Relativistic Heavy Ion Collider (RHIC), the HFT consisted of four layers of precision silicon sensors. Used in concert with the Time Projection Chamber (TPC), the HFT enables the reconstruction and topological identification of tracks arising from charmed hadron decays. The ultimate understanding of the detector efficiency and resolution demands large quantities of high quality simulations, accounting for the precise alignment of sensors, and the detailed response of the detectors and electronics to the incident tracks. The background environment presented additional challenges, as simulating the significant rates from pileup events accumulated during the long integration times of the tracking detectors could have quickly exceeded the available computational resources, and the relative contributions from different sources was unknown. STAR has long addressed these issues by embedding simulations into background events directly sampled during data taking at the experiment. This technique has the advantage of providing a completely realistic picture of the dynamic background environment while introducing minimal additional computational overhead compared to simulation of the primary collision alone, thus scaling to any luminosity. We will discuss how STAR has applied this technique to the simulation of the HFT, and will show how the careful consideration of misalignment of precision detectors and calibration uncertainties results in the detailed reproduction of basic observables, such as track projection to the primary vertex. We will further summarize the experience and lessons learned in applying these techniques to heavy-flavor simulations and discuss recent results

Transplantation of PC1/3-Expressing α-cells Improves Glucose Handling and Cold Tolerance in Leptin-resistant Mice

Type 2 diabetes (T2D) is characterized by elevated blood glucose levels owing to insufficient secretion and/or activity of the glucose-lowering hormone insulin. Glucagon-like peptide-1 (GLP-1) has received much attention as a new treatment for diabetes because of its multiple blood glucose–lowering effects, including glucose-dependent enhancement of insulin secretion, inhibition of gastric emptying, and promotion of the survival and growth of insulin-producing β-cells. GLP-1, along with GLP-2 and oxyntomodulin, is produced in the intestinal L-cell via processing of proglucagon by prohormone convertase 1/3 (PC1/3), while in the pancreatic α-cell, coexpression of proglucagon and the alternate enzyme PC2 typically results in differential processing of proglucagon to yield glucagon. We used alginate-encapsulated α-cells as a model to evaluate continuous delivery of PC1/3- or PC2-derived proglucagon products. In high fat–fed and db/db mice, PC1/3-, but not PC2-expressing α-cells improved glucose handling and transiently lowered fasting glucose levels, suggesting that continuous delivery of PC1/3-derived proglucagon products via cell therapy may be useful for diabetes treatment. In addition, we show that long-term treatment with PC1/3-expressing, but not PC2-expressing, α-cells improved cold-induced thermogenesis in db/db mice, demonstrating a previously unappreciated effect of one or more PC1/3-derived α-cell products