Rejuvenating rice proteomics: facts, challenges, and visions

Proteomics is progressing at an unprecedented pace, as can be exemplified by the progress in model organisms such as yeast, bacteria, and mammals. Proteomics research in plants, however, has not progressed at the same pace. Unscrambling of the genome sequences of the dicotyledoneous Arabidopsis thaliana (L.) and monocotyledoneous rice (Oryza sativa L.) plant species, respectively, has made them accessible reference organisms to study plant proteomics. Study of these two reference plants is expected to unravel the mystery of plant biology. Rice, a critically important food crop on the earth, has been termed a "cornerstone" and the "Rosetta stone" for functional genomics of cereal crops. Here, we look at the progress in unraveling rice proteomes and present the facts, challenges, and vision. The text is divided into two major parts: the first part presents the facts and the second part discusses the challenges and vision. The facts include the technology and its use in developing proteomes, which have been critically and constructively reviewed. The challenges and vision deal with the establishment of technologies to exhaustively investigate the protein components of a proteome, to generate high-resolution gel-based reference maps, and to give rice proteomics a functional dimension by studying PTMs and isolation of multiprotein complexes. Finally, we direct a vision on rice proteomics. This is our third review in series on rice proteomics, which aims to stimulate an objective discussion among rice researchers and to understand the necessity and impact of unraveling rice proteomes to their full potential.     

The usefulness of contrast-enhanced sonography in the differential diagnostic of adrenal tumors

INTRODUCTION: The occurrence of gland tumors causes significant clinical problem. Non hormone-secreting tumors provide the most complicated diagnostic difficulties. The application of contrast-enhanced sonography could improve the vessels visualization and point out characteristic features of benign and malignant changes. The authors believe that this new method make possible the differential adrenal tumor diagnostic process more precise and increase the specificity of ultrasonography in the recognition of benign and malignant tumors. The aim of this study was to define the usefulness of contrasting agent Levovist in differential diagnostics of adrenal tumors and its influence on sensitivity and specificity of ultrasound examination and to establish patients qualification criteria for surgical procedures. MATERIAL AND METHODS: Ultrasound examinations were made with the use of digital devise by GE Voluson 740, probe 4-6 mHz with Doppler options and volumetric probe 3D according to the following protocol: 26 patients with recognized adrenal tumor were qualified for the examination. Patients in the first stage of tumor vascularization had Doppler examination with color (CD) and power Doppler (PD). Three-dimensional ultrasonography was used to improve visualization of vascularization. In the final phase of the examination the patients were administrated of Levovist in the recommended by the producer dose: 2.5 g in the concentration of 400 mg/l. RESULTS: 26 cases of adrenal gland tumours were subjected to analysis. In standard ultrasonographic examination focal changes in 25 patients were hipoechogenic focuses and in one case the focus was hyperechogenic. Heterogeneity of focuses was observed in 16 cases. In Doppler examination with color (CD) and power Doppler (PD) vascular blood flow was revealed within 12. After using contrasting agent Levovist vascular blood flow was achieved in 4 additional cases, which constituted 61%. CONCLUSIONS: 1. 3D ultrasound could be useful in cases of big adrenal tumors--over 3 cm diameter after application of ultrasound contrast agents. 2. The use of Levovist in Doppler examination improves the visualization of tumor vascularization. However, it is impossible to differentiate benign from malignant tumors unequivocally.     

Search for novel stress-responsive protein components using a yeast mutant lacking two cytosolic Hsp70 genes, SSA1 and SSA2

Heat shock proteins (Hsp) 70 are a ubiquitous family of molecular chaperones involved in many cellular processes. A yeast strain, ssa1/2, with two functionally redundant cytosolic Hsp70s (SSA1 and SSA2) deleted shows thermotolerance comparable to mildly heat-shocked wild type yeast, as well as increased protein synthesis and ubiquitin-proteasome protein degradation. Since mRNA abundance does not always correlate well with protein expression levels it is essential to study proteins directly. We used a gel-based approach to identify stress-responsive proteins in the ssa1/2 mutant and identified 43 differentially expressed spots. These were trypsin-digested and analyzed by nano electrospray ionization liquid chromatography tandem mass spectrometry (nESI-LC-MS/MS). A total of 22 non-redundant proteins were identified, 11 of which were confirmed by N-terminal sequencing. Nine proteins, most of which were up-regulated (2-fold or more) in the ssa1/2 mutant, proved to be stress-inducible proteins such as molecular chaperones and anti-oxidant proteins, or proteins related to carbohydrate metabolism. Interestingly, a translational factor Hyp2p up-regulated in the mutant was also found to be highly phosphorylated. These results indicate that the cytosolic Hsp70s, Ssa1p and Ssa2p, regulate an abundance of proteins mainly involved in stress responses and protein synthesis.     

New protein extraction/solubilization protocol for gel-based proteomics of rat (female) whole brain and brain regions

The rat is an accepted model for studying human psychiatric/neurological disorders. We provide a protocol for total soluble protein extraction using trichloroacetic acid/acetone (TCA/A) from rat (female) whole brain, 10 brain regions and the pituitary gland, and show that two-dimensional gel electrophoresis (2-DGE) using pre-cast immobilized pH (4-7) gradient (IPG) strip gels (13 cm) in the first dimension yields clean silver nitrate stained protein profiles. Though TCA/A precipitation may not be "ideal", the important choice here is the selection of an appropriate lysis buffer (LB) for solubilizing precipitated proteins. Our results reveal enrichment of protein spots by use of individual brain regions rather than whole brain, as well as the presence of differentially expressed spots in their proteomes. Thus individual brain regions provide improved protein coverage and are better suited for differential protein detection. Moreover, using a phosphoprotein-specific dye, in-gel detection of phosphoproteins was demonstrated. Representative high-resolution silver nitrate stained proteome profiles of rat whole brain total soluble protein are presented. Shortcomings apart (failure to separate membrane proteins), gel-based proteomics remains a viable option, and 2-DGE is the method of choice for generating high-resolution proteome maps of rat brain and brain regions.     

Similarity selection and the evolution of sex: revisiting the red queen

For over 25 years, many evolutionary ecologists have believed that sexual reproduction occurs because it allows hosts to change genotypes each generation and thereby evade their coevolving parasites. However, recent influential theoretical analyses suggest that, though parasites can select for sex under some conditions, they often select against it. These models assume that encounters between hosts and parasites are completely random. Because of this assumption, the fitness of a host depends only on its own genotype (“genotypic selection”). If a host is even slightly more likely to encounter a parasite transmitted by its mother than expected by random chance, then the fitness of a host also depends on its genetic similarity to its mother (“similarity selection”). A population genetic model is presented here that includes both genotypic and similarity selection, allowing them to be directly compared in the same framework. It is shown that similarity selection is a much more potent force with respect to the evolution of sex than is genotypic selection. Consequently, similarity selection can drive the evolution of sex even if it is much weaker than genotypic selection with respect to fitness. Examination of explicit coevolutionary models reveals that even a small degree of mother–offspring parasite transmission can cause parasites to favor sex rather than oppose it. In contrast to previous predictions, the model shows that weakly virulent parasites are more likely to favor sex than are highly virulent ones. Parasites have figured prominently in discussions of the evolution of sex, but recent models suggest that parasites often select against sex rather than for it. With the inclusion of small and realistic exposure biases, parasites are much more likely to favor sex. Though parasites alone may not provide a complete explanation for sex, the results presented here expand the potential for parasites to contribute to the maintenance of sex rather than act against it.     

Immunomodulatory role of vascular endothelial growth factor and angiopoietin-1 in airway remodeling

The blood vessels formed in asthmatic airways are involved in inflammatory and airway remodeling processes in chronic asthma. Vascular endothelial cell growth factor (VEGF) and angiopoietin-1 (Ang-1) are primary angiogenic growth factors, involved in the formation of such blood vessels. VEGF has been reported to contribute to non-specific airway hyper-responsiveness, have chemotactic effects on eosinophils, and enhance airway smooth muscle cell proliferation. Furthermore, Th2 cells have receptors for VEGF, and Th2-associated cytokines increase VEGF production. There are reports that elevated levels of VEGF correlates with the severity of asthma. Ang-1 has been shown to induce pro-inflammatory effects such as eosinophil chemotaxis via tie-2 receptors. Reports indicate ang-1 contribution to increased secretion of matrix metalloproteinase-2 (MMP-2) and decreased secretion of tissue inhibitors of metalloproteinase-2 (TIMP-2). However, Ang-1 has also been shown to exhibit several anti-inflammatory properties such as suppressing expression of adhesion molecules, blocking vascular permeability and eosinophil chemotaxis induced by VEGF. These findings support the notion that apart from their roles in blood vessels formation, these angiogenic growth factors are directly involved in the pathogenesis of chronic asthma. This paper reviews individual and combined roles of VEGF and Ang-1. The potential therapeutic applications involving these factors are also discussed.     

Diversity of culturable sulfidogenic bacteria in two oil–water separation tanks in the north-eastern oil fields of India

Sulfidogenic communities in the production waters of onshore oil fields in north-eastern India were examined using a culturing approach. Production water samples were inoculated into medium selective for Sulfate reducing bacteria (SRB) and Thiosulfate Reducing Bacteria (TRB). The total number of viable sulfidogenic microorganisms in the samples obtained from the two production water tanks was approximately 10⁵ MPN ml^?1 (most probable number per ml). Most of the isolates were thermo-tolerant and could be grown between 40 and 45 °C. Hydrogen sulfide production by TRB was significantly higher than by SRB. Based on 16S rRNA gene sequencing, the isolates were grouped in nine different phylotypes. Phylogenetic analysis indicated that most of the SRB were affiliated with the phylum Proteobacteria, encompassing Gram-negative bacteria, belonging to the genera Desulfovibrio, Desulfomicrobium, and Desulfobulbus. However, five isolates grouped with the genus Desulfotomaculum were found to be gram-positive SRB. Most of the thiosulfate reducing isolates was affiliated with the phylum Firmicutes, including Clostridium and Fusibacter and also with the phylum Proteobacteria, including the genera Enterobacter and Citrobacter. Phylotypes related to Clostridium (69%) and Desulfovibrio (53%) dominated the community in the production water samples. This study demonstrates the diversity of the TRB and SRB that play a critical role in the souring mediated corrosion of the oil–water separation tanks in the north-eastern India oil fields.     

Preparation and evaluation of tubular micelles of pluronic lecithin organogel for transdermal delivery of sumatriptan

The present work focuses on the preparation and evaluation of lecithin organogel system of thermoreversible polymer pluronic F127, which would enhance the stability and absorption of sumatriptan succinate across the skin. Formulations were developed with and without co-surfactant (pluronic F127). The prepared organogels were evaluated for its appearance, organoleptic characteristics, and feel upon application, homogeneity, occlusivenes, washability, pH, viscosity, spreadability, gel transition temperature of formulations. The formulations were also evaluated for drug content, in vitro drug diffusion properties and skin irritation testing. In vivo evaluation of formulations was carried out by hot plate and writhing test method, and finally the optimized formulation was subjected to stability studies. The developed formulations were easily washable, smooth in feel, and showed no clogging which indicate superior texture of system. Formulation, containing pluronic showed greater spreadability and higher drug diffusion rate as compared to pluronic free organogel. Drug content of organogel formulations was in the range of 94-97%. The pH of the formulations was 6.48 ± 0.5 and 6.98 ± 0.1, reflecting no risk of skin irritation. Pluronic not only enhances the stability of organogel by increasing the viscosity (from 6,541 ± 234.76 to 7,826 ± 155.65 poise) but also increases the release of drug from 67.39 ± 1.53% to 74.21 ± 1.7%. The sumatriptan exhibits higher and long lasting antinociceptive effect as indicated by the persistent increase in reaction time in hot plate and inhibited abdominal contraction in acetic acid-induced writhing test (p < 0.05). The prepared optimized formulation was found to be stable without any significant changes at room temperature.     

Enantioselective cyanoformylation of aldehydes catalyzed with solid base mediated chiral V(V) salen complexes

Polymeric and monomeric V(V) chiral salen complexes‐catalyzed enantioselective ethyl cyanoformylation of aldehydes using ethyl cyanoformate as a source of cyanide was accomplished in the presence of several basic cocatalysts viz., NaOH, KOH, basic Al₂O₃ and hydrotalcite. Excellent yield (>95%) of chiral ethyl cyanohydrincarbonate with high enantioselectivity up to 94% was achieved in 24–36 h when hydrotalcite was used as an additive. The polymeric catalyst 1 is more reactive than the monomeric catalyst 2 to produce chiral ethyl cyanohydrincarbonate in high optical purity. The chiral polymeric catalyst 1 and cocatalysts hydrotalcite and basic alumina used in this study were recoverable and recyclable several times with retention of its performance. Chirality, 2010. © 2009 Wiley‐Liss, Inc.