Swapan Kumar Roy

Morpho-Physiological and Proteome Level Responses to Cadmium Stress in Sorghum

Cadmium (Cd) stress may cause serious morphological and physiological abnormalities in addition to altering the proteome in plants. The present study was performed to explore Cd-induced morpho-physiological alterations and their potential associated mechanisms in Sorghum bicolor leaves at the protein level. Ten-day-old sorghum seedlings were exposed to different concentrations (0, 100, and 150 μM) of CdCl2, and different morpho-physiological responses were recorded. The effects of Cd exposure on protein expression patterns in S. bicolor were investigated using two-dimensional gel electrophoresis (2-DE) in samples derived from the leaves of both control and Cd-treated seedlings. The observed morphological changes revealed that the plants treated with Cd displayed dramatically altered shoot lengths, fresh weights and relative water content. In addition, the concentration of Cd was markedly increased by treatment with Cd, and the amount of Cd taken up by the shoots was significantly and directly correlated with the applied concentration of Cd. Using the 2-DE method, a total of 33 differentially expressed protein spots were analyzed using MALDI-TOF/TOF MS. Of these, treatment with Cd resulted in significant increases in 15 proteins and decreases in 18 proteins. Major changes were absorbed in the levels of proteins known to be involved in carbohydrate metabolism, transcriptional regulation, translation and stress responses. Proteomic results revealed that Cd stress had an inhibitory effect on carbon fixation, ATP production and the regulation of protein synthesis. Our study provides insights into the integrated molecular mechanisms involved in responses to Cd and the effects of Cd on the growth and physiological characteristics of sorghum seedlings. We have aimed to provide a reference describing the mechanisms involved in heavy metal damage to plants.

Bead Based Proteome Enrichment Enhances Features of the Protein Elution Plate (PEP) for Functional Proteomic Profiling

A novel functional proteomics technology called PEP(Protein Elution Plate) was developed to separate complex proteomes from natural sources and analyze protein functions systematically. The technology takes advantage of the powerful resolution of two-dimensional gel electrophoresis (2-D Gels). The modification of electrophoretic conditions in combination with a high-resolution protein elution plate supports the recovery of functionally active proteins. As 2DE(2-Dimensional Electrophoresis) resolution can be limited by protein load, we investigated the use of bead based enrichment technologies, called AlbuVoid™ and KinaSorb™ to determine their effect on the proteomic features which can be generated from the PEP platform. Using a variety of substrates and enzyme activity assays, we report on the benefits of combining bead based enrichment to improve the signal report and the features generated for Hexokinase, Protein Kinase, Protease, and Alkaline Phosphatase activities. As a result, the PEP technology allows systematic analysis of large enzyme families and can build a comprehensive picture of protein function from a complex proteome, providing biological insights that could otherwise not be observed if only protein abundances were analyzed.

Relative Distribution of Free Amino Acids in Buckwheat

The most abundant amino acid in the sprouts of common buckwheat (CB) was Val (40%), followed by Tyr (28%), whereas Val accounted for 62% in tatary buckwheat (TB). The buckwheat stem and root commonly contained Gln (40–42% in stem; 30–37% in root). Thus, soluble amino nitrogen source is used for Gln in buckwheat. The main difference of amino acid distribution in 3 tissues between CB and TB was Tyr in sprouts. A low level of Tyr in TB was presumably resulted from the conversion to other phenolic metabolites. The content of essential free amino acids in TB sprout was 53% higher than that in CB. Thus, the TB sprouts are beneficial to the human nutrition.

Protein Profiling Reveals Novel Proteins in Pollen and Pistil of W22 (ga1; Ga1) in Maize

Gametophytic factors mediate pollen-pistil interactions in maize (Zea mays L.) and play active roles in limiting gene flow among maize populations and between maize and teosinte. This study was carried out to identify proteins and investigate the mechanism of gametophytic factors using protein analysis. W22 (ga1); which did not carry a gametophytic factor and W22 (Ga1), a near iso-genic line, were used for the proteome investigation. SDS-PAGE was executed to investigate proteins in the pollen and pistil of W22 (ga1) and W22 (Ga1). A total of 44 differentially expressed proteins were identified in the pollen and pistil on SDS-PAGE using LTQ-FTICR MS. Among the 44 proteins, a total of 24 proteins were identified in the pollen of W22 (ga1) and W22 (Ga1) whereas 20 differentially expressed proteins were identified from the pistil of W22 (ga1) and W22 (Ga1). However, in pollen, 2 proteins were identified only in the W22 (ga1) and 12 proteins only in the W22 (Ga1) whereas 10 proteins were confirmed from the both of W22 (ga1) and W22 (Ga1). In contrary, 10 proteins were appeared only in the pistil of W22 (ga1) and 7 proteins from W22 (Ga1) while 3 proteins confirmed in the both of W22 (ga1) and W22 (Ga1). Moreover, the identified proteins were generally involved in hydrolase activity, nucleic acid binding and nucleotide binding. These results help to reveal the mechanism of gametophytic factors and provide a valuable clue for the pollen and pistil research in maize.

Methods to Monitor the Functional Subproteomes of SERPIN Protease Inhibitors

Conformational variants of the unique family of protease inhibitors annotated as SERPINs are most often underrepresented in proteomic analyses. This limits understanding the complex regulation that this family of proteins presents to the networks within the protease web of interactions. Using bead-based separation provided by a family of proteomic enrichment products-notably AlbuVoid™ and AlbuSorb™, we demonstrate their utility to satisfy investigations of serum SERPINs. We also suggest their use to develop functional profiles of the SERPIN proteoforms, and how those can establish relationships to disease phenotypes, gene mutations, and dysregulated mechanisms.

Inheritance of Self-Compatibility in a Buckwheat Hybrid

Abstract This study was conducted to determine the inheritance of self-compatibility and homomorphic flower type when the wild species Fagopyrum homotropicum was crossed with common buckwheat (Fagopyrum esculentum). Unidirectional interspecific hybrids between cultivated F. esculentum Moench. (common buckwheat) and its wild relative F. homotropicum were produced after controlled pollination and embryo rescue culture. Cross-compatibility was found to be better when thrum-type common buckwheat was used as the female parent rather than the pin-type. The resulting F1 plants were partially fertile, late maturing, and intermediate between the parents in flower shape and plant height. They segregated into heterostylic (thrum only) and homostylic types in equal number, indicating that homostyly is controlled by a single dominant gene. The thrum-type F1 hybrids were backcrossed to common buckwheat and the progenies were raised utilizing embryo rescue culture. The homostylic F1 hybrids were advanced to the F2 and F3 generations through self-fertilization and utilized, together with the BC1F1, for the analysis of the stylar genes. The results obtained indicate that the genes coding for heterostyly and homostyly are controlled by the multiple allelic gene S. It appears that the pin/thrum complex in F. esculentum is governed by a single genetic locus S with two alleles, S and s, that control the reaction in Ss (thrum-type) as well as the ss (pin-type) plants, respectively. The homomorphic flower type of F. homotropicum is governed by the allele Sh. These genes can be characterized by a relationship of dominance, i.e., S>Sh>s. The introgression of F. homotropicum genes into common buckwheat was verified by means of electrophoretic analysis of seed proteins.

Distribution of Amino Acids in Buckwheat

Abstract The amino acids found to be abundant in common buckwheat (CB) sprouts was Val (40%), followed by Tyr (28%), whereas Val accounted for 62% in Tartary buckwheat (TB). The buckwheat stem and root commonly contained Gln (40%–42% in stem; 30%–37% in root). Thus, soluble amino nitrogen source is used for Gln in buckwheat. The main difference of amino acid distribution in 3 tissues between CB and TB was Tyr in sprouts. A low level of Tyrin TB presumably resulted from the conversion to other phenolic metabolites. The content of essential free amino acids in TB sprout was 53% higher than that in CB. Thus, the TB sprouts are beneficial to human nutrition.

In vivo Acclimatization Responses of Platycodon grandiflorum For. Duplex to Different Soil Types and Environmental Factors

This study aimed to evaluate the effects of soil types and environmental factors for optimum conditions of seedlings growth of the Platycodon grandiflorum for establishing the in vivo acclimatization system of regenerated plants derived from the in vitro culture. P. grandflorum seedlings were transferred to the in vivo condition and acclimatized under different soil types, light intensities, and various temperatures. Changes caused by environmental factors and soil types in plant growth viz. plant height, leaf width, leaf length, stem diameter, number of leaves, branches and nodes were recorded in this study. Among the nine types of soil, the best growth performances were obtained from the soil type SVP (Soil mixed with horticultural bed soil, vermiculite, and perlite @ 2:1:1). Seedlings of P. grandiflorum showed the best growth at higher levels of light intensity (60 μmol·m-2·s-1). In contrast, P. grandiflorum seedlings showed the best growth response at a moderate level of temperature (25°C). Collectively, the present study provides a better understanding of the responses of growth characteristics in P. grandiflorum seedlings exposed to various soil types, light intensities, and temperatures.

Stroma liquid biopsy™-a proteomic model of the systemic response to cancer

The advancements in “nextgen” and rapid genome sequencing have spawned new companies for liquid biopsy products and services that are quick, minimally invasive and that allow clinicians to monitor the course of therapy and to forecast recurrent disease. While these are certainly exciting prospects, challenges remain as genomic instability is a fundamental hallmark of cancer cells [1]. So in many respects, genomic driven approaches will always suffer the problem of shooting after a moving target.

Concepts, Prospects, and Potentiality in Buckwheat ( Fagopyrum esculentum Moench): A Research Perspective

Abstract Buckwheat (Fagopyrum esculentum) is an important crop grown throughout the world for its potential value to humans and livestock. It is believed to have been a popular grain and forage crop for centuries, with the origin of domestication thought to be the eastern Tibetan plateau, bordering the Chinese province of Yunnan. The main producers of buckwheat are China, Russian Federation, Ukraine, and Kazakhstan. Recently, much research progress has been attempted to investigate the biotechnological and genetic characterization as well as to mitigate the breeding barriers of buckwheat. The methods of conventional breeding are only partially applicable because of the self-incompatibility barriers among different species. However, excellent research progress related to concepts, prospects, and potentiality in buckwheat has been focused on in this review. This review critically and constructively summarizes the biotechnological advancement of buckwheat, especially tissue culture and genetic progress, such as self-incompatibility and conventional breeding. In addition, prospects and potentiality of the introduction and establishment of buckwheat and the application of modern technologies are assessed. This review aims to introduce the recent advancement of research dealing with biotechnology and genetics as well as to understand the necessity and impact of buckwheat.