A β-glucuronidase (GUS) based cell death assay.

We have developed a novel transient plant expression system that simultaneously expresses the reporter gene, β-glucuronidase (GUS), with putative positive or negative regulators of cell death. In this system, N. benthamiana leaves are co-infiltrated with a 35S driven expression cassette containing the gene to be analyzed, and the GUS vector pCAMBIA 2301 using Agrobacterium strain LBA4404 as a vehicle.

A novel multilocus sequence typing scheme for the opportunistic pathogen Propionibacterium acnes and characterization of type I cell surface-associated antigens.

We have developed a novel multilocus sequence typing (MLST) scheme and database (http://pubmlst.org/pacnes/) for Propionibacterium acnes based on the analysis of seven core housekeeping genes. The scheme, which was validated against previously described antibody, single locus and random amplification of polymorphic DNA typing methods, displayed excellent resolution and differentiated 123 isolates into 37 sequence types (STs).

HDX-analyzer: a novel package for statistical analysis of protein structure dynamics.

Background: HDX mass spectrometry is a powerful platform to probe protein structure dynamics during ligand binding, protein folding, enzyme catalysis, and such. HDX mass spectrometry analysis derives the protein structure dynamics based on the mass increase of a protein of which the backbone protons exchanged with solvent deuterium. Coupled with enzyme digestion and MS/MS analysis, HDX mass spectrometry can be used to study the regional dynamics of protein based on the m/z value or percentage of deuterium incorporation for the digested peptides in the HDX experiments.

Natural roles of antimicrobial peptides in microbes, plants and animals.

Antimicrobial peptides (AMPs) are ribosomally synthesized natural antibiotics that are crucial effectors of innate immune systems in all living organisms. AMPs are diverse peptides, differing in their amino acid composition and structure, that generally display rapid killing and broad-spectrum antimicrobial activities. Therefore, AMPs have high potential for therapeutic use in healthcare and agriculture.

Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation.

Oligomeric amyloid-β is currently of interest in amyloid-β mediated toxicity and the pathogenesis of Alzheimer's disease. Mapping the amyloid-β interaction partners could help to discover novel pathways in disease pathogenesis. To discover the amyloid-β interaction partners, we applied a protein array with more than 8100 unique recombinantly expressed human proteins.

Innate immunity effectors and virulence factors in symbiosis.

Rhizobium-legume symbiosis has been considered as a mutually favorable relationship for both partners. However, in certain phylogenetic groups of legumes, the plant directs the bacterial symbiont into an irreversible terminal differentiation. This is mediated by the actions of hundreds of symbiosis-specific plant peptides resembling antimicrobial peptides, the effectors of innate immunity.

Phosphorylation of receptor-like cytoplasmic kinases by bacterial flagellin.

Molecular mechanisms that distinguish self and non-self are fundamental in innate immunity to prevent infections in plants and animals. Recognition of the conserved microbial components triggers immune responses against a broad spectrum of potential pathogens. In Arabidopsis, bacterial flagellin was perceived by a leucine-rich repeat-receptor-like kinase (LRR-RLK) FLS2.

AtBAG7, an Arabidopsis Bcl-2-associated athanogene, resides in the endoplasmic reticulum and is involved in the unfolded protein response.

The Bcl-2-associated athanogene (BAG) family is an evolutionarily conserved, multifunctional group of cochaperones that perform diverse cellular functions ranging from proliferation to growth arrest and cell death in yeast, in mammals, and, as recently observed, in plants. The Arabidopsis genome contains seven homologs of the BAG family, including four with domain organization similar to animal BAGs. In the present study we show that an Arabidopsis BAG, AtBAG7, is a uniquely localized endoplasmic reticulum (ER) BAG that is necessary for the proper maintenance of the unfolded protein response (UPR).

Resistance against various fungal pathogens and reniform nematode in transgenic cotton plants expressing Arabidopsis NPR1.

Cotton is an economically important crop worldwide that suffers severe losses due to a wide range of fungal/bacterial pathogens and nematodes. Given its susceptibility to various pathogens, it is important to obtain a broad-spectrum resistance in cotton. Resistance to several fungal and bacterial diseases has been obtained by overexpressing the Non-expressor of Pathogenesis-Related genes-1 (NPR1) in various plant species with apparently minimal or no pleiotropic effects.

A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity.

Plants and animals rely on innate immunity to prevent infections by detection of microbe-associated molecular patterns (MAMPs) through pattern-recognition receptors (PRRs). The plant PRR FLS2, a leucine-rich repeat-receptor kinase, recognizes bacterial flagellin and initiates immune signaling by association with another leucine-rich repeat-receptor-like kinase, BAK1. It remains unknown how the FLS2/BAK1 receptor complex activates intracellular signaling cascades.

QTL mapping of a high protein digestibility trait in Sorghum bicolor.

Compared with other cereal grains, Sorghum bicolor shows lower protein digestibility. The low digestibility is thought to result from disulfide cross linking in the beta- and gamma-kafirins. In contrast, the single recessive high digestibility/high lysine content (HD) mutation which confers greater grain digestibility exists in sorghum that is thought to result from reduced accumulation of gamma-kafirin that allows greater access to the high digestible alpha-kafarin fraction.

Defense-related gene expression and enzyme activities in transgenic cotton plants expressing an endochitinase gene from Trichoderma virens in response to interaction with Rhizoctonia solani.

There are many reports on obtaining disease-resistance trait in plants by overexpressing genes from diverse organisms that encode chitinolytic enzymes. Current study represents an attempt to dissect the mechanism underlying the resistance to Rhizoctonia solani in cotton plants expressing an endochitinase gene from Trichoderma virens. Several assays were developed that provided a powerful demonstration of the disease protection obtained in the transgenic cotton plants.

A Solanum lycopersicum x Solanum pimpinellifolium linkage map of tomato displaying genomic locations of R-genes, RGAs, and candidate resistance/defense-response ESTs.

We have identified an accession (LA2093) within the tomato wild species Solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. To utilize the full genetic potential of LA2093 in tomato breeding, we have developed a linkage map based on an F(2) population of a cross between LA2093 and a tomato breeding line, using 115 RFLP, 94 EST, and 41 RGA markers. The map spanned 1002.

Expression of anti-K99 scFv in transgenic rice tissues and its functional characterization.

As a first step towards manufacturing functional anti-K99 single chain variable antibody fragment (scFv) in a plant system to prevent colibacillosis in neonatal calves, we investigated the feasibility of producing these antibodies in rice plants. Two scFv constructs, with or without the endoplasmic reticulum (ER) targeting KDEL sequence, were introduced into rice for either ER-retention of the recombinant antibody or its secretion. In agreement with several other published reports, extremely low-levels of scFv were produced in rice plants transformed with the construct lacking the ER-targeting sequence.

Plant programmed cell death: can't live with it; can't live without it.

The decision of whether a cell should live or die is fundamental for the wellbeing of all organisms. Despite intense investigation into cell growth and proliferation, only recently has the essential and equally important idea that cells control/programme their own demise for proper maintenance of cellular homeostasis gained recognition. Furthermore, even though research into programmed cell death (PCD) has been an extremely active area of research there are significant gaps in our understanding of the process in plants.

Oxalic acid is an elicitor of plant programmed cell death during Sclerotinia sclerotiorum disease development.

Accumulating evidence supports the idea that necrotrophic plant pathogens interact with their hosts by controlling cell death. Sclerotinia sclerotiorum is a necrotrophic ascomycete fungus with a broad host range (>400 species). Previously, we established that oxalic acid (OA) is an important pathogenicity determinant of this fungus.

The BAG proteins: a ubiquitous family of chaperone regulators.

The BAG (Bcl-2 associated athanogene) family is a multifunctional group of proteins that perform diverse functions ranging from apoptosis to tumorigenesis. An evolutionarily conserved group, these proteins are distinguished by a common conserved region known as the BAG domain. BAG genes have been found in yeasts, plants, and animals, and are believed to function as adapter proteins forming complexes with signaling molecules and molecular chaperones.

Enhanced fungal resistance in transgenic cotton expressing an endochitinase gene from Trichoderma virens.

Mycoparasitic fungi are proving to be rich sources of antifungal genes that can be utilized to genetically engineer important crops for resistance against fungal pathogens. We have transformed cotton and tobacco plants with a cDNA clone encoding a 42 kDa endochitinase from the mycoparasitic fungus, Trichoderma virens. Plants from 82 independently transformed callus lines of cotton were regenerated and analysed for transgene expression.

A comprehensive study of the use of a homologous promoter in antisense cotton lines exhibiting a high seed oleic acid phenotype.

As opposed to first-generation biotechnology products, such as pest-resistant crops and herbicide-resistant crops, second-generation products often utilize plant-derived, homologous or heterologous genes and/or promoters. In this study, we evaluated the ability of a promoter from a gene encoding a major storage protein in cottonseed to drive an antisense sequence of the cotton FAD2 gene to down-regulate the activity of Delta-12 desaturase enzyme in cottonseeds. The oleic acid level in the transgenic cottonseeds approximately doubled from the wild-type level of 15%, with a concomitant decrease in the level of linoleic acid.

Engineering cottonseed for use in human nutrition by tissue-specific reduction of toxic gossypol.

Global cottonseed production can potentially provide the protein requirements for half a billion people per year; however, it is woefully underutilized because of the presence of toxic gossypol within seed glands. Therefore, elimination of gossypol from cottonseed has been a long-standing goal of geneticists. Attempts were made to meet this objective by developing so-called "glandless cotton" in the 1950s by conventional breeding techniques; however, the glandless varieties were commercially unviable because of the increased susceptibility of the plant to insect pests due to the systemic absence of glands that contain gossypol and other protective terpenoids.

Cotton (Gossypium hirsutum L.).

Considering the economic importance of cotton in many developing and developed countries, there is an urgent need to accelerate the application of biotechnological tools to address the problems associated with the production of this crop and to improve the quality of fiber and seed. This requires a simple yet robust gene delivery/transformant recovery system. A protocol for the production of transgenic cotton plants was refined in our laboratory.

Tomato QM-like protein protects Saccharomyces cerevisiae cells against oxidative stress by regulating intracellular proline levels.

Exogenous proline can protect cells of Saccharomyces cerevisiae from oxidative stress. We altered intracellular proline levels by overexpressing the proline dehydrogenase gene (PUT1) of S. cerevisiae.

Sorghum bicolor's transcriptome response to dehydration, high salinity and ABA.

Genome wide changes in gene expression were monitored in the drought tolerant C4 cereal Sorghum bicolor, following exposure of seedlings to high salinity (150 mM NaCl), osmotic stress (20% polyethylene glycol) or abscisic acid (125 microM ABA). A sorghum cDNA microarray providing data on 12,982 unique gene clusters was used to examine gene expression in roots and shoots at 3- and 27-h post-treatment. Expression of approximately 2200 genes, including 174 genes with currently unknown functions, of which a subset appear unique to monocots and/or sorghum, was altered in response to dehydration, high salinity or ABA.

Seasonal variation in gene expression for loblolly pines (Pinus taeda) from different geographical regions.

In developing xylem, gene expression levels vary in different genotypes, at different stages of development, throughout a growing season, and in response to stresses. Commercially important characteristics such as wood-specific gravity are known to differ with seed source. For example, when grown on a common site, the specific gravity of Arkansas loblolly pine (Pinus taeda L.