GridMAT-MD: a grid-based membrane analysis tool for use with molecular dynamics.

GridMAT-MD is a new program developed to aid in the analysis of lipid bilayers from molecular dynamics simulations. It reads a GROMACS coordinate file and generates two types of data: a two-dimensional contour plot depicting membrane thickness, and a polygon-based tessellation of the individual lipid headgroups. GridMAT-MD can also account for proteins or small molecules within the headgroups of the lipids, closely approximating their occupied lateral area.

The involvement of the interleukin-1 receptor-associated kinases (IRAKs) in cellular signaling networks controlling inflammation.

Innate immunity and inflammation plays a key role in host defense and wound healing. However, Excessive or altered inflammatory processes can contribute to severe and diverse human diseases including cardiovascular disease, diabetes and cancer. The interleukin-1 receptor-associated kinases (IRAKs) are critically involved in the regulation of intracellular signaling networks controlling inflammation.

A comparative molecular dynamics analysis of the amyloid beta-peptide in a lipid bilayer.

Because the amyloid beta-peptide (Abeta) functions as approximately half of the transmembrane domain of the amyloid precursor protein and interaction of Abeta with membranes is proposed to result in neurotoxicity, the association of Abeta with membranes likely is important in the etiology of Alzheimer's disease. Atomic details of the interaction of Abeta with membranes are not accessible with most experimental techniques, but computational methods can provide this information. Here, we present the results of ten 100-ns molecular dynamics (MD) simulations of the 40-residue amyloid beta-peptide (Abeta40) embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer.

Loss of the innate immunity negative regulator IRAK-M leads to enhanced host immune defense against tumor growth.

IRAK-M is a negative regulator of innate immunity signaling processes. Although attenuation of innate immunity may help to prevent excessive inflammation, it may also lead to compromised immune surveillance of tumor cells and contribute to tumor formation and growth. Here, we demonstrate that IRAK-M(-/-) mice are resistant to tumor growth upon inoculation with transplantable tumor cells.

Inositol polyphosphate 5-phosphatases 1 and 2 are required for regulating seedling growth.

Signals can be perceived and amplified at the cell membrane by receptors coupled to the production of a variety of second messengers, including myoinositol 1,4,5-trisphosphate [Ins(1,4,5)P(3)]. The myoinositol polyphosphate 5-phosphatases (5PTases; EC 3.1.

Recent insights into R gene evolution.

SUMMARY Plants are under strong evolutionary pressure to maintain surveillance against pathogens. Resistance (R) gene-dependent recognition of pathogen avirulence (Avr) determinants plays a major role in plant defence. Here we highlight recent insights into the molecular mechanisms and selective forces that drive the evolution of NB-LRR (nucleotide binding-leucine-rich repeat) resistance genes.

The type III effector repertoire of Pseudomonas syringae pv. syringae B728a and its role in survival and disease on host and non-host plants.

The bacterial plant pathogen Pseudomonas syringae injects a large repertoire of effector proteins into plant cells using a type III secretion apparatus. Effectors can trigger or suppress defences in a host-dependent fashion. Host defences are often accompanied by programmed cell death, while interference with defences is sometimes associated with cell death suppression.

Terpene synthases and the regulation, diversity and biological roles of terpene metabolism.

Terpene synthases are the primary enzymes in the formation of low-molecular-weight terpene metabolites. Rapid progress in the biochemical and molecular analysis of terpene synthases has allowed significant investigations of their evolution, structural and mechanistic properties, and regulation. The organization of terpene synthases in large gene families, their characteristic ability to form multiple products, and their spatial and temporal regulation during development and in response to biotic and abiotic factors contribute to the time-variable formation of a diverse group of terpene metabolites.

Molecular modeling of the effects of mutant alleles on chalcone synthase protein structure.

Chalcone synthase (CHS) catalyzes the first committed step in flavonoid biosynthesis, a major pathway of plant secondary metabolism. An allelic series for the Arabidopsis CHS locus, tt4, was previously characterized at the gene, protein, and end-product levels. In an effort to deduce the molecular basis for the observed phenotypes, homology models were generated for five of the tt4 proteins based on the crystal structure of CHS2 from Medicago.

SIRT1: tumor promoter or tumor suppressor?

Over the past decade, an intensive research on the basic biology of aging has identified individual genes either directly or indirectly involved in regulating the aging process in various model organisms. This allows us to garner all the information available from studies of model organisms and to apply them to better understand aging and cancer in human. Among many genes thus far reported contributing to aging process, the yeast silent information regulator-2 (SIR2) and its homologues in other species, which belong to the family of type III histone and protein deacetylases, have been the subject of active discussion.

Genetic analysis of developmentally regulated resistance to downy mildew (Hyaloperonospora parasitica) in Arabidopsis thaliana.

Although developmentally regulated disease resistance has been observed in a variety of plant-pathogen interactions, the molecular basis of this phenomenon is not well understood. Arabidopsis thaliana ecotype Columbia-0 (Col-0) expresses a developmentally regulated resistance to Hyaloperonospora parasitica isolate Emco5. Col-0 seedlings support profuse mycelial growth and asexual spore formation in the cotyledons.

Metabolic channeling in plants.

The organization of cooperating enzymes into macromolecular complexes is a central feature of cellular metabolism. A major advantage of such spatial organization is the transfer of biosynthetic intermediates between catalytic sites without diffusion into the bulk phase of the cell. This so-called "metabolic channeling" offers unique opportunities for enhancing and regulating cellular biochemistry.

Association of diamine oxidase and S-adenosylhomocysteine hydrolase in Nicotiana tabacum extracts.

The oxidative deamination of methylated putrescine by a diamine oxidase activity (DAO) is an important step in the biosynthesis of nicotine in tobacco and tropane alkaloids in several Solanaceous plants. A polyclonal rabbit antiserum was previously developed to a purported purified DAO enzyme from Nicotiana tabacum. The antiserum bound to a single 53 kDa protein and immunoprecipitated 80% of DAO activity from tobacco root extracts.

Production of recombinant proteins by hairy roots cultured in plastic sleeve bioreactors.

Plant-based expression of recombinant proteins offers significant advantages over transgenic animal-and cell-based systems. Unlike bacteria, plants perform the complex protein-processing steps required to produce eukaryotic proteins in active form. In order to facilitate protein production and purification we used hairy root cultures as a secretion-based in vitro plant system.

Convergent evolution of disease resistance genes.

The resistance genes Rpg1-b in soybean and RPM1 in Arabidopsis recognize the same bacterial avirulence protein (AvrB). Recent map-based cloning of Rpg1-b has provided the first opportunity to compare functionally analogous R genes in distantly related species. Rpg1-b and RPM1 are not orthologs.

Molecular characterization of an Arabidopsis gene encoding a phospholipid-specific inositol polyphosphate 5-phosphatase.

Phosphoinositides are important molecules that serve as second messengers and bind to a complex array of proteins modulating their subcellular location and activity. The enzymes that metabolize phosphoinositides can in some cases serve to terminate the signaling actions of phosphoinositides. The inositol polyphosphate 5-phosphatases (5PTases) comprise a large protein family that hydrolyzes 5-phosphates from a variety of inositol phosphate and phosphoinositide substrates.

Strategies for avoiding reinventing the precollege education and outreach wheel.

The National Science Foundation's recent mandate that all Principal Investigators address the broader impacts of their research has prompted an unprecedented number of scientists to seek opportunities to participate in precollege education and outreach. To help interested geneticists avoid duplicating efforts and make use of existing resources, we examined several precollege genetics, genomics, and biotechnology education efforts and noted the elements that contributed to their success, indicated by program expansion, participant satisfaction, or participant learning. Identifying a specific audience and their needs and resources, involving K-12 teachers in program development, and evaluating program efforts are integral to program success.

Meiotic recombination between paralogous RBCSB genes on sister chromatids of Arabidopsis thaliana.

Paralogous genes organized as a gene cluster can rapidly evolve by recombination between misaligned paralogs during meiosis, leading to duplications, deletions, and novel chimeric genes. To model unequal recombination within a specific gene cluster, we utilized a synthetic RBCSB gene cluster to isolate recombinant chimeric genes resulting from meiotic recombination between paralogous genes on sister chromatids. Several F1 populations hemizygous for the synthRBCSB1 gene cluster gave rise to Luc+ F2 plants at frequencies ranging from 1 to 3 x 10(-6).

Genomic organization and regulation of the LeIMP-1 and LeIMP-2 genes encoding myo-inositol monophosphatase in tomato.

Myo-inositol (inositol) monophosphatase (IMP), an enzyme which catalyzes the synthesis of free inositol from various inositol monophosphates, is encoded by a small multigene family in many organisms. The tomato IMP gene family encodes three IMP isoforms with identical in vitro biochemical properties. To determine the role of each tomato LeIMP gene in plant growth, we isolated the genomic DNA copies of the LeIMP-1 and LeIMP-2 genes.

Synergistic antimicrobial activity of metabolites produced by a nonobligate bacterial predator.

A naturally occurring, gram-negative, nonobligate predator bacterial strain 679-2, exhibits broad-spectrum antimicrobial activity that is due, in part, to the production of three extracellular compounds. Antimicrobial-activity-directed fractionation of a culture of strain 679-2 against a panel of microorganisms has led to the isolation of three compounds: pyrrolnitrin, maculosin, and a new compound, which we have named banegasine. Although pyrrolnitrin is well known in the literature, it has not been found in cells with the herbicide maculosin.

An Arabidopsis inositol 5-phosphatase gain-of-function alters abscisic acid signaling.

Signals can be perceived and amplified at the cell membrane by receptors coupled to the production of a variety of second messengers, including inositol 1,4,5-trisphosphate (IP3). We previously have identified 15 putative inositol 5-phosphatases (5PTases) from Arabidopsis and shown that At5PTase1 can hydrolyze IP3. To determine whether At5PTase1 can terminate IP3-mediated signaling, we analyzed transgenic plants ectopically expressing At5PTase1.

Plant disease resistance genes: recent insights and potential applications.

Plant disease resistance genes (R genes) encode proteins that detect pathogens. R genes have been used in resistance breeding programs for decades, with varying degrees of success. Recent molecular research on R proteins and downstream signal transduction networks has provided exciting insights, which will enhance the use of R genes for disease control.

A non-toxic lectin for antigen delivery of plant-based mucosal vaccines.

RicinB, the non-toxic galactose/N-acetylgalactosamine-binding subunit of ricin, was fused to a model antigen, green fluorescent protein (GFP), and expressed in tobacco plants and hairy root cultures to test for utility in mucosal vaccine delivery/adjuvancy. The fusion protein retained both GFP fluorescence and galactose/galactosamine-binding activity. Intranasal immunization of mice with galactosamine-affinity purified ricinB:GFP recovered from tobacco root cultures triggered significant increases in GFP-specific serum IgGs.