Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis>)

Background  

Cultivated peanut or groundnut (Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut.     

S-Nitrosylation of Surfactant Protein-D Controls Inflammatory Function

The pulmonary collectins, surfactant proteins A and D (SP-A and SP-D) have been implicated in the regulation of the innate immune system within the lung. In particular, SP-D appears to have both pro- and anti-inflammatory signaling functions. At present, the molecular mechanisms involved in switching between these functions remain unclear. SP-D differs in its quaternary structure from SP-A and the other members of the collectin family, such as C1q, in that it forms large multimers held together by the N-terminal domain, rather than aligning the triple helix domains in the traditional “bunch of flowers” arrangement. There are two cysteine residues within the hydrophobic N terminus of SP-D that are critical for multimer assembly and have been proposed to be involved in stabilizing disulfide bonds. Here we show that these cysteines exist within the reduced state in dodecameric SP-D and form a specific target for S-nitrosylation both in vitro and by endogenous, pulmonary derived nitric oxide (NO) within a rodent acute lung injury model. S-nitrosylation is becoming increasingly recognized as an important post-translational modification with signaling consequences. The formation of S-nitrosothiol (SNO)-SP-D both in vivo and in vitro results in a disruption of SP-D multimers such that trimers become evident. SNO-SP-D but not SP-D, either dodecameric or trimeric, is chemoattractive for macrophages and induces p38 MAPK phosphorylation. The signaling capacity of SNO-SP-D appears to be mediated by binding to calreticulin/CD91. We propose that NO controls the dichotomous nature of this pulmonary collectin and that posttranslational modification by S-nitrosylation causes quaternary structural alterations in SP-D, causing it to switch its inflammatory signaling role. This represents new insight into both the regulation of protein function by S-nitrosylation and NO's role in innate immunity.     

Clioquinol inhibits peroxide-mediated toxicity through up-regulation of phosphoinositol-3-kinase and inhibition of p53 activity

A growing body of evidence supports a central role for biometals in neurodegenerative disorders. Biometals induce oxidative stress through the generation of reactive oxygen species and contribute to neuronal cell dysfunction in Alzheimer's disease (AD), prion disorders and Parkinson's disease (PD). Therapies based on modulation of biometal metabolism are currently being developed and the metal ligand, 5-chloro-7-iodo-8-hydroxyquinoline (clioquinol or CQ) has been investigated for the treatment of AD. CQ has also shown therapeutic benefits in an animal model of PD. However, little is known about the neuroprotective processes of CQ in vivo. In this study, we examined the effect of CQ in BE(2)-M17 human neuroblastoma cells exposed to increased oxidative stress (hydrogen peroxide (H2O2) treatment). Although CQ alone induced a moderate toxic effect on cells, when added to H2O2-treated M17 cells, CQ induced a significant inhibition of H2O2 toxicity. This correlated with up-regulation of phosphoinositol-3-kinase (PI3K) activity in CQ-treated cells. The protective action of CQ was not observed in murine N2a neuroblastoma cells treated with H2O2 and this cell-line did not reveal CQ-mediated increases in PI3K activation. The protective effect was specific for CQ and was not induced by a number of different metal ligands. Inhibition of PI3K activity with LY294002 prevented CQ protection against H2O2 toxicity, demonstrating a crucial role for CQ activation of PI3K in protection against oxidative stress. Furthermore, CQ inhibited H2O2-mediated up-regulation of p53 activity in the M17 cells and this was dependent on PI3K activation. Our studies demonstrate that in human M17 cells, CQ can protect against oxidative stress by activating the PI3K-dependent survival pathway and blocking p53-mediated cell death. These findings have important implications for the development of protective metal ligand-based therapies for treatment of disorders involving oxidative stress.     

Estimating a Treatment Effect in Residual Time Quantiles Under the Additive Hazards Model

For randomized clinical trials where the endpoint of interest is a time-to-event subject to censoring, estimating the treatment effect has mostly focused on the hazard ratio from the Cox proportional hazards model. Since the model’s proportional hazards assumption is not always satisfied, a useful alternative, the so-called additive hazards model, may instead be used to estimate a treatment effect on the difference of hazard functions. Still, the hazards difference may be difficult to grasp intuitively, particularly in a clinical setting of, e.g., patient counseling, or resource planning. In this paper, we study the quantiles of a covariate’s conditional survival function in the additive hazards model. Specifically, we estimate the residual time quantiles, i.e., the quantiles of survival times remaining at a given time t, conditional on the survival times greater than t, for a specific covariate in the additive hazards model. We use the estimates to translate the hazards difference into the difference in residual time quantiles, which allows a more direct clinical interpretation. We determine the asymptotic properties, assess the performance via Monte-Carlo simulations, and demonstrate the use of residual time quantiles in two real randomized clinical trials.     

Processing of type II procollagen amino propeptide by matrix metalloproteinases.

In many embryonic tissues, type IIA procollagen is synthesized and deposited into the extracellular matrix containing the NH(2)-propeptide, the cysteine-rich domain of which binds to bone morphogenic proteins. To investigate whether matrix metalloproteinases (MMPs) synthesized during development and disease can cleave the NH(2) terminus of type II procollagens, we tested eight types of enzymes. Recombinant trimeric type IIA collagen NH(2)-propeptide encoded by exons 1-8 fused to the lectin domain of rat surfactant protein D was used as a substrate. The latter allowed trimerization of the propeptide domain and permitted isolation by saccharide affinity chromatography. Although MMPs 1, 2, and 8 did not show cleavage, MMPs 3, 7, 9, 13, and 14 cleaved the recombinant protein both at the telopeptide region and at the procollagen N-proteinase cleavage site. MMPs 7 and 13 demonstrated other cleavage sites in the type II collagen-specific region of the N-propeptide; MMP-7 had another cleavage site close to the COOH terminus of the cysteine-rich domain. To prove that an MMP can cleave the native type IIA procollagen in situ, we demonstrated that MMP-7 removes the NH(2)-propeptide from collagen fibrils in the extracellular matrix of fetal cartilage and identified the cleavage products. Because the N-proteinase and telopeptidase cleavage sites are present in both type IIA and type IIB procollagens and the telopeptide cleavage site is retained in the mature collagen fibril, this processing could be important to type IIB procollagen and to mature collagen fibrils as well.     

Categorizing reactivity of bacteriorhodopsin cysteine mutants crosslinking to 4-bromoretinal.

The structure of bacteriorhodopsin (bR) has been probed by a large number of experimental methods. In earlier work distance constraints measured from the 1BRD Brookhaven structure (1, 2) were used to guide site-directed mutagenesis/affinity labeling experiments (3-5). In the present study we report on the use of limited molecular dynamics (MD) investigations of the same bR/affinity label system. We show here that the chiral center introduced when 4-bromo-all-trans retinal is synthesized produces variable impact on potential crosslinking. Our MD analysis suggests the following ranking of binding site mutants in order of reactivity: R118C > S118C > S121C > R141C > S141C > R121C, R138C, S138C. Chirality appears to have limited effect for the M118C mutants but shows more dramatic impact for the T121C and S141C mutants. These results are in excellent agreement with the experimental observations and offer encouragement that MD can be a useful component of experimental design with considerable predictive power.     

Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM–ligand interactions

Deciphering how enzymes interact, modify, and recognize carbohydrates has long been a topic of interest in academic, pharmaceutical, and industrial research. Carbohydrate-binding modules (CBMs) are noncatalytic globular protein domains attached to carbohydrate-active enzymes that strengthen enzyme affinity to substrates and increase enzymatic efficiency via targeting and proximity effects. CBMs are considered auspicious for various biotechnological purposes in textile, food, and feed industries, representing valuable tools in basic science research and biomedicine. Here, we present the first crystallographic structure of a CBM8 family member (CBM8), DdCBM8, from the slime mold Dictyostelium discoideum, which was identified attached to an endo-β-1,4-glucanase (glycoside hydrolase family 9). We show that the planar carbohydrate-binding site of DdCBM8, composed of aromatic residues, is similar to type A CBMs that are specific for crystalline (multichain) polysaccharides. Accordingly, pull-down assays indicated that DdCBM8 was able to bind insoluble forms of cellulose. However, affinity gel electrophoresis demonstrated that DdCBM8 also bound to soluble (single chain) polysaccharides, especially glucomannan, similar to type B CBMs, although it had no apparent affinity for oligosaccharides. Therefore, the structural characteristics and broad specificity of DdCBM8 represent exceptions to the canonical CBM classification. In addition, mutational analysis identified specific amino acid residues involved in ligand recognition, which are conserved throughout the CBM8 family. This advancement in the structural and functional characterization of CBMs contributes to our understanding of carbohydrate-active enzymes and protein–carbohydrate interactions, pushing forward protein engineering strategies and enhancing the potential biotechnological applications of glycoside hydrolase accessory modules.     

Neurospora crassa ribosomal DNA: sequence of internal transcribed spacer and comparison with N. intermedia and N. sitophila

Using [32P]DNA probes from a clone containing 17S, 5.8S and 26S rRNA of Neurospora crassa, the remainder of the repeat unit (RU) for ribosomal DNA (rDNA) has been cloned. Combining restriction analysis of the cloned DNA and restriction digests of genomic DNA, the RU was found to be 8.7 kb. The nucleotide sequence was determined for the internal transcribed spacer (ITS) regions one and two, for 5.8S rRNA and for portions of 17S and 26S rRNAs immediately flanking the ITS regions, and compared to the corresponding region of Saccharomyces carlsbergensis. In addition, a comparative restriction analysis of two other Neurospora species was performed using twelve restriction endonucleases. Genomic DNA blots of rDNA from N. intermedia and N. sitophila revealed rDNA RUs of 8.4 kb. The majority of differences in restriction patterns were confined to sequences outside the mature rRNA regions. However, one SmaI recognition site was found in 26S rRNA of N. crassa and N. sitophila but not in N. intermedia.     

Effect of seaweed concentrate fromEcklonia maxima (Osbeck) Papenfuss onMeloidogyne incognita infestation on tomato

Seaweed concentrate (SWC), prepared fromEcklonia maxima, when applied as a soil drench to tomato seedlings, significantly increased plant growth and reduced infestation byMeloidogyne incognita. Foliar applied SWC had little effect on plant growth and increased nematode galling. Ashing SWC reduced the suppressive effect on nematode infestation. In anin vitro experiment, SWC lessened infestation of root-knot nematodes on excised roots of a susceptible cultivar of tomato. Application of the same concentrations of SWC to a nematode-resistant cultivar increased the number of egg masses.