Molecular evolution of chloroplast DNA sequences

Comparative data on the evolution of chloroplast genes are reviewed. The chloroplast genome has maintained a similar structural organization over most plant taxa so far examined. Comparisons of nucleotide sequence divergence among chloroplast genes reveals marked similarity across the plant kingdom and beyond to the cyanobacteria (blue-green algae). Estimates of rates of nucleotide substitution indicate a synonymous rate of 1.1 x 10(-9) substitutions per site per year. Noncoding regions also appear to be constrained in their evolution, although addition/deletion events are common. There have also been evolutionary changes in the distribution of introns in chloroplast encoded genes. Relative to mammalian mitochondrial DNA, the chloroplast genome evolves at a conservative rate.      

Land-Use History and Forest Regeneration in the Cayey Mountains, Puerto Rico

Although deforestation continues to be a major threat to tropical biodiversity, abandonment of agricultural land in Puerto Rico provides an opportunity to study long-term patterns of secondary forest regeneration. Using aerial photographs from 1937, 1967, and 1995, we determined land-use history for 2443 ha in the Cayey Mountains. Pastures were the dominant land cover in 1937 and <20% of the area was classified as forest. Between 1937 and 1995, forest cover increased to 62% due to widespread abandonment of agriculture. To examine the effect of historic land use on current forest structure and species composition, we sampled secondary forests in 24 abandoned pastures, 9 abandoned coffee plantations and 4 old-growth forest sites. Sites were located on two soil types along an elevational gradient (125–710 m) and included a chronosequence from 4 to over 80 years old. After 25–30 years, basal area and species richness in secondary forest sites derived from abandoned pastures and coffee plantations were similar to old-growth forest sites. The species composition of secondary forests derived from abandoned pastures and coffee plantations remained distinct from old-growth forest. In addition to historic land use, age and elevation were important environmental variables explaining variation in secondary forest species composition. Non-indigenous species were common in recently abandoned pastures and coffee plantations, but their importance declined in the older sites. This study demonstrates that secondary forests on private land can be an important component of the conservation of tropical tree biodiversity. Received 16 June 1999; Accepted 8 October 1999.     

Forest Regeneration in a Chronosequence of Tropical Abandoned Pastures: Implications for Restoration Ecology

During the mid‐1900s, most of the island of Puerto Rico was deforested, but a shift in the economy from agriculture to small industry beginning in the 1950s resulted in the abandonment of agricultural lands and recovery of secondary forest. This unique history provides an excellent opportunity to study secondary forest succession and suggest strategies for tropical forest restoration. To determine the pattern of secondary succession, we describe the woody vegetation in 71 abandoned pastures and forest sites in four regions of Puerto Rico. The density, basal area, aboveground biomass, and species richness of the secondary forest sites were similar to those of the old growth forest sites (>80 yr) after approximately 40 years. The dominant species that colonized recently abandoned pastures occurred over a broad elevational range and are widespread in the neotropics. The species richness of Puerto Rican secondary forests recovered rapidly, but the species composition was quite different in comparison with old growth forest sites, suggesting that enrichment planting will be necessary to restore the original composition. Exotic species were some of the most abundant species in the secondary forest, but their long‐term impact depended on life history characteristics of each species. These data demonstrate that one restoration strategy for tropical forest in abandoned pastures is simply to protect the areas from fire, and allow natural regeneration to produce secondary forest. This strategy will be most effective if remnant forest (i.e., seed sources) still exist in the landscape and soils have not been highly degraded. Patterns of forest recovery also suggest strategies for accelerating natural recovery by planting a suite of generalist species that are common in recently abandoned pastures in Puerto Rico and throughout much of the neotropics.     

PROTEUS: a suite of programs for prediction of structural features of proteins using an Apple lie

We have implemented several algorithms, developed by variousauthors for predicting structural features of proteins fromtheir primary structure, on an Apple lle and collected themin a suite, named PROTEUS. This suite incorporates: (i) methodsfor predicting secondary structure; (ii) the algorithm for computingthe hydropathy profile using one out of five available setsof parameters; (ii) the algorithms for calculating the hydrophobicmoment plot; and (iv) for performing the amphipathic analysisusing one out of four available sets of parameters. The suitehas a utility program for storing on a disk the sequence tobe analysed. As an example, we applied some of the methods includedin PROTEUS to predict the structure of a mitochondnal leaderpeptide. The results suggest the occurrence of structural featurespossibly related to the import of proteins into mitochondria. Received on April 30, 1987; accepted on July 21, 1987     

Antioxidant efficacy of iridoid and phenylethanoid glycosides from the medicinal plant Teucrium chamaedris in cell-free systems

Twelve glycosides, seven iridoids and five phenylethanoids, have been isolated from leaf and root methanolic extracts of Wall Germander (Teucrium chamaedrys), a Mediterranean species historically used as a medicinal plant. Among them, three iridoid and one phenylethanoid glycosides have been isolated and characterized for the first time. All of the structures have been elucidated on the basis of their spectral data, especially 1D and 2D NMR experiments.The antioxidative properties of pure metabolites, as well as of crude organic extracts of the plant, have been analyzed on the basis of their DPPH radical scavenging capability. The antioxidant capacity in cell-free systems of the isolated metabolites was carried out by measuring their capabilities to inhibit the synthesis of thiobarbituric acid reactive species in assay media using as oxidable substrates a vegetable fat and the pentose sugar 2-deoxyribose and to prevent oxidative damage of the hydrosoluble bovine serum albumin (BSA) protein. Phenylethanoid glycosides resulted efficacious DPPH radical, while iridoid glycosides prevent massively the 2-deoxyribose and BSA oxidations in assay media.     

Characterization of low-molecular-mass trypsin isoinhibitors from oil-rape (Brassica napus var. oleifera) seed.

A new low-molecular-mass (6767.8 Da) serine proteinase isoinhibitor has been isolated from oil-rape (Brassica napus var. oleifera) seed, designated 5-oxoPro1-Gly62-RTI-III. The 5-oxoPro1-Gly62-RTI-III isoinhibitor is longer than the Asp2-Pro61-RTI-III and the Ser3-Pro61-RTI-III forms, all the other amino acid residues being identical. In RTI-III isoinhibitors, the P1-P1' reactive site bond (where residues forming the reactive site have been identified as PnellipsisP1 and P1'ellipsisPn', where P1-P1' is the inhibitor scissile bond) has been identified at position Arg21-Ile22. The inhibitor disulphide bridges pattern has been determined as Cys5-Cys27, Cys18-Cys31, Cys42-Cys52 and Cys54-Cys57. The disulphide bridge arrangement observed in the RTI-III isoinhibitors is reminiscent of that found in a number of toxins (e.g. erabutoxin b). Moreover, the organization of the three disulphide bridges subset Cys5-Cys27, Cys18-Cys31 and Cys42-Cys52 is reminiscent of that found in epidermal growth factor domains. Preliminary 1H-NMR data indicates the presence of alphaalphaNOEs and 3JalphaNH coupling constants, typical of the beta-structure(s). These data suggest that the three-dimensional structure of the RTI-III isoinhibitors may be reminiscent of that of toxins and epidermal growth factor domains, consisting of three-finger shaped loops extending from the crossover region. Values of the apparent association equilibrium constant for RTI-III isoinhibitors binding to bovine beta-trypsin and bovine alpha-chymotrypsin are 3.3 x 109 m-1 and 2.4 x 106 m-1, respectively, at pH 8.0 and 21.0 degrees C. The serine proteinase : inhibitor complex formation is a pH-dependent entropy-driven process. RTI-III isoinhibitors do not show any similarity to other serine proteinase inhibitors except the low molecular mass white mustard trypsin isoinhibitor, isolated from Sinapis alba L. seed (MTI-2). Therefore, RTI-III and MTI-2 isoinhibitors could be members of a new class of plant serine proteinase inhibitors.     

Whole Grain Intakes in the Diets Of Malaysian Children and Adolescents – Findings from the MyBreakfast Study

Background

Diets rich in whole grain are associated with several health benefits. Little is known however, about whole grain consumption patterns in Malaysia. The aim of this study was to assess whole grain intakes and dietary source in Malaysian children and adolescents.

Methods

This analysis is from the MyBreakfast study, a national cross sectional study investigating eating habits among primary and secondary school children throughout Malaysia, conducted in 2013. Children (n = 5,165) and adolescents (n = 2,947) who completed two days of dietary assessment using a food record or recall respectively were included. The whole grain content of foods was estimated mainly through the use of quantitative ingredient declarations on food labels. All wholegrain foods were considered irrespective of the amount of whole grain they contained.

Results

Overall, only 25% of children and 19% of adolescents were wholegrain consumers. Mean daily intakes in the total sample were 2.3g/d (SD 5.8g/d) in children and 1.7g/d (SD 4.7g/d) in adolescents and in the consumer’s only sample, mean intakes reached 9.1g/d (SD 8.6) and 9.2g/d (SD 7.1g/d) respectively. Wheat was the main grain source of whole grain while ready to eat breakfast cereals and hot cereals were the main food contributors. Less than 3% of the children and adolescents reached the US quantitative whole grain recommendation of 48g/day.

Conclusion

Whole grain is consumed by only a minority of Malaysian children and adolescents and even among consumers, intakes are well below recommendations. Efforts are needed to firstly understand the barriers to whole grain consumption among Malaysian children in order to design effective health promotion initiatives to promote an increase in whole grain consumption.     

Structural adaptation of extreme halophilic proteins through decrease of conserved hydrophobic contact surface

Background

Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding.

Results

In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed in silico structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin) into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces.

Conclusions

NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.     

Cigarette smoke-induced accumulation of lung dendritic cells is interleukin-1α-dependent in mice

Background

Evidence suggests that dendritic cells accumulate in the lungs of COPD patients and correlate with disease severity. We investigated the importance of IL-1R1 and its ligands IL-1α and β to dendritic cell accumulation and maturation in response to cigarette smoke exposure.

Methods

Mice were exposed to cigarette smoke using a whole body smoke exposure system. IL-1R1-, TLR4-, and IL-1α-deficient mice, as well as anti-IL-1α and anti-IL-1β blocking antibodies were used to study the importance of IL-1R1 and TLR4 to dendritic cell accumulation and activation.

Results

Acute and chronic cigarette smoke exposure led to increased frequency of lung dendritic cells. Accumulation and activation of dendritic cells was IL-1R1/IL-1α dependent, but TLR4- and IL-1β-independent. Corroborating the cellular data, expression of CCL20, a potent dendritic cells chemoattractant, was IL-1R1/IL-1α-dependent. Studies using IL-1R1 bone marrow-chimeric mice revealed the importance of IL-1R1 signaling on lung structural cells for CCL20 expression. Consistent with the importance of dendritic cells in T cell activation, we observed decreased CD4⁺ and CD8⁺ T cell activation in cigarette smoke-exposed IL-1R1-deficient mice.

Conclusion

Our findings convey the importance of IL-1R1/IL-1α to the recruitment and activation of dendritic cells in response to cigarette smoke exposure.