The infrared spectrum, equilibrium structure and harmonic and anharmonic force field of thioborine, HBS

Infrared spectra of the two stretching fundamentals of both HBS and DBS have been observed, using a continuous flow system through a multiple reflection long path cell at a pressure around 1 Torr and a Nicolet Fourier Transform spectrometer with a resolution of about 0•1 cm-1. The v3 BS stretching fundamental of DBS, near 1140 cm-1, is observed in strong Fermi resonance with the overtone of the bend 2v2. The bending fundamental v2 has not been observed and must be a very weak band. The analysis of the results in conjunction with earlier work gives the equilibrium structure (re(BH) = 1•1698(12) , re(BS) = 1•5978(3) ) and the harmonic and anharmonic force field.

Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily.

This review summarizes the recent discovery of the cupin superfamily (from the Latin term "cupa," a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic beta-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1, 2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications.

Germin and germin-like proteins: evolution, structure, and function

Germin and germin-like proteins (GLPs) are encoded by a family of genes found in all plants. They are part of the cupin superfamily of biochemically diverse proteins, a superfamily that has a conserved tertiary structure, though with limited similarity in primary sequence. The subgroups of GLPs have different enzyme functions that include the two hydrogen peroxide-generating enzymes, oxalate oxidase (OxO) and superoxide dismutase. This review summarizes the sequence and structural details of GLPs and also discusses their evolutionary progression, particularly their amplification in gene number during the evolution of the land plants. In terms of function, the GLPs are known to be differentially expressed during specific periods of plant growth and development, a pattern of evolutionary subfunctionalization. They are also implicated in the response of plants to biotic (viruses, bacteria, mycorrhizae, fungi, insects, nematodes, and parasitic plants) and abiotic (salt, heat/cold, drought, nutrient, and metal) stress. Most detailed data come from studies of fungal pathogenesis in cereals. This involvement with the protection of plants from environmental stress of various types has led to numerous plant breeding studies that have found links between GLPs and QTLs for disease and stress resistance. In addition the OxO enzyme has considerable commercial significance, based principally on its use in the medical diagnosis of oxalate concentration in plasma and urine. Finally, this review provides information on the nutritional importance of these proteins in the human diet, as several members are known to be allergenic, a feature related to their thermal stability and evolutionary connection to the seed storage proteins, also members of the cupin superfamily.

Influence of agricultural management, sward structure and food resources on grassland field use by birds in lowland England.

Agricultural management of grassland in lowland Britain has changed fundamentally in the last 50 years, resulting in spatial and structural uniformity within the pastoral landscape. The full extent to which these changes may have reduced the suitability of grassland as foraging habitat for birds is unknown. This study investigated the mechanisms by which these changes have impacted on birds and their food supplies. We quantified field use by birds in summer and winter in two grassland areas of lowland England (Devon and Buckinghamshire) over 3 years, relating bird occurrence to the management, sward structure and seed and invertebrate food resources of individual fields. Management intensity was defined in terms of annual nitrogen input. There was no consistent effect of management intensity on total seed head production, although those of grasses generally increased with inputs while forbs were rare throughout. Relationships between management intensity and abundance of soil and epigeal invertebrates were complex. Soil beetle larvae were consistently lower in abundance, and surface-active beetle larvae counts consistently higher, in intensively managed fields. Foliar invertebrates showed more consistent negatively relationships with management intensity. Most bird species occurred at low densities. There were consistent relationships across regions and years between the occurrence of birds and measures of field management. In winter, there was a tendency towards higher occupancy of intensively managed fields by species feeding on soil invertebrates. In summer, there were few such relationships, although many species avoided fields with tall swards. Use of fields by birds was generally not related to measures of seed or invertebrate food abundance. While granivorous species were perhaps too rare to detect a relationship, in insectivores the strong negative relationships (in summer) with sward height suggested that access to food may be the critical factor. While it appears that intensification of grassland management has been deleterious to the summer food resources of insectivorous birds that use insects living within the grass sward, intensification may have been beneficial to several species in winter through the enhancement of soil invertebrates. Synthesis and applications. We suggest that attempts to restore habitat quality for birds in grassland landscapes need to create a range of management intensities and sward structures at the field and farm scales. A greater understanding of methods to enhance prey accessibility, as well as abundance, for insectivorous birds is required.

Social bees and food plant associations in the Nilgiri Biosphere Reserve, India

The diversity of social bees was assessed at 15 sites across five locations of the Nilgiri Biosphere Reserve, Western Ghats, India, from January to December 2007. We also conducted floristic analyses of local vegetation in each site using one-hectare sample plots. All woody species with a dbh (diameter at breast height) : 30 cm were recorded within the plots. A total area of 9.72 ha was assessed for floristic composition. Similarity of floristic composition between sites was determined using the Jaccard's distance measure and a dendrogram constructed based on the hierarchical clustering of floristic dissimilarities between sites. A Bee Importance Index (BII) was developed to give a measure of the bee diversity at each site. This index was a sum of the species richness of bee species in a site and their visitation frequencies to flowers, calculated as mean flower visits hour 1 within 2 focal patches within one hectare plots. The visits of bee species to flowers were also recorded. The Jaccard distance measure indicated that the montane sites were quite dissimilar to the low elevation sites in floristic diversity. The BII was 7-9 for the wet forest sites and ranged from 4-6 for drier forest sites. Seventy three plant species were identified as social bee plants and of them 45% were visited by one species of bee, 37% by two bee species and 18% by more than two bee species, indicating a certain degree of floral specialization among bees.

Macrophyte community structure and species occurrence in relation to environmental determinants in the ephemeral aquatic habitats of Gavdos, Greece

The aims of this study were to explore the environmental factors that determine the distribution of plant communities in temporary rock pools and provide a quantitative analysis of vegetation-environment relationships for five study sites on the island of Gavdos, southwest of Crete, Greece. Data from 99 rock pools were collected and analysed using Two-Way Indicator Species Analysis (TWINSPAN), Detrended Correspondence Analysis (DCA) and Canonical Correspondence Analysis (CCA) to identify the principal communities and environmental gradients that are linked to community distribution. A total of 46 species belonging to 21 families were recorded within the study area. The dominant families were Labiatae, Gramineae and Compositae while therophytes and chamaephytes were the most frequent life forms. The samples were classified into six community types using TWINSPAN, which were also corroborated by CCA analysis. The principal gradients for vegetation distribution, identified by CCA, were associated with water storage and water retention ability, as expressed by pool perimeter and water depth. Generalised Additive Models (GAMs) were employed to identify responses of four dominant rock pool species to water depth. The resulting species response curves showed niche differentiation in the cases of Callitriche pulchra and Tillaea vaillantii and revealed competition between Zannichellia pedunculata and Chara vulgaris. The use of classification in combination with ordination techniques resulted in a good discrimination between plant communities. Generalised Additive Models are a powerful tool in investigating species response curves to environmental gradients. The methodology adopted can be employed for improving baseline information on plant community ecology and distribution in Mediterranean ephemeral pools.

Genetic structure and systematic relationships within the Ophrys fuciflora aggregate (Orchidaceae: Orchidinae): high diversity in Kent and a wind-induced discontinuity bisecting the Adriatic

A recent phylogenetic study based on multiple datasets is used as the framework for a more detailed examination of one of the ten molecularly circumscribed groups identified, the Ophrys fuciflora aggregate. The group is highly morphologically variable, prone to phenotypic convergence, shows low levels of sequence divergence and contains an unusually large proportion of threatened taxa, including the rarest Ophrys species in the UK. The aims of this study were to (a) circumscribe minimum resolvable genetically distinct entities within the O. fuciflora aggregate, and (b) assess the likelihood of gene flow between genetically and geographically distinct entities at the species and population levels. Fifty-five accessions sampled in Europe and Asia Minor from the O. fuciflora aggregate were studied using the AFLP genetic fingerprinting technique to evaluate levels of infraspecific and interspecific genetic variation and to assess genetic relationships between UK populations of O. fuciflora s.s. in Kent and in their continental European and Mediterranean counterparts. The two genetically and geographically distinct groups recovered, one located in England and central Europe and one in south-eastern Europe, are incongruent with current species delimitation within the aggregate as a whole and also within O. fuciflora s.s. Genetic diversity is higher in Kent than in the rest of western and central Europe. Gene flow is more likely to occur between populations in closer geographical proximity than those that are morphologically more similar. Little if any gene flow occurs between populations located in the south-eastern Mediterranean and those dispersed throughout the remainder of the distribution, revealing a genetic discontinuity that runs north-south through the Adriatic. This discontinuity is also evident in other clades of Ophrys and is tentatively attributed to the long-term influence of prevailing winds on the long-distance distribution of pollinia and especially seeds. A cline of gene flow connects populations from Kent and central and southern Europe; these individuals should therefore be considered part of an extensive meta-population. Gene flow is also evident among populations from Kent, which appear to constitute a single metapopulation. They show some evidence of hybridization, and possibly also introgression, with O. apifera.

The structure and mechanism of serine acetyltransferase from Escherichia coli

Serine acetyltransferase (SAT) catalyzes the first step of cysteine synthesis in microorganisms and higher plants. Here we present the 2.2 Angstrom crystal structure of SAT from Escherichia coli, which is a dimer of trimers, in complex with cysteine. The SAT monomer consists of an amino-terminal alpha-helical domain and a carboxyl- terminal left-handed beta-helix. We identify His(158) and Asp(143) as essential residues that form a catalytic triad with the substrate for acetyl transfer. This structure shows the mechanism by which cysteine inhibits SAT activity and thus controls its own synthesis. Cysteine is found to bind at the serine substrate site and not the acetyl-CoA site that had been reported previously. On the basis of the geometry around the cysteine binding site, we are able to suggest a mechanism for the O-acetylation of serine by SAT. We also compare the structure of SAT with other left-handed beta-helical structures.

Structure and function analysis of the poliovirus cis-acting replication element (CRE)

The poliovirus cis-acting replication element (CRE) templates the uridylylation of VPg, the protein primer for genome replication. The CRE is a highly conserved structural RNA element in the enteroviruses and located within the polyprotein-coding region of the genome. We have determined the native structure of the CRE, defined the regions of the structure critical for activity, and investigated the influence of genomic location on function. Our results demonstrate that a 14-nucleotide unpaired terminal loop, presented on a suitably stable stem, is all that is required for function. These conclusions complement the recent analysis of the 14-nucleotide terminal loop in the CRE of human rhinovirus type 14. The CRE can be translocated to the 5' noncoding region of the genome, at least 3.7-kb distant from the native location, without adversely influencing activity, and CRE duplications do not adversely influence replication. We do not have evidence for a specific interaction between the CRE and the RNA-binding 3CD(pro) complex, an essential component of the uridylylation reaction, and the mechanism by which the CRE is coordinated and orientated during the reaction remains unclear. These studies provide a detailed overview of the structural determinants required for CRE function, and will facilitate a better understanding of the requirements for picornavirus replication.