Fusion of carbohydrate binding modules from <Emphasis Type="Italic">Thermotoga neapolitana</Emphasis> with a family 10 xylanase from <Emphasis Type="Italic">Bacillus halodurans</Emphasis> S7

Xylanase A of Thermotoga neapolitana contains binding domains both at the N- and C-terminal ends of the catalytic domain. In the N-terminal position it contains two carbohydrate-binding modules (CBM) which belong to family 22. These CBMs bind xylan but not to cellulose. The gene encoding the mature peptide of these CBMs was fused with an alkaline active GH10 xylanase from Bacillus halodurans S7 and expressed in Escherichia coli. The (His)₆ tagged hybrid protein was purified by immobilized metal affinity chromatography and characterized. Xylan binding by the chimeric protein was influenced by NaCl concentration and pH of the binding medium. Binding increased with increasing salt concentration up to 200 mM. Higher extent of binding was observed under acidic conditions. The fusion of the CBM structures enhanced the hydrolytic efficiency of the xylanase against insoluble xylan, but decreased the stability of the enzyme. The optimum temperature and pH for the activity of the xylanase did not change.     

Analysis of Protein Three-Dimension Structure Using Amino Acids Depths

The issue of amino acid depth in proteins gives important insights to our understanding of protein’s three-dimensional structure. There has already been much research done in mathematical and statistical sciences regarding the general definitions, properties and algorithms describing the particle depth of spatially extended systems. We constructed a method of calculating the amino acids depths and applied it to a set of 527 protein structures. We propose the introduction of amino acid depth tendency factors for three-dimensional structures of proteins. The depth tendency factors relate not only to the hydrophobicity indices but also to the electrostatic charge. We found a relationship between the protein size and the number of residues using the distance between the deepest residue and surface residues. We made a prediction regarding the number of residues on the surface of a protein, the deepest amino acid, and the average depth, all of which are fitted well to a linear functional relationship with the length of the protein. Finally, we have predicted the depths of multiple peptides in protein’s three-dimension structure. Electronic supplementary material The online version of this article () contains supplementary material, which is available to authorized users.     

Water column oxygen demand and sediment oxygen flux: patterns of oxygen depletion in tidal creeks

Low dissolved oxygen (DO) levels often occur during summer in tidal creeks along the southeastern coast of the USA. We analyzed rates of oxygen loss as water-column biochemical oxygen demand (BOD₅) and sediment oxygen flux (SOF) at selected tidal creek sites monthly over a 1-year period. Ancillary physical, chemical and biological data were collected to identify factors related to oxygen loss. BOD₅ rates ranged from 0.0 mg l^?1 to 7.6 mg l^?1 and were correlated positively with organic suspended solids, total suspended solids, chlorophyll a concentrations, temperature, and dissolved oxygen, and negatively with pH and nitrate + nitrite. SOF rates ranged from 0.0 to 9.3 g O₂ m^?2 d^?1, and were positively correlated with temperature, chlorophyll a, and total suspended solids, but negatively with dissolved oxygen. Both forms of oxygen uptake were seasonally dependent, with BOD₅ elevated in spring and summer and SOF elevated in summer and fall. Average oxygen loss to sediments was greater and more variable than oxygen loss in the water column. Oxygen deficits at three of five locations were significantly related to BOD₅ and SOF, but not at two sites where ground water discharges were observed. Correlation and principal component analyses suggested that BOD₅ and SOF responded to somewhat different suites of environmental variables. BOD₅ was driven by a set of parameters linked to warm season storm water inputs that stimulated organic seston loads, especially chlorophyll a, while SOF behaved less strongly so. Runoff processes that increase loads of organic material and nutrients and ground water discharges low in dissolved oxygen contribute to occurrences of low dissolved oxygen in tidal creeks.     

The contribution of cacao agroforests to the conservation of lower canopy ant and beetle diversity in Indonesia

The ongoing destruction of tropical rainforests has increased the interest in the potential value of tropical agroforests for the conservation of biodiversity. Traditional, shaded agroforests may support high levels of biodiversity, for some groups even approaching that of undisturbed tropical forests. However, it is unclear to what extent forest fauna is represented in this diversity and how management affects forest fauna in agroforests. We studied lower canopy ant and beetle fauna in cacao agroforests and forests in Central Sulawesi, Indonesia, a region dominated by cacao agroforestry. We compared ant and beetle species richness and composition in forests and cacao agroforests and studied the impact of two aspects of management intensification (the decrease in shade tree diversity and in shade canopy cover) on ant and beetle diversity. The agroforests had three types of shade that represented a decrease in tree diversity (high, intermediate and low diversity). Species richness of ants and beetles in the canopies of the cacao trees was similar to that found in lower canopy forest trees. However, the composition of ant and beetle communities differed greatly between the agroforest and forest sites. Forest beetles suffered profoundly from the conversion to agroforests: only 12.5% of the beetle species recorded in the forest sites were also found in the agroforests and those species made up only 5% of all beetles collected from cacao. In contrast, forest ants were well represented in agroforests, with 75% of all species encountered in the forest sites also occurring on cacao. The reduction of shade tree diversity had no negative effect on ants and beetles on cacao trees. Beetle abundances and non-forest ant species richness even increased with decreasing shade tree diversity. Thinning of the shade canopy was related to a decrease in richness of forest ant species on cacao trees but not of beetles. The contrasting responses of ants and beetles to shade tree management emphasize that conservation plans that focus on one taxonomic group may not work for others. Overall ant and beetle diversity can remain high in shaded agroforests but the conservation of forest ants and beetles in particular depends primarily on the protection of natural forests, which for forest ants can be complemented by the conservation of adjacent shaded cacao agroforests.     

Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges

Natural products isolated from sponges are an important source of new biologically active compounds. However, the development of these compounds into drugs has been held back by the difficulties in achieving a sustainable supply of these often-complex molecules for pre-clinical and clinical development. Increasing evidence implicates microbial symbionts as the source of many of these biologically active compounds, but the vast majority of the sponge microbial community remain uncultured. Metagenomics offers a biotechnological solution to this supply problem. Metagenomes of sponge microbial communities have been shown to contain genes and gene clusters typical for the biosynthesis of biologically active natural products. Heterologous expression approaches have also led to the isolation of secondary metabolism gene clusters from uncultured microbial symbionts of marine invertebrates and from soil metagenomic libraries. Combining a metagenomic approach with heterologous expression holds much promise for the sustainable exploitation of the chemical diversity present in the sponge microbial community.     

Impact of urban fragmentation on the genetic structure of the eastern red-backed salamander

Urban development is a major cause of habitat loss and fragmentation. Few studies, however, have dealt with fragmentation in an urban landscape. In this paper, we examine the genetic structure of isolated populations of the eastern red-backed salamander (Plethodon cinereus) in a metropolitan area. We sampled four populations located on a mountain in the heart of Montréal (Québec, Canada), which presents a mosaic of forested patches isolated by roads, graveyards and buildings. We assessed the genetic structure of these populations using microsatellite loci and compared it to the genetic structure of four populations located in a continuous habitat in southern Québec. Our results indicate that allelic richness and heterozygosity are lower in the urban populations. Exact differentiation tests and pairwise F _ST also show that the populations found in the fragmented habitat are genetically differentiated, whereas populations located in the continuous habitat are genetically homogeneous. These results raise conservation concerns for these populations as well as for rare or threatened species inhabiting urban landscapes.     

Depth-related changes to density,diversity and structure of benthic megafaunal assemblages in the Fimbul ice shelf region,Weddell Sea,Antarctica

The depth-related patterns in the benthic megafauna of the NE Weddell Sea shelf at the edge of the Fimbul Ice Shelf were investigated at seven sites using towed camera platform photographs. Megafaunal density decreased with depth from 77,939 ha⁻¹ at 245 m to 8,895 ha⁻¹ at 510 m. While diversity was variable, with H′ ranging between 1.34 and 2.28, there were no depth related patterns. Multivariate analyses revealed two distinct assemblages; a shallow assemblage with dense patches of suspension feeders in undisturbed areas and a deep assemblage where these were not present. Disturbance from icebergs explained many observed patterns in faunal distribution. In shallow waters probable effects of disturbance were observed as changes in successional stages; in deeper waters changes in habitat as a result of past disturbance explained faunal distributions. In deeper areas ice ploughing created a mosaic landscape of fine and coarse sediments. Total megafaunal density was highest in areas of coarse sediment (up to 2.9 higher than in finer sediment areas) but diversity was highest in intermediate areas (H′ = 2.35).     

Biochemical Characterization and Phylogenetic Analysis Based on 16S rRNA Sequences for V-Factor Dependent Members of <Emphasis Type="Italic">Pasteurellaceae</Emphasis> Derived from Laboratory Rats

Phylogenetic analysis based on 16S rRNA sequences with sequence data of some bacterial species of Pasteurellaceae related to rodents deposited in GenBank was performed along with biochemical characterization for the 20 strains of V-factor dependent members of Pasteurellaceae derived from laboratory rats to obtain basic information and to investigate the taxonomic positions. The results of biochemical tests for all strains were identical except for three tests, the ornithine decarboxylase test, and fermentation tests of D(+) mannose and D(+) xylose. The biochemical properties of 8 of 20 strains that showed negative results for the fermentation test of D(+) xylose agreed with those of Haemophilus parainfluenzae complex. By phylogenetic analysis, the strains were divided into two clusters that agreed with the results of the fermentation test of xylose (group I: negative reaction for xylose, group II: positive reaction for xylose). The clusters were independent of other bacterial species of Pasteurellaceae tested. The sequences of the strains in group I showed 99.7–99.8% similarity and the strains in group II showed 99.3–99.7% similarity. None of the strains in group I had a close relation with Haemophilus parainfluenzae by phylogenetic analysis, although they showed the same biochemical properties. In conclusion, the strains had characteristic biochemical properties and formed two independent groups within the “rodent cluster” of Pasteurellaceae that differed in the results of the fermentation test of xylose. Therefore, they seemed to be hitherto undescribed taxa in Pasteurellaceae.     

General Information

A novel cDNA clone encoding a COR413-like gene was isolated by suppression subtraction hybridization and cDNA library screening from sea-island cotton (Gossypium barbadense). This gene (designated as GbCOR413, Accession number: AY761065) has a total length of 893 bp with an open reading frame of 600 bp, encoding a predicated polypeptide of 200 amino acids with a molecular weight of 22.74 kDa and a predicated pI of 9.2. Bioinformatics analyses revealed that this gene belonged to a novel stress-regulated multi-spanning transmembrane protein family without signal peptide. By means of semi-quantities RT-PCR analysis, the expression of GbCOR413 under short-term cold treatment at 4°C, water submergence and abscic acid treatment was investigated. Our studies suggested that the cloned gene was a new member of COR gene family which was slowly responsive to cold stress in cotton. Jin Wang and Kai-Jing Zuo are co-first authors of this paper.