Role of acidic amino acid residues in chitooligosaccharide-binding to Streptomyces sp. N174 chitosanase

We examined the oligosaccharide binding to Streptomyces sp. N174 chitosanase by fluorescence spectroscopy. By means of the tryptophan fluorescence quenching, the oligosaccharide binding abilities were evaluated using the three mutant enzymes (D57A, E197A, and D201A). The enzymatic activities of the mutant enzymes were 0.5%, 20.0%, and 38.5% of that of the wild type, respectively. Scatchard plot obtained for the wild type enzyme showed a biphasic profile, suggesting that the oligosaccharide binds to the chitosanase with two different binding sites (the high affinity site and the low affinity site). In contrast, Scatchard plot for E197A exhibited a monophasic profile, in which the slope of the line corresponds to that for the low affinity binding of the wild type enzyme. A monophasic profile was also obtained for D201A, but the slope of the line was similar to that of the high affinity binding. Thus, we conclude that Glu197 and Asp201 are responsible for oligosaccharide binding at the high affinity site and the low affinity site, respectively, which correspond to the (-n) subsites and the (+n) subsites (n=1, 2, and 3). The fluorescence quenching was very weak in D57A, suggesting a strong contribution of this residue to the oligosaccharide binding.     

Dry granulation and compression of spray-dried plant extracts

The purpose of this research was to evaluate the influence of dry granulation parameters on granule and tablet properties of spray-dried extract (SDE) fromMaytenus ilicifolia, which is widely used in Brazil in the treatment of gastric disorders. The compressional behavior of the SDE and granules of the SDE was characterized by Heckel plots. The tablet properties of powders, granules, and formulations containing a high extract dose were compared. The SDE was blended with 2% magnesium stearate and 1% colloidal silicon dioxide and compacted to produce granules after slugging or roll compaction. The influences of the granulation process and the roll compaction force on the technological properties of the granules were studied. The flowability and density of spray-dried particles were improved after granulation. Tablets produced by direct compression of granules showed lower crushing strength than the ones obtained from nongranulated material. The compressional analysis by Heckel plots revealed that the SDE undergoes plastic deformation with a very low tendency to rearrangement at an early stage of compression. On the other hand, the granules showed an intensive rearrangement as a consequence of fragmentation and rebounding. However, when the compaction pressure was increased, the granules showed plastic deformation. The mean yield pressure values showed that both granulation techniques and the roll compaction force were able to reduce the material's ability to undergo plastic deformation. Finally, the tablet containing a high dose of granules showed a close dependence between crushing strength and the densification degree of the granules (ie, roll compaction force). Published: October 14, 2005     

Mapping of origin of replication in Themococcales

Genome replication is a crucial and essential process for the continuity of life.In all organisms it starts at a specific region of the genome known as origin of replication (Ori) site. The number of Ori sites varies in prokaryotes and eukaryotes. Replication starts at a single Ori site in bacteria, but in eukaryotes multiple Ori sites are used for fast copying across all chromosomes. The situation becomes complex in archaea, where some groups have single and others have multiple origins of replication. Themococcales, are a hyperthermophilic order of archaea. They are anaerobes and heterotrophs-peptide fermenters, sulphate reducers, methanogens being some of the examples of metabolic types. In this paper we have applied a combination of multiple in silico approaches - Z curve, the cell division cycle (cdc6) gene location and location of consensus origin recognition box (ORB) sequences for location of origin of replication in Thermococcus onnurineus, Thermococcus gammatolerans and other Themococcales and compared the results to that of the well-documented case of Pyrococcus abyssi. The motivation behind this study is to find the number of Ori sites based on the data available for members of this order. Results from this in silico analysis show that the Themococcales have a single origin of replication.     

Importance of short-term dynamics in carbon isotope ratios of ecosystem respiration (delta13C(R)) in a Mediterranean oak woodland and linkage to environmental factors

Temporal dynamics in carbon isotope ratios of ecosystem respiration (delta13C(R)) were evaluated on hourly, daily and annual timescales in a Mediterranean woodland. Emphasis was given to the periods of transition from wet to dry season and vice versa, when the system turns from a net carbon sink to a source. The constancy of nocturnal delta13C(R) was tested. The relationship between delta13C(R) (determined through Keeling plots) and environmental factors was evaluated through time-lag analysis. Delta13C(R) exhibited high annual variation (> 7). During the transition periods, delta13C(R) correlated significantly with factors influencing photosynthetic discrimination, soil respiration, and whole-canopy conductance. Time-lags differed between below- and above-ground variables, and between seasons. A shift in regression parameters with environmental factors indicated seasonal differences in ecosystem responsiveness (e.g. temperature acclimation). Delta13C(R) exhibited substantial nocturnal enrichment (> 4) from dusk to dawn. These data indicate pronounced short-term dynamics in delta13C(R) at hourly to daily timescales and a modulated response to environmental drivers. Substantial short-term changes in nocturnal delta13C(R) may have important implications for the sampling protocols of nocturnal Keeling plots.     

INCREASED RESIDUAL VARIANCE AT DEVELOPMENTAL SWITCH POINTS: STATISTICAL ARTIFACT OR INDICATOR OF EXPOSED GENOTYPIC INFLUENCE?

Discussing the organization of developmental switches, West-Eberhard (2003) proposed the use of regression residual plots to locate the neutral point of the switch, which is characterized by maximum genotypic influence on the resulting phenotype. However, statistical artifacts due to measurement error in nonlinear models might account for a substantial proportion of the increase of residuals variance at the switch point. Simulations based on field data show that increases in residual variance occur as artifacts when normal amounts of measurement error are present, even in absence of any genotypic variance. The results suggest that interpretation of nonlinear variation in thresold traits is problematic and requires considering this statistical effect. A method to estimate the weight of genotypic contribution to residual variance is proposed, and its assumptions and limitations are discussed.     

Functional analysis and structure determination of alkaline protease from Aspergillus flavus

Proteases are one of the highest value commercial enzymes as they have broad applications in food, pharmaceutical, detergent, and dairy industries and serve as vital tools in determination of structure of proteins and polypeptides. Multiple application of these enzymes stimulated interest to discover them with novel properties and considerable advancement of basic research into these enzymes. A broad understanding of the active site of the enzyme and of the mechanism of its inactivation is essential for delineating its structure-function relationship. Primary structure analysis of alkaline protease showed 42% of its content to be alpha helix making it stable for three dimensional structure modeling. Homology model of alkaline protease has been constructed using the X-ray structure (3F7O) as a template and swiss model as the workspace. The model was validated by ProSA, SAVES, PROCHECK, PROSAII and RMSD. The results showed the final refined model is reliable. It has 53% amino acid sequence identity with the template, 0.24 Å as RMSD and has -7.53 as Z-score, the Ramachandran plot analysis showed that conformations for 83.4 % of amino acid residues are within the most favored regions and only 0.4% in the disallowed regions.     

Synonymous codon usage in chloroplast genome of Coffea arabica

Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to find out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as chloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz., leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A₃, T₃, G₃, C₃, GC₃) revealed that compositional constraints played crucial role in shaping the codon usage pattern of C. arabica chloroplast genome. ENC Vs GC₃ plot grouped majority of the analyzed genes on or just below the left side of the expected GC₃ curve indicating the influence of base compositional constraints in regulating codon usage. But some of the genes lie distantly below the continuous curve confirmed the influence of some other factors on the codon usage across those genes. Influence of compositional constraints was further confirmed by correspondence analysis as axis 1 and 3 had significant correlations with silent base contents. Correlation of ENC with axis 1, 4 and CAI with 1, 2 prognosticated the minor influence of selection in nature but exact separation of highly and lowly expressed genes could not be seen. From the present study, we concluded that mutational pressure combined with weak selection influenced the pattern of synonymous codon usage across the genes in the chloroplast genomes of C. arabica.     

Prediction of membrane protein types by means of wavelet analysis and cascaded neural networks

In this study, membrane proteins were classified using the information hidden in their sequences. It was achieved by applying the wavelet analysis to the sequences and consequently extracting several features, each of them revealing a proportion of the information content present in the sequence. The resultant features were made normalized and subsequently fed into a cascaded model developed in order to reduce the effect of the existing bias in the dataset, rising from the difference in size of the membrane protein classes. The results indicate an improvement in prediction accuracy of the model in comparison with similar works. The application of the presented model can be extended to other fields of structural biology due to its efficiency, simplicity and flexibility.     

Lineages-through-time plots of neutral models for speciation

Drawing inferences about macroevolutionary processes from phylogenetic trees is a fundamental challenge in evolutionary biology. Understanding stochastic models for speciation is an essential step in solving this challenge. We consider a neutral class of stochastic models for speciation, the constant rate birth-death process. For trees with n extant species - which might be derived from bigger trees via random taxon sampling - we calculate the expected time of the kth speciation event (k=1,...,n-1). Further, for a tree with n extant species, we calculate the density and expectation for the number of lineages at any time between the origin of the process and the present. With the developed methods, expected lineages-through-time (LTT) plots can be drawn analytically. The effect of random taxon sampling on LTT plots is discussed.     

美国东部杜克森林长期定位研究综述

 该文比较系统地综述了美国东部杜克森林76年来植物种类变化、种群动态和森林演替研究的基本情况。重点介绍了该森林内永久性森林样地的 设置和调查规范,以及最近10年来利用永久样地数据进行树木空间格局和自然干扰研究的最新进展,并将杜克森林永久样地监测规范和数据管 理方法与目前主要的森林监测网络进行了一定的比较,旨在对目前国际上蓬勃开展的长期定位植物多样性监测和空间格局研究有所启示和帮助 。