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.     

Mark‐resight abundance and survival estimation of Indo‐Pacific bottlenose dolphins,Tursiops aduncus,in the Swatch‐of‐No‐Ground,Bangladesh

A mark‐resight analysis under Pollock's robust design was applied to Indo‐Pacific bottlenose dolphins Tursiops aduncus in the Swatch‐of‐No‐Ground (SoNG) submarine canyon, Bangladesh, during the winter seasons of 2005–2009. Information from sightings of photo‐identified individuals (1,144) and unmarked individuals generated abundance estimates of 1,701 (95% confidence interval [CI]= 1,533–1,888), 1,927 (95% CI = 1,851–2,006), 2,150 (95% CI = 1,906–2,425), and 2,239 (95% CI = 1,985–2,524) individuals for seasons 1–4, respectively. This makes the population among the largest assessed of the species. Overall apparent survival was estimated as 0.958 (95% CI = 0.802–0.992). Interseasonal probabilities of transitioning to an unobservable state were estimated as 0.045, 0.363, and 0.300 for years 1–2, 2–3, and 3–4, respectively, and the overall probability of remaining in an unobservable state was 0.688. These probabilities, together with an apparent increase in abundance during the study period, indicate that the identified dolphins are part of a larger superpopulation moving throughout a more extensive geographic area. Of the photo‐identified dolphins, 28.2% exhibited injuries related to entanglements with fishing gear. This implies a strong potential for fatal interactions that could jeopardize the conservation status of the population, which otherwise appears favorable.     

The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness

We explore factors affecting patterns of polymorphism and divergence (as captured by the neutrality index) at mammalian mitochondrial loci. To do this, we develop a population genetic model that incorporates a fraction of neutral amino acid sites, mutational bias, and a probability distribution of selection coefficients against new nonsynonymous mutations. We confirm, by reanalyzing publicly available datasets, that the mitochondrial cyt-b gene shows a broad range of neutrality indices across mammalian taxa, and explore the biological factors that can explain this observation. We find that observed patterns of differences in the neutrality index, polymorphism, and divergence are not caused by differences in mutational bias. They can, however, be explained by a combination of a small fraction of neutral amino acid sites, weak selection acting on most amino acid mutations, and differences in effective population size among taxa.     

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.     

Thirty‐eight years of change in a tropical forest: plot data from Mpanga Forest Reserve,Uganda

Variations in the composition and structure of mid‐altitude, semi‐deciduous topical forest in a 0.64‐ha plot in Mpanga Forest Reserve, Uganda, are described for a 38‐year period to 2006. Repeat surveys of trees in the plot with a girth ≥30 cm at reference height in 1982, 1993 and 2006, following a baseline survey in 1968, indicate only relatively minor fluctuations in density, Shannon diversity, evenness, basal area (BA) and estimated above ground biomass. The largest trees [diameter at breast height (dbh) > 40 cm] and main canopy taxa (e.g. Celtis mildbraedii) accounted for the largest fraction of BA. Mortality was the highest amongst taxa classed as early seral, understorey and/or in the smallest size category (dbh = 9.5–20 cm), while new recruits were predominantly understorey taxa. Only one tree was recorded as felled for human use between the surveys of 1968 and 1993. In contrast, a considerable increase in anthropogenic disturbance was evident at the time of the 2006 survey, and illegal logging now poses a substantial threat to future resource availability and carbon storage in what was for a time one of the most protected areas of forest in Uganda.