An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem

Background  

The protein folding problem is a fundamental problems in computational molecular biology and biochemical physics. Various optimisation methods have been applied to formulations of the ab-initio folding problem that are based on reduced models of protein structure, including Monte Carlo methods, Evolutionary Algorithms, Tabu Search and hybrid approaches. In our work, we have introduced an ant colony optimisation (ACO) algorithm to address the non-deterministic polynomial-time hard (NP-hard) combinatorial problem of predicting a protein's conformation from its amino acid sequence under a widely studied, conceptually simple model – the 2-dimensional (2D) and 3-dimensional (3D) hydrophobic-polar (HP) model.     

1,2,3-Triazole Fused Quinoline-Peptidomimetics: Studies on Synthesis, DNA Binding and Photonuclease Activity

Abstract  

We present, simple approach for the accession of 1,2,3-triazole fused quinoline peptide analogues from 3-(azidomethyl)-2-chloroquinoline in a three-step mechanistic pathway. The UV–Visible absorbance plot shows dynamic interaction of parent triazole derivative with CT DNA as efficient DNA intercalator (K _b = 4.6 × 10⁻⁴ M⁻¹). Finally, the efficient DNA damage was observed on photo-irradiation at 360 nm in the presence of 2-(9H-Fluoren-9-ylmethoxycarbonylamino)-propionic acid 1-(2-chloro-quinolin-3-ylmethyl)-1H-[1,2,3]triazole-4-ylmethyl ester (6a).     

Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter

Background  

Gradients of morphogens pattern cell fate – a phenomenon that is especially important during development. A simple model system for studying how morphogens pattern cell behavior would overcome difficulties inherent in the study of natural morphogens in vivo. A synthetic biology approach to building such a system is attractive.     

Environmental adversity and uncertainty favour cooperation

Background  

A major cornerstone of evolutionary biology theory is the explanation of the emergence of cooperation in communities of selfish individuals. There is an unexplained tendency in the plant and animal world – with examples from alpine plants, worms, fish, mole-rats, monkeys and humans – for cooperation to flourish where the environment is more adverse (harsher) or more unpredictable.     

Experimental manipulation of immune-mediated disease and its fitness costs for rodent malaria parasites

Background  

Explaining parasite virulence (harm to the host) represents a major challenge for evolutionary and biomedical scientists alike. Most theoretical models of virulence evolution assume that virulence arises as a direct consequence of host exploitation, the process whereby parasites convert host resources into transmission opportunities. However, infection-induced disease can be immune-mediated (immunopathology). Little is known about how immunopathology affects parasite fitness, or how it will affect the evolution of parasite virulence. Here we studied the effects of immunopathology on infection-induced host mortality rate and lifetime transmission potential – key components of parasite fitness – using the rodent malaria model, Plasmodium chabaudi chabaudi.     

Role of subtyping in detecting Salmonella cross contamination in the laboratory

Background  

With the exception of M. tuberculosis, little has been published on the problems of cross-contamination in bacteriology laboratories. We performed a retrospective analysis of subtyping data from the National Salmonella Reference Laboratory (Ireland) from 2000–2007 to identify likely incidents of laboratory cross contamination.     

An EST database from saffron stigmas

Background  

Saffron (Crocus sativus L., Iridaceae) flowers have been used as a spice and medicinal plant ever since the Greek-Minoan civilization. The edible part – the stigmas – are commonly considered the most expensive spice in the world and are the site of a peculiar secondary metabolism, responsible for the characteristic color and flavor of saffron.     

Sleep in Kcna2 knockout mice

Background  

Shaker codes for a Drosophila voltage-dependent potassium channel. Flies carrying Shaker null or hypomorphic mutations sleep 3–4 h/day instead of 8–14 h/day as their wild-type siblings do. Shaker-like channels are conserved across species but it is unknown whether they affect sleep in mammals. To address this issue, we studied sleep in Kcna2 knockout (KO) mice. Kcna2 codes for Kv1.2, the alpha subunit of a Shaker-like voltage-dependent potassium channel with high expression in the mammalian thalamocortical system.     

Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models

Background  

Identifying large gene regulatory networks is an important task, while the acquisition of data through perturbation experiments (e.g., gene switches, RNAi, heterozygotes) is expensive. It is thus desirable to use an identification method that effectively incorporates available prior knowledge – such as sparse connectivity – and that allows to design experiments such that maximal information is gained from each one.     

Phenotypic plasticity and morphological integration in a marine modular invertebrate

Background  

Colonial invertebrates such as corals exhibit nested levels of modularity, imposing a challenge to the depiction of their morphological evolution. Comparisons among diverse Caribbean gorgonian corals suggest decoupling of evolution at the polyp vs. branch/internode levels. Thus, evolutionary change in polyp form or size (the colonial module sensu stricto) does not imply a change in colony form (constructed of modular branches and other emergent features). This study examined the patterns of morphological integration at the intraspecific level. Pseudopterogorgia bipinnata (Verrill) (Octocorallia: Gorgoniidae) is a Caribbean shallow water gorgonian that can colonize most reef habitats (shallow/exposed vs. deep/protected; 1–45 m) and shows great morphological variation.     

Process Optimization,Characterization and Pharmacokinetic Evaluation in Rats of Ursodeoxycholic Acid–Phospholipid Complex

The purpose of this research was to study whether the bioavailability of ursodeoxycholic acid could be improved by administering ursodeoxycholic acid–phospholipid complex (UDCA–PLC) orally to rats. A central composite design approach was used for process optimization in order to obtain the acceptable UDCA–PLC. The physicochemical properties of the complex obtained by optimal parameters were investigated by means of scanning electron microscopy and X-ray diffraction. The pharmacokinetic parameters and bioavailability studies were conducted in rats of UDCA after oral administration of UDCA–PLC and UDCA tablet. Multiple linear regression analysis for process optimization revealed that the acceptable UDCA–PLC was obtained wherein the optimal values of X ₁, X ₂ and X ₃ were 3, 60°C and 3 h, respectively. The XRD studies of UDCA–PLC obtained by the optimal parameters demonstrated that UDCA and phospholipids in the UDCA–PLC were combined by non-covalent bonds, not form new compounds. But pharmacokinetic parameters of the complex in rats were T _max 1.6 h, C _max 0.1346 μg/ml, 11.437 μg·h/ml, respectively. The relative bioavailability of UDCA of UDCA–PLC was increased by 241%,compared with the reference ursodeoxycholic acid tablet.     

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

Background  

Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions. One approach to recover this information is to use 3D templates – structure-function motifs that consist of a few functionally critical amino acids and may suggest functional similarity when geometrically matched to other structures. Since experimentally determined functional sites are not common enough to define 3D templates on a large scale, this work tests a computational strategy to select relevant residues for 3D templates.     

Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

Background  

Model violations constitute the major limitation in inferring accurate phylogenies. Characterizing properties of the data that are not being correctly handled by current models is therefore of prime importance. One of the properties of protein evolution is the variation of the relative rate of substitutions across sites and over time, the latter is the phenomenon called heterotachy. Its effect on phylogenetic inference has recently obtained considerable attention, which led to the development of new models of sequence evolution. However, thus far focus has been on the quantitative heterogeneity of the evolutionary process, thereby overlooking more qualitative variations.     

Field applications of a bio-trickling filter for the removal of nitrogen oxides from flue gas

A bio-trickling filter (BTF) packed with polyhedral spheres was used to remove nitrogen oxides (NOx) from the flue gas of a coal-fired power plant. The BTF system consistently removed 64–95% of the NOx after start-up and acclimation under dynamic conditions (e.g., 120–240 m³/h flue gas flow rate and inlet 300–900 mg NOx/m³). Scanning electron microscopy of the biofilms that were formed showed a shift in the predominating bacteria. Analyses by PCR-denaturing gradient gel electrophoresis showed that the naturally-selected mixed cultures in the biofilm under a flue gas environment were mainly Klebsiella sp. and Pseudomonas sp.     

Viable nonsense mutants for the essential gene <Emphasis Type="Italic">SUP45</Emphasis> of <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Background  

Termination of protein synthesis in eukaryotes involves at least two polypeptide release factors (eRFs) – eRF1 and eRF3. The highly conserved translation termination factor eRF1 in Saccharomyces cerevisiae is encoded by the essential gene SUP45.     

DNA sequence diversity and the origin of cultivated safflower (<Emphasis Type="Italic">Carthamus tinctorius</Emphasis>L.; Asteraceae)

Background  

Safflower (Carthamus tinctorius L.) is a diploid oilseed crop whose origin is largely unknown. Safflower is widely believed to have been domesticated over 4,000 years ago somewhere in the Fertile Crescent. Previous hypotheses regarding the origin of safflower have focused primarily on two other species from sect. Carthamus – C. oxyacanthus and C. palaestinus – as the most likely progenitors, although some attention has been paid to a third species (C. persicus) as a possible candidate. Here, we describe the results of a phylogenetic analysis of the entire section using data from seven nuclear genes.     

ParaHaplo: A program package for haplotype-based whole-genome association study using parallel computing

Background  

Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region for use in BLAST-based similarity searches in the International Nucleotide Sequence Databases. These searches are time-consuming and regularly require a significant amount of manual intervention and complementary analyses. We here present software – in the form of an identification pipeline for large sets of fungal ITS sequences – developed to automate the BLAST process and several additional analysis steps. The performance of the pipeline was evaluated on a dataset of 350 ITS sequences from fungi growing as epiphytes on building material.     

Maintenance of adaptive differentiation by Wolbachia induced bidirectional cytoplasmic incompatibility: the importance of sib-mating and genetic systems

Background  

Bacteria of the genus Wolbachia are reproductive parasites widespread among arthropods. The most common effect arising from the presence of Wolbachia in a population is Cytoplasmic Incompatibility (CI), whereby postmating reproductive isolation occurs in crosses between an infected male and an uninfected female, or when a male is infected with a different strain of Wolbachia to that of the female (bidirectional CI). Previous theoretical models have demonstrated that bidirectional CI can contribute to the genetic divergence of populations in haploid and diploid organisms. However, haplodiploid organisms were not considered in these models even though they include Nasonia parasitoid wasps – the best example of the implication of Wolbachia in ongoing speciation. Moreover, previous work did not investigate inbreeding mating systems, which are frequently observed in arthropod species.     

Heterotrophic nitrification–aerobic denitrification by novel isolated bacteria

Three novel strains capable of heterotrophic nitrification–aerobic denitrification were isolated from the landfill leachate treatment system. Based on their phenotypic and phylogenetic characteristics, the isolates were identified as Agrobacterium sp. LAD9, Achromobacter sp. GAD3 and Comamonas sp. GAD4, respectively. Batch tests were carried out to evaluate the growth and the ammonia removal patterns. The maximum growth rates as determined from the growth curve were 0.286, 0.228, and 0.433 h⁻¹ for LAD9, GAD3 and GAD4, respectively. The maximum aerobic nitrification–denitrification rate was achieved by the strain GAD4 of 0.381 mmol/l h, followed by LAD9 of 0.374 mmol/l h and GAD3 of 0.346 mmol/l h. Moreover, hydroxylamine oxidase and periplasmic nitrate reductase were successfully expressed in all the isolates. The relationship between the enzyme activities and the aerobic nitrification–denitrification rates revealed that hydroxylamine oxidation may be the rate-limiting step in the heterotrophic nitrification–aerobic denitrification process. The study results are of great significance to the wastewater treatment systems where simultaneous removal of carbon and nitrogen is desired.