Genome-wide codon usage profiling of ocular infective Chlamydia trachomatis serovars and drug target identification

Chlamydia trachomatis (C.t) is a Gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B and C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering potential drug targets and genomic influence on pathogenesis. Hence, in this study we performed deep statistical profiling of codon usage in these serovars. The overall base composition analysis reveals that these serovars are over biased to AU than GC. Similarly, relative synonymous codon usage also showed preference towards A/U ending codons. Parity Rule 2 analysis inferred unequal distribution of AT and GC, indicative of other unknown factors acting along with mutational pressure to influence codon usage bias (CUB). Moreover, absolute quantification of CUB also revealed lower bias across these serovars. The effect of natural selection on CUB was also confirmed by neutrality plot, reinforcing natural selection under mutational pressure turned to be a pivotal role in shaping the CUB in the strains studied. Correspondence analysis (COA) clarified that, C.t C/TW-3 to show a unique trend in codon usage variation. Host influence analysis on shaping the codon usage pattern also inferred some speculative relativity. In a nutshell, our finding suggests that mutational pressure is the dominating factor in shaping CUB in the strains studied, followed by natural selection. We also propose potential drug targets based on cumulative analysis of strand bias, CUB and human non-homologue screening.     

The dose dependent effects of betulin on porcine chondrocytes

The past two decades triterpenes have attracted attention because of their pharmacological potential, especially its anti-oxidant activity. The present study was aimed to evaluate the possible protective effects of the triterpene betulin on porcine chondrocytes. For this, the cells were treated with different doses of betulin (0.02, 0.32 and 5.12 μg/mL) and without betulin. Biochemical measures of necrosis, mitochondrial activity, DNA content and sulphated glycosaminoglycans (sGAG) were reported. In addition, the gene expression of extracellular matrix molecules (ECM), proteases and soluble factors were examined. The abundance of reactive oxygen species (ROS) was also reported. Among the concentrations tried 0.32 μg/mL of betulin was found to be optimum because it effectively promoted the gene expressions of type II collagen, aggrecan and inhibited the gene expression of matrix metalloproteinase 2 (MMP-2). The chemiluminescence (CL) assay indicated that betulin treated chondrocytes had better free radical scavenging activity than the chondrocytes cultured without betulin. Alcian blue staining revealed that the chondrocytes were functionally active and able to synthesis sGAG. The free radical scavenging activity ensures betulin as protectant of chondrocytes and it further maintains the proliferation and basic activities of chondrocytes.     

Evaluation of hypoglycemic therapeutics and nutritional supplementation for type 2 diabetes mellitus management: An insight on molecular approaches

Biotechnology Letters - This review aims to summarize the current management of type 2 diabetes principles, including oral hypoglycemic agents, types of insulin administration, diet maintenance,...     

Modification of paper properties by the pretreatment of wastepaper pulp with Graphiumputredinis, Trichodermaharzianum and fusant xylanases

Graphiumputredinis, Trichodermaharzianum and fusant were used in the present study to produce extracellular xylanases, an important industrial enzyme used in pulp and paper industry produced in a minimal medium supplemented with oat spelt xylan (1%, w/v) pH 7.0 at 27+/-2 degrees C. The enzyme was purified to homogeneity by DEAE-Cellulose and Superdex 75 FPLC column, respectively. The enzyme was found to be a monomer as determined by SDS gel electrophoresis. The optimum pH and temperature for purified G. putredinis, T. harzianum and fusant xylanases were 5.0-6.0 and 50-70 degrees C, respectively. Pretreatment of paper pulp with G. putredinis, T. harzianum and fusant xylanases decreased pulp kappa number. Xylanases particularly that of fusant at 5 IU/g pulp concentration and 1.5% pulp consistency at 60 degrees C for 18 h followed by EDED process yielded good quality paper from waste paper pulp. A significant increase in pulp brightness and improvement in various pulp properties, viz. burst capacity, thickness and bulkness of the treated pulp were observed in comparison to the conventional chemical bleaching. Easy purification and high stability of these enzymes makes it amicable for industrial applications.     

Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae)

Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo‐Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co‐amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent–offspring relationships in natural populations, with over 99.6% accuracy in parent–offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28–96% of loci. The multiplex PCRs developed here provide a reliable and cost‐effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species.     

Redox-mediated decolorization of recalcitrant textile dyes by <Emphasis Type="Italic">Trichoderma harzianum</Emphasis> WL1 laccase

The efficiency of crude and partially purified Trichoderma harzianum WL1 laccase for the decolorization of synthetic dyes (Rhodamine 6G, Erioglaucine and Trypan blue) with complex aromatic structures were evaluated. Selection of dyes was based on their extensive usage in local dyeing and textile industries around the study area. Studies on the role of redox potential of laccases on dye decolorization are rarely discussed and hence, for the first time we have shown the redox mediated dye decolorizing efficiency of T. harzianum WL1 laccase with the commonly employed redox mediator 1-hydroxybenzotriazole (HBT). The process parameters such as initial dye concentration, enzyme load and HBT concentration were studied and found that they had a great influence on dye removal process. When the dyes were treated with increased concentration of enzyme, it showed a greater percentage of decolorization. Compared to the crude laccase, partially purified laccase accounts for maximum decolorization of all the dyes studied. In addition, the rate of dye decolorization was considerably enhanced in presence of 4 mM HBT. Maximum and minimum decolorization were recorded for Rhodamine 6G and Trypan blue, respectively. The results of this study further confirmed that, T. harzianum laccase was found to be suitable with HBT and this laccase-mediator system (LMS) could be applied for the decolorization of various classes of dyes.     

Feasibility of using <Emphasis Type="Italic">Trichoderma harzianum</Emphasis> biomass for the removal of erioglaucine from aqueous solution

The test fungus Trichoderma harzianum was isolated from the Western Ghats area of Tamilnadu, India. The study involves the feasibility of using T.harzianum to remove erioglaucine from an aqueous solution in batch mode. The batch mode experimental parameters such as effect of agitation time and initial dye concentration, adsorbent mass and pH were determined. The results revealed that, the fungal biomass at 1.5 g/50 ml adsorbent mass removed 75.67–88.05% of dye (10–50 mg/l) in 105 min at pH 4.0. The adsorption equilibrium data followed both Langmuir and Freundlich isotherms. From the Langmuir isotherm, the adsorbent had adsorption capacity (Q ₀ ) of 3.09 mg/g. Pseudo first and second order rate kinetic equations were applied to the experimental adsorption data. The results indicate that the adsorbent system followed second order rate kinetics.     

Identification of potential drugs targeting L,L-diaminopimelate aminotransferase of Chlamydia trachomatis: An integrative pharmacoinformatics approach

Chlamydia trachomatis (C.t) is a gram-negative obligate intracellular bacteria, which is a major causative of infectious blindness and sexually transmitted diseases. A surge in multidrug resistance among chlamydial species has posed a challenge to adopt alternative drug targeting strategies. Recently, in C.t, L,L-diaminopimelate aminotransferase (CtDAP-AT) is proven to be a potential drug target due its essential role in cell survival and host nonspecificity. Hence, in this study, a multilevel precision-based virtual screening of CtDAP-AT was performed to identify potential inhibitors, wherein, an integrative stringent scoring and filtration were performed by coupling, glide docking score, binding free energy, ADMET (absorption, distribution, metabolism, and excretion, toxicity) prediction, density functional theory (quantum mechanics), and molecular dynamics simulation (molecular mechanics). On cumulative analysis, NSC_5485 (1,3-bis((7-chloro-4-quinolinyl)amino)-2-propanol) was found to be the most potential lead, as it showed higher order significance in terms of binding affinity, bonded interactions, favorable ADMET, chemical reactivity, and greater stabilization during complex formation. This is the first report on prioritization of small molecules from National Cancer Institute (NCI) and Maybridge data sets (341 519 compounds) towards targeting CtDAP-AT. Thus, the proposed compound shall aid in effective combating of a broad spectrum of C.t infections as it surpassed all the levels of prioritization.