Metabolic pathway analysis and molecular docking analysis for identification of putative drug targets in Toxoplasma gondii: novel approach

Toxoplasma gondii is an obligate intracellular apicomplexan parasite that can infect a wide range of warm-blooded animals including humans. In humans and other intermediate hosts, toxoplasma develops into chronic infection that cannot be eliminated by host's immune response or by currently used drugs. In most cases, chronic infections are largely asymptomatic unless the host becomes immune compromised. Thus, toxoplasma is a global health problem and the situation has become more precarious due to the advent of HIV infections and poor toleration of drugs used to treat toxoplasma infection, having severe side effects and also resistance have been developed to the current generation of drugs. The emergence of these drug resistant varieties of T. gondii has led to a search for novel drug targets. We have performed a comparative analysis of metabolic pathways of the host Homo sapiens and the pathogen T. gondii. The enzymes in the unique pathways of T. gondii, which do not show similarity to any protein from the host, represent attractive potential drug targets. We have listed out 11 such potential drug targets which are playing some important work in more than one pathway. Out of these, one important target is Glutamate dehydrogenase enzyme; it plays crucial part in oxidation reduction, metabolic process and amino acid metabolic process. As this is also present in the targets of tropical diseases of TDR (Tropical disease related Drug) target database and no PDB and MODBASE 3D structural model is available, homology models for Glutamate dehydrogenase enzyme were generated using MODELLER9v6. The model was further explored for the molecular dynamics simulation study with GROMACS, virtual screening and docking studies with suitable inhibitors against the NCI diversity subset molecules from ZINC database, by using AutoDock-Vina. The best ten docking solutions were selected (ZINC01690699, ZINC17465979, ZINC17465983, ZINC18141294_03, ZINC05462670, ZINC01572309, ZINC18055497_01, ZINC18141294, ZINC05462674 and ZINC13152284_01). Further the Complexes were analyzed through LIGPLOT. On the basis of Complex scoring and binding ability it is deciphered that these NCI diversity set II compounds, specifically ZINC01690699 (as it has minimum energy score and one of the highest number of interactions with the active site residue), could be promising inhibitors for T. gondii using Glutamate dehydrogenase as Drug target.     

Transpiration difference under high evaporative demand in chickpea (Cicer arietinum L.) may be explained by differences in the water transport pathway in the root cylinder

• Terminal drought substantially reduces chickpea yield. Reducing water use at vegetative stage by reducing transpiration under high vapor pressure deficit (VPD), i.e. under dry/hot conditions, contributes to drought adaptation. We hypothesized that this trait could relate to differences in a genotype's dependence on root water transport pathways and hydraulics.
• Transpiration rate responses in conservative and profligate chickpea genotypes were evaluated under increasing VPD in the presence/absence of apoplastic and cell‐to‐cell transport inhibitors.
• Conservative genotypes ICC 4958 and ICC 8058 restricted transpiration under high VPD compared to the profligate genotypes ICC 14799 and ICC 867. Profligate genotypes were more affected by aquaporin inhibition of the cell‐to‐cell pathway than conservative genotypes, as measured by the root hydraulic conductance and transpiration under high VPD. Aquaporin inhibitor treatment also led to a larger reduction in root hydraulic conductivity in profligate than in conservative genotypes. In contrast, blockage of the apoplastic pathway in roots decreased transpiration more in conservative than in profligate genotypes. Interestingly, conservative genotypes had high early vigour, whereas profligate genotypes had low early vigour.
• In conclusion, profligate genotypes depend more on the cell‐to‐cell pathway, which might explain their higher root hydraulic conductivity, whereas water‐saving by restricting transpiration led to higher dependence on the apoplastic pathway. This opens the possibility to screen for conservative or profligate chickpea phenotypes using inhibitors, itself opening to the search of the genetic basis of these differences.

     

Microbial–meiofaunal interrelationships in coastal sediments of the Red Sea

Population density and biomass of bacteria and meiofauna were investigated seasonally in the sediments of the north-western bank of Red Sea. Samples of sediments were collected seasonally from three different stations to determine microphytobenthic biomass (chlorophyll a), protein, lipid, carbohydrate, and total organic matter concentrations. These investigations revealed that microbial components tended to increase their dominancy, whereas sensitive meiofauna were extremely reduced during the entire study period. Thus a very low density of the total meiofauna (with an annual average of 109 ± 26 ind./10 cm²) was recorded whilst the benthic microbial population densities exhibited higher values (ranging from 0.31 ± 0.02 × 10⁸ to 43.67 ± 18.62 × 10⁸/g dry sediment). These changes in the relative importance analysis of benthic microbial components versus meiofaunal ones seem to be based on the impact of organic matter accumulation on the function and structure of these benthic communities. Proteins, lipids and carbohydrates showed very low concentration values, and the organic matter mostly consisted of carbohydrates, reflecting lower nutritional values for benthic fauna in general and meiofauna in particular. The distribution of microbial and meiofaunal communities seems to be dependent on the quality of the organic matter rather than on its quantity. Total organic matter concentrations varied between 5.8 and 7.6 mg/g, with organic carbon accounting for only 32% of the total organic matter. Chlorophyll a attained very low values, fluctuating between 0.11 and 0.56 μg/g, indicating the oligotrophy of the studied area. The very low concentration of chlorophyll a in the Red Sea sediment suggests that the sedimentary organic matter, heterotrophic bacteria and/or protozoa constitute an alternative resource that is consumed by meiofauna when algae are less abundant. Protozoa, therefore, represent the “missing link in bacteria–meiofauna interaction in the Red Sea marine sediment ecosystem.     

TDZ-induced direct shoot organogenesis and somatic embryogenesis on cotyledonary node explants of lentil (Lens culinaris Medik.)

An efficient and simple procedure for inducing high frequency direct shoot organogenesis and somatic embryogenesis in lentil from cotyledonary node explants (without both the cotyledons) in response to TDZ alone is reported. TDZ at concentration lower than 2.0 μM induced shoot organogenesis whereas at higher concentration (2.5–15 μM) it caused a shift in regeneration from shoot organogenesis to somatic embryogenesis. The cotyledonary node and seedling cultures developed only shoots even at high concentrations of BAP and TDZ, respectively. TDZ at 0.5 and 5.0 μM was found to be optimal for inducing an average of 4–5 shoots per cotyledonary node in 93 % of the cultures and 55 somatic embryos in 68 % of the cultures, respectively. The somatic embryos were germinated when transferred to lower TDZ concentration (0.5–1.0 μM). The shoots were rooted on MS basal medium containing 2.5 μM IBA. The plantlets were obtained within 8 weeks from initiation of culture and were morphologically similar to seed-raised plants. The possible role of stress in thidiazuron induced somatic embryogenesis is discussed.Key words: Thidiazuron, Lens culinaris, Somatic embryogenesis, Organogenesis     

一株蓝麻黄内生放线菌的分离、鉴定和活性研究

目的:分离对农作物致病菌具有拮抗作用的株内生放线菌,并对其进行系统鉴定.方法:经表面消毒采用研磨法从蓝麻黄中分离内生放线菌;再通过琼脂扩散法筛选具有抗农作物致病菌活性的内生放线菌;利用菌株形态特征、培养特征、生理生化特性和16S rRNA序列分析对拮抗菌进行鉴定;并对代谢产物做了生物碱的检测.结果:从蓝麻黄中分离到菌7株内生放线菌而其中的XJEG-GA-16具有较好拮抗作用,该菌对7种植物病原菌具有较好的拮抗作用,尤其是对玉米大斑病菌的拮抗作用显著抑菌圈大于20mm.经形态学观察,培养特征、生理生化特和分子分类学分析鉴定与Streptomyces albus subsp.albus在同一个分支上,同源性为99%.该菌株代谢产物中含有生物碱.结论:蓝麻黄内生放线菌XJEG-GA-16对农作物致病菌有明显的拮抗作用,最终鉴定为链霉菌Streptomyces albus subsp.Albus.     

Adaptive glenoid bone remodeling simulation

Glenoid prosthesis loosening is the most common cause for revision total shoulder arthroplasty. Stress-induced bone remodeling may compromise long-term prosthesis fixation and significantly contribute to loosening. Realistic, robust analysis of bone-prosthesis constructs need to look beyond initial post-implantation mechanics provided by static finite element (FE) simulation. Adaptive bone remodeling simulations based on Wolff's law are needed for evaluating long-term glenoid prostheses fixation. The purpose of this study was to take a first step towards this goal and create and validate two-dimensional FE simulations, using the intact glenoid, for computing subject-specific adaptive glenoid remodeling. Two-dimensional glenoid FE models were created from scapulae computed tomography images. Two distinct processes, “element” and “node” simulations, used the forward-Euler method to compute bone remodeling. Initial bone density was homogeneous. Center and offset load combinations were iteratively applied. To validate the simulations we performed location-specific statistical comparisons between predicted and actual bone density, load combinations, and “element” and “node” processes. Visually and quantitatively “element” simulations produced better results (p>0.22), and correlation coefficients ranged 0.51–0.69 (p<0.001). Having met this initial work's goals, we expect subject-specific FE glenoid bone remodeling simulations together with static FE stress analyses to be effective tools for designing and evaluating glenoid prostheses.     

Genotoxic potential of medroxyprogesterone acetate in cultured human peripheral blood lymphocytes

Medroxyprogesterone acetate was studied at three different concentrations (1, 5 and 10 microM), for its genotoxic effects in human peripheral blood lymphocyte culture using chromosomal aberrations and sister chromatid exchanges as parameters. Duplicate peripheral blood cultures were treated with three different concentrations (1, 5 and 10 microM) of medroxyprogesterone acetate. The study was carried out both in the absence as well as in the presence of metabolic activation (S9 mix) with and without NADP. Medroxyprogesterone acetate was found genotoxic at 5 and 10 microM in the presence of S9 mix with NADP. To study the possible mechanism of the genotoxicity of medroxyprogesterone acetate, superoxide dismutase and catalase at different doses were used separately and in combination with 10 microM of medroxyprogesterone at different doses in the presence of S9 mix with NADP. Superoxide dismutase treatment results in an increase of the genotoxic damage but catalase treatment reduce the genotoxic damage of medroxyprogesterone acetate. Catalase treatment in combination with superoxide dismutase also results in the further reduction of the genotoxic damage. The results of the present study reveal that medroxyprogesterone acetate is genotoxic only in the presence of metabolic activation (S9 mix) with NADP. Treatments with superoxide dismutase and catalase suggests the possible generation of reactive oxygen species by redox cycling of various forms of quinones, similar to estrogens, that are the results of aromatic hydroxylation by cytochrome P450s.     

The essential role of centrosomal NDE1 in human cerebral cortex neurogenesis

We investigated three families whose offspring had extreme microcephaly at birth and profound mental retardation. Brain scans and postmortem data showed that affected individuals had brains less than 10% of expected size (≤10 standard deviation) and that in addition to a massive reduction in neuron production they displayed partially deficient cortical lamination (microlissencephaly). Other body systems were apparently unaffected and overall growth was normal. We found two distinct homozygous mutations of NDE1, c.83+1G>T (p.Ala29GlnfsX114) in a Turkish family and c.684_685del (p.Pro229TrpfsX85) in two families of Pakistani origin. Using patient cells, we found that c.83+1G>T led to the use of a novel splice site and to a frameshift after NDE1 exon 2. Transfection of tagged NDE1 constructs showed that the c.684_685del mutation resulted in a NDE1 that was unable to localize to the centrosome. By staining a patient-derived cell line that carried the c.83+1G>T mutation, we found that this endogeneously expressed mutated protein equally failed to localize to the centrosome. By examining human and mouse embryonic brains, we determined that NDE1 is highly expressed in neuroepithelial cells of the developing cerebral cortex, particularly at the centrosome. We show that NDE1 accumulates on the mitotic spindle of apical neural precursors in early neurogenesis. Thus, NDE1 deficiency causes both a severe failure of neurogenesis and a deficiency in cortical lamination. Our data further highlight the importance of the centrosome in multiple aspects of neurodevelopment.     

A novel multi-planar radiography method for three dimensional pose reconstruction of the patellofemoral and tibiofemoral joints after arthroplasty

Determining the 3D pose of the patella after total knee arthroplasty is challenging. The commonly used single-plane fluoroscopy is prone to large errors in the clinically relevant mediolateral direction. A conventional fixed bi-planar setup is limited in the minimum angular distance between the imaging planes necessary for visualizing the patellar component, and requires a highly flexible setup to adjust for the subject-specific geometries. As an alternative solution, this study investigated the use of a novel multi-planar imaging setup that consists of a C-arm tracked by an external optoelectric tracking system, to acquire calibrated radiographs from multiple orientations. To determine the accuracies, a knee prosthesis was implanted on artificial bones and imaged in simulated 'Supine' and 'Weightbearing' configurations. The results were compared with measures from a coordinate measuring machine as the ground-truth reference. The weightbearing configuration was the preferred imaging direction with RMS errors of 0.48 mm and 1.32 ° for mediolateral shift and tilt of the patella, respectively, the two most clinically relevant measures. The 'imaging accuracies' of the system, defined as the accuracies in 3D reconstruction of a cylindrical ball bearing phantom (so as to avoid the influence of the shape and orientation of the imaging object), showed an order of magnitude (11.5 times) reduction in the out-of-plane RMS errors in comparison to single-plane fluoroscopy. With this new method, complete 3D pose of the patellofemoral and tibiofemoral joints during quasi-static activities can be determined with a many-fold (up to 8 times) (3.4mm) improvement in the out-of-plane accuracies compared to a conventional single-plane fluoroscopy setup.