Multivariate PLS Modeling of Apicomplexan FabD-Ligand Interaction Space for Mapping Target-Specific Chemical Space and Pharmacophore Fingerprints

Biomolecular recognition underlying drug-target interactions is determined by both binding affinity and specificity. Whilst, quantification of binding efficacy is possible, determining specificity remains a challenge, as it requires affinity data for multiple targets with the same ligand dataset. Thus, understanding the interaction space by mapping the target space to model its complementary chemical space through computational techniques are desirable. In this study, active site architecture of FabD drug target in two apicomplexan parasites viz. Plasmodium falciparum (PfFabD) and Toxoplasma gondii (TgFabD) is explored, followed by consensus docking calculations and identification of fifteen best hit compounds, most of which are found to be derivatives of natural products. Subsequently, machine learning techniques were applied on molecular descriptors of six FabD homologs and sixty ligands to induce distinct multivariate partial-least square models. The biological space of FabD mapped by the various chemical entities explain their interaction space in general. It also highlights the selective variations in FabD of apicomplexan parasites with that of the host. Furthermore, chemometric models revealed the principal chemical scaffolds in PfFabD and TgFabD as pyrrolidines and imidazoles, respectively, which render target specificity and improve binding affinity in combination with other functional descriptors conducive for the design and optimization of the leads.

Comments on ``Influence of chemical reaction and viscous dissipation on MHD mixed convection flow'' by K. Das JMST 28 (5) (2014) 1881 similar to 1885] and ``Cu-water nanofluid flow and heat transfer over a shrinking sheet'' by K. Das JMST 28 (12) 5089 similar to 5094]

In this letter, we submit our comment on the following recently published papers by Kalidas Das: (1) ``Influence of chemical reaction and viscous dissipation on MHD mixed convection flow,'' Journal of Mechanical Science and Technology 28 (5) (2014) 1881-1885; and (2) ``Cu-water nanofluid flow and heat transfer over a shrinking sheet,'' Journal of Mechanical Science and Technology 28 (12) (2014) 5089-5094. The authors attempt to present the similarity solutions in both papers. We comment that the similarity transformations considered in Refs. 1, 2] are incorrect. Thus, the results presented by Kalidas Das lead to invalid conclusions.

Bulk Randall-Sundrum models, electroweak precision tests, and the 125 GeV Higgs

We present up-to-date electroweak fits of various Randall-Sundrum (RS) models. We consider the bulk RS, deformed RS, and the custodial RS models. For the bulk RS case we find the lightest Kaluza-Klein (KK) mode of the gauge boson to be similar to 8 TeV, while for the custodial case it is similar to 3 TeV. The deformed model is the least fine-tuned of all which can give a good fit for KK masses < 2 TeV depending on the choice of the model parameters. We also comment on the fine-tuning in each case.

Different methods of manufacturing FE-based oxygen carrier particles for reforming via chemical looping, and their effect on performance

Chemical looping combustion (CLC) is a means of combusting carbonaceous fuels, which inherently separates the greenhouse gas carbon dioxide from the remaining combustion products, and has the potential to be used for the production of high-purity hydrogen. Iron-based oxygen carriers for CLC have been subject to considerable work; however, there are issues regarding the lifespan of iron-based oxygen carriers over repeated cycles. In this work, haematite (Fe2O3) was reduced in an N2+CO+CO2 mixture within a fluidised bed at 850°C, and oxidised back to magnetite (Fe3O4) in a H2O+N2 mixture, with the subsequent yield of hydrogen during oxidation being of interest. Subsequent cycles started from Fe3O4 and two transition regimes were studied; Fe3O4↔Fe0.947O and Fe 3O4↔Fe. Particles were produced by mechanical mixing and co-precipitation. In the case of co-precipitated particles, Al was added such that the ratio of Fe:Al by weight was 9:1, and the final pH of the particles during precipitation was investigated for its subsequent effect on reactivity. This paper shows that co-precipitated particles containing additives such as Al may be able to achieve consistently high H2 yields when cycling between Fe3O4 and Fe, and that these yields are a function of the ratio of [CO2] to [CO] during reduction, where thermodynamic arguments suggest that the yield should be independent of this ratio. A striking feature with our materials was that particles made by mechanical mixing performed much better than those made by co-precipitation when cycling between Fe3O4 and Fe0.947O, but much worse than co-precipitated particles when cycling between Fe3O 4 and Fe.

Cavity-enhanced spectroscopies for applications of remote sensing, chemical kinetics and detection of radical species

This thesis describes applications of cavity enhanced spectroscopy towards applications of remote sensing, chemical kinetics and detection of transient radical molecular species. Both direct absorption spectroscopy and cavity ring-down spectroscopy are used in this work. Frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) was utilized for measurements of spectral lineshapes of O₂ and CO₂ for obtaining laboratory reference data in support of NASA’s OCO-2 mission. FS-CRDS is highly sensitive (> 10 km absorption path length) and precise (> 10000:1 SNR), making it ideal to study subtle non-Voigt lineshape effects. In addition, these advantages of FS-CRDS were further extended for measuring kinetic isotope effects: A dual-wavelength variation of FS-CRDS was used for measuring precise D/H and ¹³C/¹²C methane isotope ratios (sigma>0.026%) for the purpose of measuring the temperature dependent kinetic isotope effects of methane oxidation with O(¹D) and OH radicals. Finally, direct absorption spectroscopic detection of the trans-DOCO radical via a frequency combs spectrometer was conducted in collaboration with professor Jun Ye at JILA/University of Colorado.

Ionic Liquids and Cellulose: Dissolution, Chemical Modification and Preparation of New Cellulosic Materials

Due to its abundance and a wide range of beneficial physical and chemical properties, cellulose has become very popular in order to produce materials for various applications. This review summarizes the recent advances in the development of new cellulose materials and technologies using ionic liquids. Dissolution of cellulose in ionic liquids has been used to develop new processing technologies, cellulose functionalization methods and new cellulose materials including blends, composites, fibers and ion gels.

Physico-chemical factors and bacteria in fish ponds

Analyses of pond water and mud samples show that nitrifying bacteria (including ammonifying bacteria, nitrite bacteria, nitrobacteria and denitrifying bacteria) are in general closely correlated with various physico-chemical factors, ammonifying bacteria are mainly correlated with dissolved oxygen; denitrifying bacteria are inversely correlated with phosphorus; nitrite bacteria are closely correlated with nitrites, nitrobacteria are inversely correlated with ammoniac nitrogen. The nitrifying bacteria are more closely correlated with heterotrophic bacteria. Nitrobacteria are inversely correlated with anaerobic heterotrophic bacteria. The correlation is quite weak between all the nitrite bacteria which indicates that the nitrite bacteria have a controlling and regulating function in water quality and there is no interdependence as each plays a role of its own. The paper also discusses how the superficial soil (pond mud down to 3.5 cm deep) and different layers of the mud affect the biomass of bacteria. The study shows that the top superficial layer (down to 1.5 cm deep) is the major area for decomposing and converting organic matter.

Environmental and social impact monitoring of the Bujagali Hydropower Project (BHPP), Uganda Fisheries Component: monthly patterns in physico-chemical conditions and fish catch in the immediate vicinity of the Bujagali Hydropower construction site, 29th September - 28th October 2007

Following the commencement of construction works of a 250 MW hydropower plant at Dumbbell Island in the Upper Victoria Nile in September 2007, BEL requested NaFIRRI to conduct continuous monitoring of fish catches at two transects i.e. the immediate upstream transect of the project site (Kalange-Makwanzi) and the immediate downstream .transect (Buyala-Kikubamutwe). The routine monitoring surveys were designed to be conducted twice a week at each of the tWo transects. It was anticipated that major immediate impacts were to occur during construction, and these needed to be known by BEL as part of a mitigation strategy. For example, the construction of it cofferdam could be accompanied by rapid changes in water quality and quantity downstream of the construction. These changes in turn could affect the fish catch and would probably be missed by the quarterly monitoring already in place. Therefore, a major cbjective of the more regular and rapid monitoring was to discern immediate impacts of construction activities by focusing on selected water quality parameters (total suspended solids, water conductivity, temperature, dissolved oxygen and pH) and fish catch characteristics (total catch, catch rates and value of the catch)

Evaluation of quality of shark livers using bio-chemical properties and organoleptic score sheet

Shark livers are considered as an important raw material providing a quality fish oil. It has been reported to aid white — blood-cell production and act as an active ingredient in hemorrhoid treatments. It is also reported that liver oil as a good supplement of vitamin A and poly-unsaturated fatty acids which are important to the development of brain cells in human. Freshness of livers is very important to extract better quality oil. In Sri Lanka, the annual shark production amounts to 8000t, however the quality of livers collected from landing sites has not being measured yet. Present study was conducted to evaluate the quality of silky (Charcarninus fakiformis) shark livers available in Negombo and Beruwala landing sites in the West Coast of Sri Lanka and also to study the relationship between organoleptic and bio-chemical correlation on freshness of shark livers. Liver samples which were collected from landing sites in the West coast of Sri Lanka, were evaluated for external and internal colour, texture and odour. Total volatile nitrogen (TVN), pH value, free fatty acid (FFA%) and peroxide (PV) values of livers were also determined to assess quality. According to the organoleptic scoring system 4.3% of liver samples were categorized as best in quality while 30.4%, 56.5% and 8.7% rated as good, medium and poor in quality respectively at the Negombo and Beruwala landing sites. Bio-chemical analysis showed that the better quality livers had the highest score for sensory evaluation and low values for TVN, FFA and peroxide value while low quality livers gave low score for sensory evaluation and high TVN, FFA, peroxide values. Correlation coefficient of organoleptic scores against total volatile nitrogen value, pH value, free fatty acid % and peroxide value of shark livers were determined by statistical analysis. Organoleptic score of shark livers was found to be highly.

Squilla protein: chemical composition and nutritive value

Protein extract prepared from squilla (Grato squilla nepa), a commercially unexploited crustacean, was analysed for crude protein and essential amino acids. All the essential amino acids except tryptophan and threonine were present in nutritionally adequate amounts. The protein was evaluated for its nutritional quality in respect of growth rate, protein efficiency ratio (PER) and liver nitrogen content by feeding on rats. Growth rates and protein efficiency ratios were similar in rats fed on casein, squilla protein and a combination of squilla protein and casein (1:1) diet. The weight of liver and kidneys were normal.

Monthly patterns in physico-chemical conditions and fish catch in the immediate vicinity of the Bujagali hydropower construction site 29th September - 28th October 2007

The specific objectives were to: WATER QUALITY 1. To measure the water physical variables as indicators of environmental conditions in the upstream and downstream transects of Kalange (1) and Buyala (2), respectively, 2. To determine the concentrations of total suspended solids as a major constituent likely to be released into the waters at any time during the construction activities, by comparing the concentrations at the two transects. FISH CATCH 1. To follow up trends in fish catch as construction activity progresses, and to precision of the estimate; 2. To estimate the prevailing fish catch rates, total fish catches and the total value of the fish catch to the local fishers at the two transects.