When identical functional groups are not identical: A DFT study of the effects of molecular environment on sulfur K-edge X-ray absorption spectra

Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations have been used to elucidate differences in the sulfur K-edge spectra of three pairs of related compounds: methionine and , cystine and (±)6-thioctic amide, and (Me)₂SO₃ and (CH₂)₂SO₃. TD-DFT is shown to accurately reproduce all the experimental XAS spectra. The 2 eV energy difference in the sulfur K-edge rising edge position between methionine and trimethylsulfonium is shown to derive from changes in bonding rather than the increase in effective nuclear charge. A similar insensitivity to effective nuclear charge is found in the XAS spectra of cystine and (±)6-thioctic amide. These surprising results are traced back to the fact that XAS spectra reflect orbital energy differences, rather than a measure of the atomic potential. The change in atomic potential following oxidation or reduction affects the core and valence orbitals almost equally. In all cases DFT calculations showed that the dramatic differences in sulfur K-edge spectra found between functional groups in alternative molecular environments derive from the variations in orbital mixing and energies following from bonding. However, XAS rising-edge energy positions have a near linear correlation with oxidation state. This is attributed to the fact that bond strength typically increases with oxidation state. Therefore, although XAS rising-edge energies are an approximate measure of the oxidation state of the absorbing atom, it is important to recognize that the correlation of XAS edge energy with effective nuclear charge is not direct. This result is finally applied to the question of quantitative sulfur speciation in complex materials of chemical, biological, or geological origin.     

IL-10 and natural regulatory T cells: two independent anti-inflammatory mechanisms in herpes simplex virus-induced ocular immunopathology

Two prominent anti-inflammatory mechanisms involved in controlling HSV-1-induced corneal immunopathology (stromal keratitis or SK) are the production of the cytokine IL-10 and the activity of natural regulatory T cells (nTregs). It is not known whether, under in vivo conditions, IL-10 and nTregs influence the corneal pathology independently or in concert. In the current study using wild-type and IL-10(-/-) animals, we have assessed the activity of nTregs in the absence of IL-10 both under in vitro and in vivo conditions. The IL-10(-/-) animals depleted of nTregs before ocular infection showed more severe SK lesions as compared with the undepleted IL-10(-/-) animals. In addition, nTregs purified from naive WT and IL-10(-/-) animals were equally able to suppress the proliferation and the cytokine production from anti-CD3-stimulated CD4(+)CD25(-) T cells in vitro. Furthermore, intracellular cytokine staining results indicated that nonregulatory cells expressing B220 and CD25 markers were the major IL-10-producing cell types in the lymphoid tissues of HSV-infected mice. In contrast, in the infected corneas, cells with the CD11b(+)Gr1(+) phenotype along with a minor population of Foxp3(-)CD4(+) and a few F4/80(+) cells produced IL-10. Our current investigations indicate that at least two independent anti-inflammatory mechanisms are involved in limiting the corneal lesions in SK, both of which may need to be modulated to control SK therapeutically.     

Evaluation of water productivity and fish yield in sewage-fed vis-à-vis fertilized based carp culture

Reuse of wastewater in aquaculture provides a scope to enhance water productivity of the system. Quantification of nutrient inputs incorporated through treated domestic sewage with varying dosages viz. 79.3 x 10(5)lha(-1) and 67.7 x 10(5)lha(-1) and water productivity in a controlled carp culture system were assessed in comparison to those involved in a fertilized based one, with a view to correlate among physical, chemical and biological processes involved in fish yield under the systems. The net water productivities were measured on the basis of net return values (in Indian rupees; INR) from the carp production systems at a stocking density @ 5000 per ha with four species combination. Selected relevant water parameters such as dissolved oxygen, total alkalinity, biochemical oxygen demand (BOD5) in sewage effluent and fertilizer based systems were monitored along with certain biological parameters viz. gross primary productivity, fish production and water productivity. The nutrient inputs in terms of total ammonia-nitrogen (TAN) in effluents, total nitrogen (TN) in fertilizers and phosphorus (P2O5) in both effluents and fertilizers were found significantly correlated with biological production. The results of the experiment revealed that the sewage incorporation at 79.3 x 10(5)lha(-1) yielded similar gross fish production as recorded from fertilizer based system, whereas net water productivity using sewage as nutrient source was found 64% higher than that of a fertilizer based system.     

Probing sequence variation in the receptor-targeting domain of feline leukemia virus envelope proteins with peptide display libraries

Determinants of cellular tropism and receptor targeting lie within a short peptide in the Vr1 region of the envelope (Env) proteins of feline leukemia virus (FeLV) subgroups A and C. Libraries of FeLV Env proteins with random amino acid substitutions in the peptide were screened for their ability to deliver a marker gene to D17 and AH927 cells. Screening on D17 canine cells yielded D17-specific Env proteins that used the FeLV-C receptor. Screening on AH927 cells yielded Env proteins with a broader host range, with maximal titers on AH927 cells and similar or lower titers on other cells. These Env proteins used an unidentified non-FeLV receptor for entry. The A5 isolate obtained from the AH927 screen was readily concentrated to yield titers of 10(5) on human PC-3 prostate tumor cells. The sequence divergence observed among targeting peptides of library-selected Env proteins was greater than that found in parental FeLV isolates. Substitution analyses of a conserved R in the middle of the targeting peptide held constant during screening indicated that maximal titers were obtained only when R was present in both a D17 selected isolate and an AH927 selected isolate. The ability to isolate Env proteins with unique tropisms dependent on the cells on which the library is screened has direct implications for targeting gene delivery vectors.     

SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations

Background

Structural variation (SV) represents a significant, yet poorly understood contribution to an individual’s genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints.

Results

We developed and validated SoftSearch using real and synthetic datasets. SoftSearch’s key features are 1) not requiring secondary (or exhaustive primary) alignment, 2) portability into established sequencing workflows, and 3) is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.). SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call.

Conclusions

We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance.     

GC/MS Profiling and Evaluation of Leaf Essential Oil for Bactericidal Effect and Free Radical Scavenging Activity of Plectranthus amboinicus (Lour.) Spreng Collected from Odisha,India

Plectranthus amboinicus (Lour.) Spreng, known as the Indian borage or Mexican mint, is one of the most documented species in the family Lamiaceae for its therapeutic and pharmaceutical values. It is found in the tropical and subtropical regions of the world. The leaf essential oil has immense medicinal benefits like treating illnesses of the skin and disorders like colds, asthma, constipation, headaches, coughs, and fevers. After analyzing earlier reports with regard to the quantity and quality of leaf oil yield, we discovered that the germplasm taken from Odisha is preferable to other germplasms. The objective of the present work is to evaluate the free radical scavenging activity and bactericidal effect of leaf essential oil (EO) of Plectranthus amboinicus (Lour.) Spreng collected from the state of Odisha, India. The hydro distillation technique has been used for essential oil extraction. Upon GC/MS analysis, approximately 57 compounds were identified with Carvacrol as the major compound (peak area=20.25 %), followed by p-thymol (peak area=20.17 %), o-cymene (peak area=19.41 %) and carene (peak area=15.89 %). On evaluation of free radical scavenging activity, it was recorded that the best value of inhibitory concentration, was for DPPH with IC₅₀=18.64 ppm and for H₂O₂ with IC₅₀=9.35 ppm. The EO showed efficient bactericidal effect against both gram positive (Mycobacterium smegmatis, Staphylococcus aureus, Enterococcus faecium) and gram negative (Escherichia coli, Vibrio cholerae, Klebsiella pneumoniae) bacteria studied through well diffusion method. Fumigatory action of the essential oil was found against M. smegmatis, the model organism for tuberculosis study. Alamar Blue assay, gave a result with MIC value for M. smegmatis i. e., 0.12 μg/ml and the MBC value of 0.12 μg/ml. Hence, P. amboinicus found in Odisha can be suggested as an elite variety and should be further investigated for efficient administration in drug formulation.     

Genome subtraction for novel target definition in Salmonella typhi

Large genomic sequencing projects of pathogens as well as human genome leads to immense genomic and proteomic data which would be very beneficial for the novel target identification in pathogens. Subtractive genomic approach is one of the most useful strategies helpful in identification of potential targets. The approach works by subtracting the genes or proteins homologous to both host and the pathogen and identify those set of gene or proteins which are essential for the pathogen and are exclusively present in the pathogen. Subtractive genomic approach is employed to identify novel target in salmonella typhi. The pathogen has 4718 proteins out of which 300 are found to be essential (“ indispensable to support cellular life”) in the pathogen with no human homolog. Metabolic pathway analyses of these 300 essential proteins revealed that 149 proteins are exclusively involved in several metabolic pathway of S. typhi. 8 metabolic pathways are found to be present exclusively in the pathogen comprising of 27 enzymes unique to the pathogen. Thus, these 27 proteins may serve as prospective drug targets. Sub-cellular localization prediction of the 300 essential proteins was done which reveals that 11 proteins lie on the outer membrane of the pathogen which could be probable vaccine candidates.     

Qualitative and Dynamical Analysis of a Bionomic Fishery Model with Prey Refuge

Acta Biotheoretica - Viruses are the simplest of pathogens, but possess sophisticated molecular mechanisms to manipulate host behavior, frequently utilizing molecular mimicry. Severe acute...