Role of Interferon Gamma Release Assay in Active TB Diagnosis among HIV Infected Individuals

Background

A rapid and specific test is urgently needed for tuberculosis (TB) diagnosis especially among human immunodeficiency virus (HIV) infected individuals. In this study, we assessed the sensitivity of Interferon gamma release assay (IGRA) in active tuberculosis patients who were positive for HIV infection and compared it with that of tuberculin skin test (TST).

Methodology/Principal Findings

A total of 105 HIV-TB patients who were naïve for anti tuberculosis and anti retroviral therapy were included for this study out of which 53 (50%) were culture positive. Of 105 tested, QuantiFERON-TB Gold in-tube (QFT-G) was positive in 65% (95% CI: 56% to 74%), negative in 18% (95% CI: 11% to 25%) and indeterminate in 17% (95% CI: 10% to 24%) of patients. The sensitivity of QFT-G remained similar in pulmonary TB and extra-pulmonary TB patients. The QFT-G positivity was not affected by low CD4 count, but it often gave indeterminate results especially in individuals with CD4 count <200 cells/µl. All of the QFT-G indeterminate patients whose sputum culture were positive, showed ≤0.25 IU/ml of IFN-γ response to phytohemagglutinin (PHA). TST was performed in all the 105 patients and yielded the sensitivity of 31% (95% CI: 40% to 22%). All the TST positives were QFT-G positives. The sensitivity of TST was decreased, when CD4 cell counts declined.

Conclusions/Significance

Our study shows neither QFT-G alone or in combination with TST can be used to exclude the suspicion of active TB disease. However, unlike TST, QFT-G yielded fewer false negative results even in individuals with low CD4 count. The low PHA cut-off point for indeterminate results suggested in this study (≤0.25 IU/ml) may improve the proportion of valid QFT-G results.     

Biofuels: opportunities and challenges in India

Energy plays a vital role in the economic growth of any country. Current energy supplies in the world are unsustainable from environmental, economic, and societal standpoints. All over the world, governments have initiated the use of alternative sources of energy for ensuring energy security, generating employment, and mitigating CO₂ emissions. Biofuels have emerged as an ideal choice to meet these requirements. Huge investments in research and subsidies for production are the rule in most of the developed countries. India started its biofuel initiative in 2003. This initiative differs from other nations’ in its choice of raw material for biofuel production—molasses for bioethanol and nonedible oil for biodiesel. Cyclicality of sugar, molasses, and ethanol production resulted in a fuel ethanol program which suffered from inconsistent production and supply. The restrictive policies, availability of molasses, and cost hampered the fuel ethanol program. Inconsistent policies, availability of land, choice of nonnative crops, yield, and market price have been major impediments for biodiesel implementation. However, a coherent, consistent, and committed policy with long-term vision can sustain India’s biofuel effort. This will provide energy security, economic growth, and prosperity and ensure a higher quality of life for India.     

An integrated treatment system for coffee processing wastewater using anaerobic and aerobic process

The experiment was conducted to develop an integrated treatment system for coffee processing wastewater (CPWW) through the combination of biomethanation with aeration and wetland plants treatment. The biomethanation was carried out at different hydraulic retention times (HRTs) using upflow anaerobic hybrid reactor (UAHR) and 18 h of HRT was found to be optimum. The maximum biochemical oxygen demand (BOD), chemical oxygen demand (COD) and total solids (TS) reduction were 66.0%, 61.0% and 58.0%, respectively with organic loading rate of 9.55 kg m^?3 day^?1. The reduction of pollution load of the wastewater by microbial action augmented by aeration resulted in the reduction of electrical conductivity (EC), BOD, COD, and total solids (TS). Continuous aeration of wastewater resulted in maximum reduction of BOD (74.6%), COD (68.6%) and TS (49.3%). The wetland plant, Typha latifolia reduced 85.4% and 78.0% of BOD and COD, respectively in biomethanated cum aerated CPWW.     

The Benefits of Ambiol® in Promoting Germination, Growth, and Drought Tolerance can be Passed on to Next-Generation Tomato Seedlings

Seed preconditioning with Ambiol^® has been shown to improve germination, growth, and drought tolerance in seedlings of many species. Attempts to understand the mode of action of Ambiol have found that seed preconditioning triggers several new proteins, which suggests that Ambiol-induced benefits may persist beyond seedlings and, perhaps, into the next generation. Seeds were preconditioned with 0 and 10 mg l^?1 Ambiol to determine effects on germination, seedling growth, and yield of parent tomato plants. Seeds were collected from plants in each treatment and then sown to determine effects on germination and seedling growth in the next generation. Key parameters such as percent germination, leaf area, shoot mass, root mass, and photosynthesis were significantly improved in parents and in progeny. In addition, there was a 141% increase in tomato yield in preconditioned parents. It was concluded that Ambiol-induced benefits continue throughout plant development and into the next generation, potentially having significant horticultural and economic ramifications.     

Partitioning of Minimotifs Based on Function with Improved Prediction Accuracy

Background

Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions.

Methodology/Principal Findings

Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein have a related cellular or molecular function, the prediction is more likely to be accurate. This filter was implemented in Minimotif Miner using function annotations from the Gene Ontology. We have also combined two filters that are based on entirely different principles and this combined filter has a better predictability than the individual components.

Conclusions/Significance

Testing these functional filters on known and random minimotifs has revealed that they are capable of separating true motifs from false positives. In particular, for the cellular function filter, the percentage of known minimotifs that are not removed by the filter is ∼4.6 times that of random minimotifs. For the molecular function filter this ratio is ∼2.9. These results, together with the comparison with the published frequency score filter, strongly suggest that the new filters differentiate true motifs from random background with good confidence. A combination of the function filters and the frequency score filter performs better than these two individual filters.     

Minimotif Miner: a tool for investigating protein function

In addition to large domains, many short motifs mediate functional post-translational modification of proteins as well as protein-protein interactions and protein trafficking functions. We have constructed a motif database comprising 312 unique motifs and a web-based tool for identifying motifs in proteins. Functional motifs predicted by MnM can be ranked by several approaches, and we validated these scores by analyzing thousands of confirmed examples and by confirming prediction of previously unidentified 14-3-3 motifs in EFF-1.     

Recognition of ferric catecholates by FepA

Escherichia coli FepA transports certain catecholate ferric siderophores, but not others, nor any noncatecholate compounds. Direct binding and competition experiments demonstrated that this selectivity originates during the adsorption stage. The synthetic tricatecholate Fe-TRENCAM bound to FepA with 50- to 100-fold-lower affinity than Fe-enterobactin (FeEnt), despite an identical metal center, and Fe-corynebactin only bound at much higher concentrations. Neither Fe-agrobactin nor ferrichrome bound at all, even at concentrations 10(6)-fold above the Kd. Thus, FepA only adsorbs catecholate iron complexes, and it selects FeEnt among even its close homologs. We used alanine scanning mutagenesis to study the contributions of surface aromatic residues to FeEnt recognition. Although not apparent from crystallography, aromatic residues in L3, L5, L7, L8, and L10 affected FepA's interaction with FeEnt. Among 10 substitutions that eliminated aromatic residues, Kd increased as much as 20-fold (Y481A and Y638A) and Km increased as much as 400-fold (Y478), showing the importance of aromaticity around the pore entrance. Although many mutations equally reduced binding and transport, others caused greater deficiencies in the latter. Y638A and Y478A increased Km 10- and 200-fold more, respectively, than Kd. N-domain loop deletions created the same phenotype: Delta60-67 (in NL1) and Delta98-105 (in NL2) increased Kd 10- to 20-fold but raised Km 500- to 700-fold. W101A (in NL2) had little effect on Kd but increased Km 1,000-fold. These data suggested that the primary role of the N terminus is in ligand uptake. Fluorescence and radioisotopic experiments showed biphasic release of FeEnt from FepA. In spectroscopic determinations, k(off1) was 0.03/s and k(off2) was 0.003/s. However, FepAY272AF329A did not manifest the rapid dissociation phase, corroborating the role of aromatic residues in the initial binding of FeEnt. Thus, the beta-barrel loops contain the principal ligand recognition determinants, and the N-domain loops perform a role in ligand transport.     

The effect of finger millet feeding on the early responses during the process of wound healing in diabetic rats

In the present study, the role of finger millet feeding on skin antioxidant status, nerve growth factor (NGF) production and wound healing parameters in healing impaired early diabetic rats is reported. Hyperglycemic rats received food containing 50 g/100 g finger millet (FM). Non-diabetic controls and diabetic controls received balanced nutritive diet. Full-thickness excision skin wounds were made after 2 weeks prior feeding of finger millet diet. The rate of wound contraction, and the levels of collagen, hexosamine and uronic acid in the granulation tissue were determined. The skin antioxidant status and lipid peroxide concentration were also monitored during the study. In hyperglycemic rats fed with finger millet diet, the healing process was hastened with an increased rate of wound contraction. Skin levels of glutathione (GSH), ascorbic acid and alpha-tocopherol in alloxan-induced diabetic rat were lower as compared to non-diabetics. Altered activities of superoxide dismutase (SOD) and catalase (CAT) were also recorded in diabetics. Interestingly, thiobarbituric acid reactive substances (TBARS) were elevated in the wound tissues of all the groups, when compared to normal (unwounded) skin tissues. However, in diabetic rats the TBARS levels of both normal and wounded skin tissues were significantly elevated (P < 0.001) when compared with control (non-diabetic) and diabetics fed with FM. Impaired production of NGF, determined by ELISA, in diabetic rats was improved upon FM feeding and further confirmed by immunocytochemical observations reflects the increased expression of NGF in hyperglycemic rats supplemented with FM-enriched diet. Histological and electron microscopical evaluations revealed the epithelialization, increased synthesis of collagen, activation of fibroblasts and mast cells in FM-fed animals. Thus, increased levels of oxidative stress markers accompanied by decreased levels of antioxidants play a vital role in delaying wound healing in diabetic rats. However, FM feeding to the diabetic animals, for 4 weeks, controlled the glucose levels and improved the antioxidant status, which hastened the dermal wound healing process.     

Characterisation of Soybean and Wheat Seeds by Nuclear Magnetic Resonance Spectroscopy

The effects of equilibration under different air relative humidities (RH, 1 – 90 %) and temperatures (35 and 45 °C) on soybean (Glycine max) and wheat (Triticum aestivum) seeds were studied using different techniques. Seed moisture content, electrical conductivity (EC) of seed leachate and per cent seed germination were measured following standard procedures, and compared with nuclear magnetic resonance spin-spin relaxation time (T₂) measurements. Moisture contents of soybean and wheat seeds, following the reverse sigmoidal trend, were greater at 35 than at 45 °C at any particular RH. Changes in T₂ were related to the changes in germination percentage and leachate EC of both soybean and wheat seeds. Equilibrating soybean seeds at RH 11 % decreased germination percentage with corresponding decrease in T₂. On the contrary, EC of seed leachate increased. In wheat seeds equilibrated at 45 °C, T² was maximal at RH 5.5 %. T₂ declined in seeds equilibrated at high RH (> 80 %) together with low germination percentage.