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.     

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.     

Na,K-ATPase inhibition alters tight junction structure and permeability in human retinal pigment epithelial cells

Na,K-ATPase regulates avariety of transport functions in epithelial cells. In cultures ofhuman retinal pigment epithelial (RPE) cells, inhibition of Na,K-ATPaseby ouabain and K⁺ depletion decreased transepithelialelectrical resistance (TER) and increased permeability of tightjunctions to mannitol and inulin. Electrophysiological studiesdemonstrated that the decrease in TER was due to an increase inparacellular shunt conductance. At the light microscopy level, thisincreased permeability was not accompanied by changes in thelocalization of the tight junction proteins ZO-1, occludin, andclaudin-3. At the ultrastructural level, increased tight junctionpermeability correlated with a decrease in tight junction membranecontact points. Decreased tight junction membrane contact points andincreased tight junction permeability were reversible inK⁺-repletion experiments. Confocal microscopy revealed thatin control cells, Na,K-ATPase was localized at both apical andbasolateral plasma membranes. K⁺ depletion resulted in alarge reduction of apical Na,K-ATPase, and after K⁺repletion the apical Na,K-ATPase recovered to control levels. Theseresults suggest a functional link exists between Na,K-ATPase and tightjunction function in human RPE cells.

     

I-conotoxin superfamily revisited.

The I-conotoxin superfamily (I-Ctx) is known to have four disulfide bonds with the cysteine arrangement C-C-CC-CC-C-C, and the members inhibit or modify ion channels of nerve cells. Recently, Olivera and co-workers (FEBS J. 2005; 272: 4178-4188) have suggested that the previously described I-Ctx should now be divided into two different gene superfamilies, namely, I1 and I2, in view of their having two different types of signal peptides and exhibiting distinct functions. We have revisited the 28 entries presently grouped as I-Ctx in UniProt Swiss-Prot knowledgebase, and on the basis of in silico analysis have divided them into I1 and I2 superfamilies. The sequence analysis has provided a framework for in silico annotation enabling us to carry out computer-based functional characterization of the UniProtKB/TrEMBL entry Q59AA4 from Conus miles and to predict it as a member of the I2 superfamily. Furthermore, we have predicted the mature toxin of this entry and have proposed that it may be an inhibitor of voltage-gated potassium channels.     

Early growth invigoration of jack pine seedlings by natural plant growth regulators

 Survival of conifer transplants is often poor on exposed planting sites in the boreal forest. More than one-third of all conifers do not become established. To enhance the competitive ability of jack pine seedlings, seeds were treated with natural plant growth regulators (PGRs; viz., homobrassinolide, salicylic acid, and two polyamines, spermine and spermidine) and growth promotion was studied for 16 days. Homobrassinolide (5 ng l^–1), salicylic acid (100 μg l^–1) and spermine (10 μg l^–1) enhanced elongation growth and elongation rate of whole plant. Homobrassinolide (5 ng l^–1) and salicylic acid (100 μg l^–1) stimulated root elongation by 38% and 10% respectively while spermine (1000 μg l^–1) increased needle growth by 14%. Homobrassinolide stimulated dry weight growth and growth rate. Homobrassinolide recorded over 20% increase in dry matter production, apportioned equally to root and needles, whereas spermine enhanced total dry matter production by almost 10%, mostly by increasing needle weight. Homobrassinolide facilitated nearly 19% increase in growth rate while spermine recorded only a 7% growth promotion. Spermidine inhibited both elongation and dry weight growth at all concentrations. Growth promotion by homobrassinolide, salicylic acid and spermine may be through an acceleration of processes connected to cell elongation, cell division and C allocation and these PGRs showed most promise for the early invigoration and improvement of jack pine seedling growth. Received: 27 August 1997 / Accepted: 8 January 1998     

Thermophilic fungi: An assessment of their potential for growth in soil

An attempt has been made to forecast the potential of thermophilic fungi to grow in soil in the laboratory and in the field in the presence of a predominantly mesophilic fungal flora at usual temperature. The respiratory rate of thermophilic fungi was markedly responsive to changes in temperature, but that of mesophilic fungi was relatively independent of such changes. This suggested that in a thermally fluctuating environment, thermophilic fungi may be at a physiological disadvantage compared to mesophilic fungi. In mixed cultures in soil plates, thermophilic fungi outgrew mesophilic fungi under a fluctuating temperature regime only when the amplitude of the fluctuating temperatures was small and approached their temperature optima for growth. An antibody probe was used to detect the activity of native or an introduced strain of a thermophilic fungus,Thermomyces lanuginosus, under field conditions. The results suggest that although widespread, thermophilic fungi are ordinarily not an active component of soil microflora. Their presence in soil most likely may be the result of the aerial dissemination of propagules from composting plant material.