Fish Reliance on Littoral–Benthic Resources and the Distribution of Primary Production in Lakes

Pelagic, littoral, and terrestrial resources can all play a role in supporting consumers in lakes. The role of benthic algal-derived food web pathways in lakes is perhaps the least understood because limnologists have historically focused on pelagic (open-water) production and processes. We compiled carbon stable isotope data from 546 fish populations (75 lakes), and used a two end-member mixing model to calculate littoral–benthic reliance for each fish species in each lake. Fish littoral–benthic reliance values were averaged by lake to assess overall fish species benthic reliance for each lake. Lake-specific mean littoral reliance (BR_L; fish species not weighted according to production or biomass) averaged 57% and was independent of lake morphological and limnological attributes. For these same lakes, water column nutrients, light, and morphometry data were used to estimate whole-lake benthic algal and phytoplankton primary production. On average, benthic algae comprised 36% of whole-lake primary production (BP_f = 0.36). BP_f and BR_L were weakly correlated: BR_L tends to be high even in large/deep lakes in which benthic algae is a minor contributor to whole-lake primary production. The high littoral–benthic contribution to individual fish species appears to reflect the high concentration of fish species diversity in the littoral zone. Our work cannot be extrapolated to whole-lake fish production. However, the result is consistent with other work indicating that most fish species inhabit the littoral zone, whereas relatively few exclusively inhabit the pelagic. Our results suggest that it takes less primary production to support a single fish species in the littoral zone than is required to support a species in the pelagic.     

An improved protein structure evaluation using a semi-empirically derived structure property

Background

In the backdrop of challenge to obtain a protein structure under the known limitations of both experimental and theoretical techniques, the need of a fast as well as accurate protein structure evaluation method still exists to substantially reduce a huge gap between number of known sequences and structures. Among currently practiced theoretical techniques, homology modelling backed by molecular dynamics based optimization appears to be the most popular one. However it suffers from contradictory indications of different validation parameters generated from a set of protein models which are predicted against a particular target protein. For example, in one model Ramachandran Score may be quite high making it acceptable, whereas, its potential energy may not be very low making it unacceptable and vice versa. Towards resolving this problem, the main objective of this study was fixed as to utilize a simple experimentally derived output, Surface Roughness Index of concerned protein of unknown structure as an intervening agent that could be obtained using ordinary microscopic images of heat denatured aggregates of the same protein.

Result

It was intriguing to observe that direct experimental knowledge of the concerned protein, however simple it may be, might give insight on acceptability of its particular structural model out of a confusion set of models generated from database driven comparative technique for structure prediction. The result obtained from a widely varying structural class of proteins indicated that speed of protein structure evaluation can be further enhanced without compromising with accuracy by recruiting simple experimental output.

Conclusion

In this work, a semi-empirical methodological approach was provided for improving protein structure evaluation. It showed that, once structure models of a protein were obtained through homology technique, the problem of selection of a best model out of a confusion set of Pareto-optimal structures could be resolved by employing a structure agent directly obtainable through experiment with the same protein as experimental ingredient. Overall, in the backdrop of getting a reasonably accurate protein structure of pathogens causing epidemics or biological warfare, such approach could be of use as a plausible solution for fast drug design.

     

Effective Skin Cancer Treatment by Topical Co-delivery of Curcumin and STAT3 siRNA Using Cationic Liposomes

The aim of the present study was to evaluate the effectiveness of iontophoretic co-delivery of curcumin and anti-STAT3 siRNA using cationic liposomes against skin cancer. Curcumin was encapsulated in DOTAP-based cationic liposomes and then complexed with STAT3 siRNA. This nanocomplex was characterized for the average particle size, zeta-potential, and encapsulation efficiency. The cell viability studies in B16F10 mouse melanoma cells have shown that the co-delivery of curcumin and STAT3 siRNA significantly (p < 0.05) inhibited the cancer cell growth compared with either liposomal curcumin or STAT3 siRNA alone. The curcumin-loaded liposomes were able to penetrate up to a depth of 160 μm inside the skin after iontophoretic (0.47 mA/cm²) application. The in vivo efficacy studies were performed in the mouse model of melanoma skin cancer. Co-administration of the curcumin and STAT3 siRNA using liposomes significantly (p < 0.05) inhibited the tumor progression as measured by tumor volume and tumor weight compared with either liposomal curcumin or STAT3 siRNA alone. Furthermore, the iontophoretic administration of curcumin-loaded liposome-siRNA complex showed similar effectiveness in inhibiting tumor progression and STAT3 protein suppression compared with intratumoral administration. Taken together, cationic liposomes can be utilized for topical iontophoretic co-delivery of small molecule and siRNA for effective treatment of skin diseases.     

A novel synthesis of 2-arylbenzimidazoles in molecular sieves-MeOH system and their antitubercular activity

Arylbenzimidazoles have been synthesized as antimycobacterial agents. An efficient synthesis has been developed for 2-arylbenzimidazoles from o-phenylenediamines and aromatic aldehydes in molecular sieves-methanol system. The methodology is straightforward to get 2-arylbenzimidazoles (3a–3z) in excellent yields with high chemoselectivity over 2-aryl-1-benzylbenzimidazoles (4a–4z). All these benzimidazole analogues were evaluated against M. tuberculosis in BACTEC radiometric assay. The compounds 4y and 4z exhibited potential antitubercular activity against M. tuberculosis H₃₇R_V, MIC at 16?µM and 24?µM respectively. The best compound of the series i.e. compound 4y was well tolerated by Swiss-albino mice in acute oral toxicity. Compound 4y possessing a diarylbenzimidazole core, can further be optimized for better activity.     

Carbon catabolite repression of the Aspergillus nidulans xlnA gene

Expression of the Aspergillus nidulans 22 kDa endoxylanase gene, xlnA , is controlled by at least three mechanisms: specific induction by xylan or xylose; carbon catabolite repression (CCR); and regulation by ambient pH. Deletion analysis of xlnA upstream sequences has identified two positively acting regions: one that mediates specific induction by xylose; and another that mediates the influence of ambient pH and contains two PacC consensus binding sites. The extreme derepressed mutation creA^d 30 results in considerable, although not total, loss of xlnA glucose repressibility, indicating a major role for CreA in its CCR. Three consensus CreA binding sites are present upstream of the structural gene. Point mutational analysis using reporter constructs has identified a single site, xlnA .C1, that is responsible for direct CreA repression in vivo . Using the creA^d 30 derepressed mutant background, our results indicate the existence of indirect repression by CreA.     

Fluorescent analogs of UDP-glucose and their use in characterizing substrate binding by toxin A from Clostridium difficile.

Uridine-5'-diphospho-1-alpha-d-glucose (UDP-Glc) is a common substrate used by glucosyltransferases, including certain bacterial toxins such as Toxins A and B from Clostridium difficile. Fluorescent analogs of UDP-Glc have been prepared for use in our studies of the clostridial toxins. These compounds are related to the methylanthraniloyl-ATP compounds commonly used to probe the chemistry of ATP-dependent enzymes. The reaction of excess methylisatoic anhydride with UDP-Glc in aqueous solution yields primarily the 2' and 3' isomers of methylanthraniloyl-UDP-Glc (MUG). As the 2' and 3' isomers readily interconvert, this isomeric mixture was copurified by HPLC away from the other isomeric products, and was characterized by a combination of NMR, fluorescence and mass spectrometric methods. TcdA binds MUG competitively with respect to UDP-Glc with an affinity of 15 +/- 2 microm in the absence of Mg2+. There is currently no evidence that the fluorescent substrate analog is turned over by the toxin in either glucosyltransferase or glucosylhydrolase reactions. Using a competition assay, the affinity of UDP-Glc was determined to be 45+/-10 microm in the absence of Mg2+. The binding of UDP-Glc and Mg2+ are highly coupled with Mg2+ affinities in the range of 90-600 microm, depending on the experimental conditions. These results imply that one of the significant roles of the metal ion might be to stabilize the enzyme-substrate complex prior to initiation of the transferase chemistry.     

Regulation of cell structure and function by actin-binding proteins: villin's perspective

Villin is a tissue-specific actin modifying protein that is associated with actin filaments in the microvilli and terminal web of epithelial cells. It belongs to a large family of actin-binding proteins which includes actin-capping, -nucleating and/or -severing proteins such as gelsolin, severin, fragmin, adseverin/scinderin and actin crosslinking proteins such as dematin and supervillin. Studies done in epithelial cell lines and villin knock-out mice have demonstrated the function of villin in regulating actin dynamics, cell morphology, epithelial-to-mesenchymal transition, cell migration and cell survival. In addition, the ligand-binding properties of villin (F-actin, G-actin, calcium, phospholipids and phospholipase C-gamma1) are mechanistically important for the crosstalk between signaling pathways and actin reorganization in epithelial cells.     

Mechanism of activation and inhibition of the HER4/ErbB4 kinase

HER4/ErbB4 is a ubiquitously expressed member of the EGF/ErbB family of receptor tyrosine kinases that is essential for normal development of the heart, nervous system, and mammary gland. We report here crystal structures of the ErbB4 kinase domain in active and lapatinib-inhibited forms. Active ErbB4 kinase adopts an asymmetric dimer conformation essentially identical to that observed to be important for activation of the EGF receptor/ErbB1 kinase. Mutagenesis studies of intact ErbB4 in Ba/F3 cells confirm the importance of this asymmetric dimer for activation of intact ErbB4. Lapatinib binds to an inactive form of the ErbB4 kinase in a mode equivalent to its interaction with the EGF receptor. All ErbB4 residues contacted by lapatinib are conserved in the EGF receptor and HER2/ErbB2, which lapatinib also targets. These results demonstrate that key elements of kinase activation and inhibition are conserved among ErbB family members.