Spectral tuning and evolution of short wave-sensitive cone pigments in cottoid fish from Lake Baikal

The cottoid fishes of Lake Baikal in eastern Siberia provide a unique opportunity to study the evolution of visual pigments in a group of closely related species exposed to different photic environments. Members of this species flock are adapted to different depth habitats down to >1000 m, and both the rod and cone visual pigments display short wave shifts as depth increases. The blue-sensitive cone pigments of the SWS2 class cluster into two species groups with lambda(max) values of 450 and 430 nm, with the pigment in Cottus gobio, a cottoid fish native to Britain, forming a third group with a lambda(max) of 467 nm. The sequences of the SWS2 opsin gene from C. gobio and from two representatives of the 450 and 430 nm Baikal groups are presented. Approximately 6 nm of the spectral difference between C. gobio and the 450 nm Baikal group can be ascribed to the presence of a porphyropsin/rhodopin mixture in C. gobio. Subsequent analysis of amino acid substitutions by site-directed mutagenesis demonstrates that the remainder of the shift from 461 to 450 nm arises from a Thr269Ala substitution and the shift from 450 to 430 nm at least partly from Thr118Ala and Thr118Gly substitutions. The underlying adaptive significance of these substitutions in terms of spectral tuning and signal-to-noise ratio is discussed.     

Laboratory studies on the life cycle of Leydigia acanthocercoides Fisher (1854) (Cladocera: Chydoridae)

The biology of Leydigia acanthocercoides has been studied under laboratory conditions with reference to longevity, instar duration, growth, fecundity and embryonic development at a temperature range of 28–30 °C. It has three preadult and thirteen adult instars. Under the given laboratory conditions this species produces 20 eggs during a life span of 23 days. The number of eggs produced is uniformly constant in all adult instars. The growth rate seems to be exponential in the early phase of the life cycle as in other Cladocera. The general pattern of embryonic development of L. acanthocercoides is similar to those of other tropical cladocerans though differences in the duration of total developmental period have been recorded.Part of Ph.D. thesis.     

Prediction of MHC class II binding peptides based on an iterative learning model

Background

Prediction of the binding ability of antigen peptides to major histocompatibility complex (MHC) class II molecules is important in vaccine development. The variable length of each binding peptide complicates this prediction. Motivated by a text mining model designed for building a classifier from labeled and unlabeled examples, we have developed an iterative supervised learning model for the prediction of MHC class II binding peptides.

Results

A linear programming (LP) model was employed for the learning task at each iteration, since it is fast and can re-optimize the previous classifier when the training sets are altered. The performance of the new model has been evaluated with benchmark datasets. The outcome demonstrates that the model achieves an accuracy of prediction that is competitive compared to the advanced predictors (the Gibbs sampler and TEPITOPE). The average areas under the ROC curve obtained from one variant of our model are 0.753 and 0.715 for the original and homology reduced benchmark sets, respectively. The corresponding values are respectively 0.744 and 0.673 for the Gibbs sampler and 0.702 and 0.667 for TEPITOPE.

Conclusion

The iterative learning procedure appears to be effective in prediction of MHC class II binders. It offers an alternative approach to this important predictionproblem.     

Human umbilical cord tissue stem cells and neuronal lineages in an injectable caffeic acid–bioconjugated gelatin hydrogel for transplantation

Present-day scaffolds are useful in cell therapy to a reasonable extent, but in pursuit of improvising the scaffold to improve the outcome, we tested a new injectable caffeic acid–bioconjugated gelatin hydrogel scaffold (CBGH; with tunable stiffness −10%). Two-dimensional (2D) form of human umbilical cord tissue-derived mesenchymal stem cells (HUCMSCs) culture performed based on our previously reported methods and characterized by using multipotent and pluripotent analysis. In addition, neurogenesis was induced in the presence of retinoic acid or neural growth factor or epidermal growth factor categorized by neuronal markers. The viability, proliferation rate, and vascular endothelial growth factor expression of HUCMSCs increased significantly in the CBGH scaffold. In addition, there was an increase in CD90 and TRA-1-81 phenotypic expressions and SOX-2, MAP-2, TAU, NeuN, and NF, which confirmed the neurogenesis of encapsulated HUCMSCs. Topographical elucidation by scanning electron microscopy data showed that the HUCMSCs proliferated and migrated inside the construct. Hematoxylin and eosin staining demonstrated a more viable structural pattern and cresyl violet staining showed the Nissl synthesis, confirming the presence of functional neurons in the encapsulated form. The molecular-level analysis further substantiated that HUCMSCs cultured in CBGH expressed significantly greater upregulation of stemness, neuronal genes, and protein expression compared with the adherent culture. Correspondingly, this is the first time that we have measured the fluorescence intensity variation of the HUCMSCs-stained cell segmentation process using customized MATLAB code execution to reduce the background noise and autofluorescence. We conclude that this novel CBGH scaffold increases the viability, proliferation, stemness, and also neuronal transdifferentiation of HUCMSCs in a three-dimensional culture than the 2D plastic adherent culture.     

The biology of simocephalus acutirostratus king (Cladocera: Daphnidae)-hatchability of the parthenogenetic egg cultured in artificial media

The development of the parthenogenetic egg of the daphnid, Simocephalus acutirostratus was studied in different artificial media. The hatchability is found to be 100% in 0.001 M to 0.01 M of sodium chloride. 100% hatchability is noticed in concentrations ranging from 0.001 M to 0.05 M of calcium chloride. Apart from minor fluctuations, a high percentage of hatchability is recorded when isotonic solutions of sodium and calcium chloride are mixed. The hatchability of the different stages of the embryo is studied in an artificial medium which contains various proportions of sodium chloride, potassium chloride and calcium chloride. The results are discussed and compared with those from an allied temperate form, Simocephalus vetulus (O. F. Muller).     

Synthesis and antimycobacterial activity of 4-[5-(substituted phenyl)-4, 5-dihydro-3-isoxazolyl]-2-methylphenols

Compounds based on the isoxazoline moiety were screened for their antimycobacterial activity in vitro against Mycobacterium tuberculosis H37R (MTB), and INH (isoniazid) resistant Mycobacterium tuberculosis (INHR-MTB) using the agar dilution method and bactec 460. Among the synthesized compounds, 4-[5-(4-bromophenyl)-4,5-dihydro-3-isoxazolyl]-2-methylphenol (4l) was found to be the most active agent against MTB and INHR-MTB with minimum inhibitory concentration of 0.62 μM. When compared to INH, compound (4l) was 1.12 fold and 3.0 fold more active against MTB and INHR-MTB, respectively.