The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations

Background: Phosphorylation by protein kinases is central to cellular signal transduction. Abnormal functioning of kinases has been implicated in developmental disorders and malignancies. Their activity is regulated by second messengers and by the binding of associated domains, which are also influential in translocating the catalytic component to their substrate sites, in mediating interaction with other proteins and carrying out their biological roles. Results: Using sensitive profile-search methods and manual analysis, the human genome has been surveyed for protein kinases. A set of 448 sequences, which show significant similarity to protein kinases and contain the critical residues essential for kinase function, have been selected for an analysis of domain combinations after classifying the kinase domains into subfamilies. The unusual domain combinations in particular kinases suggest their involvement in ubiquitination pathways and alternative modes of regulation for mitogen-activated protein kinase kinases (MAPKKs) and cyclin-dependent kinase (CDK)-like kinases. Previously unexplored kinases have been implicated in osteoblast differentiation and embryonic development on the basis of homology with kinases of known functions from other organisms. Kinases potentially unique to vertebrates are involved in highly evolved processes such as apoptosis, protein translation and tyrosine kinase signaling. In addition to coevolution with the kinase domain, duplication and recruitment of non-catalytic domains is apparent in signaling domains such as the PH, DAG-PE, SH2 and SH3 domains. Conclusions: Expansion of the functional repertoire and possible existence of alternative modes of regulation of certain kinases is suggested by their uncommon domain combinations. Experimental verification of the predicted implications of these kinases could enhance our understanding of their biological roles.

Typical and atypical domain combinations in human protein kinases: functions, disease causing mutations and conservation in other primates

Ser/Thr and Tyr protein kinases orchestrate many signalling pathways and hence loss in this balance leads to many disease phenotypes. Due to their high abundance, diversity and importance, efforts have been made in the past to classify kinases and annotate their functions at both gross and fine levels. These kinases are conventionally classified into subfamilies based on the sequences of catalytic domains. Usually the domain architecture of a full-length kinase is consistent with the subfamily classification made based on the sequence of kinase domain. Important contributions of modular domains to the overall function of the kinase are well known. Recently occurrence of two kinds of outlier kinases-''Hybrid'' and ``Rogue'' has been reported. These show considerable deviations in their domain architectures from the typical domain architecture known for the classical kinase subfamilies. This article provides an overview of the different subfamilies of human kinases and the role of non-kinase domains in functions and diseases. Importantly this article provides analysis of hybrid and rogue kinases encoded in the human genome and highlights their conservation in closely related primate species. These kinases are examples of elegant rewiring to bring about subtle functional differences compared to canonical variants.

Analogous Synaptic Plasticity Profiles Emerge from Disparate Channel Combinations

An open question within the Bienenstock-Cooper-Munro theory for synaptic modification concerns the specific mechanism that is responsible for regulating the sliding modification threshold (SMT). In this conductance-based modeling study on hippocampal pyramidal neurons, we quantitatively assessed the impact of seven ion channels (R- and T-type calcium, fast sodium, delayed rectifier, A-type, and small-conductance calcium-activated (SK) potassium and HCN) and two receptors (AMPAR and NMDAR) on a calcium-dependent Bienenstock-Cooper-Munro-like plasticity rule. Our analysis with R- and T-type calcium channels revealed that differences in their activation-inactivation profiles resulted in differential impacts on how they altered the SMT. Further, we found that the impact of SK channels on the SMT critically depended on the voltage dependence and kinetics of the calcium sources with which they interacted. Next, we considered interactions among all the seven channels and the two receptors through global sensitivity analysis on 11 model parameters. We constructed 20,000 models through uniform randomization of these parameters and found 360 valid models based on experimental constraints on their plasticity profiles. Analyzing these 360 models, we found that similar plasticity profiles could emerge with several nonunique parametric combinations and that parameters exhibited weak pairwise correlations. Finally, we used seven sets of virtual knock-outs on these 360 models and found that the impact of different channels on the SMT was variable and differential. These results suggest that there are several nonunique routes to regulate the SMT, and call for a systematic analysis of the variability and state dependence of the mechanisms underlying metaplasticity during behavior and pathology.

Do carboximide-carboxylic acid combinations form co-crystals? The role of hydroxyl substitution on the formation of co-crystals and eutectics

Carboxylic acids, amides and imides are key organic systems which provide understanding of molecular recognition and binding phenomena important in biological and pharmaceutical settings. In this context, studies of their mutual interactions and compatibility through co-crystallization may pave the way for greater understanding and new applications of their combinations. Extensive co-crystallization studies are available for carboxylic acid/amide combinations, but only a few examples of carboxylic acid/imide co-crystals are currently observed in the literature. The non-formation of co-crystals for carboxylic acid/imide combinations has previously been rationalized, based on steric and computed stability factors. In the light of the growing awareness of eutectic mixtures as an alternative outcome in co-crystallization experiments, the nature of various benzoic acid/cyclic imide combinations is established in this paper. Since an additional functional group can provide sites for new intermolecular interactions and, potentially, promote supramolecular growth into a co-crystal, benzoic acids decorated with one or more hydroxyl groups have been systematically screened for co-crystallization with one unsaturated and two saturated cyclic imides. The facile formation of an abundant number of hydroxybenzoic acid/cyclic carboximide co-crystals is reported, including polymorphic and variable stoichiometry co-crystals. In the cases where co-crystals did not form, the combinations are shown invariably to result in eutectics. The presence or absence and geometric disposition of hydroxyl functionality on benzoic acid is thus found to drive the formation of co- crystals or eutectics for the studied carboxylic acid/imide combinations.

Investigation of the Mechanical Properties of Thin Films by Nanoindentation, Considering the Effects of Thickness and Different Coating-Substrate Combinations

In order to further investigate nanoindentation data of film-substrate systems and to learn more about the mechanical properties of nanometer film-substrate systems, two kinds of films on different substrate systems have been tested with a systematic variation in film thickness and substrate characteristics. The two kinds of films are aluminum and tungsten, which have been sputtered on to glass and silicon substrates, respectively. Indentation experiments were performed with a Nano Indent XP II with indenter displacements typically about two times the nominal film thicknesses. The resulting data are analyzed in terms of load-displacement curves and various comparative parameters, such as hardness, Young's modulus, unloading stiffness and elastic recovery. Hardness and Young's modulus are investigated when the substrate effects are considered. The results show how the composite hardness and Young's modulus are different for different substrates, different films and different film thicknesses. An assumption of constant Young's modulus is used for the film-substrate system, in which the film and substrate have similar Young's moduli. Composite hardness obtained by the Joslin and Oliver method is compared with the directly measured hardness obtained by the Oliver and Pharr method.

Propagation properties of off-axis Hermite-cosh-Gaussian beam combinations through a first-order optical system

Based on the Collins integral formula, the analytic expressions of propagation of the coherent and the incoherent off-axis Hermite-cosh-Gaussian (HChG) beam combinations with rectangular symmetry passing through a paraxial first-order optical system are derived, and corresponding numerical examples are given and analysed. The resulting beam quality is discussed in terms of power in the bucket (PIB). The study suggests that the resulting beam cannot keep the initial intensity shape during the propagation and the beam quality for coherent mode is not always better than that for incoherent mode. Reviewing the numerical simulations of Gaussian, Hermite-Gaussian (HG) and cosh Gaussian (ChG) beam combinations indicates that the Hermite polynomial exerts a chief influence on the irradiance profile of composite beam and far field power concentration.

Effect of dietary supplementation of tocoferol acetate alone and with varying combinations on growth, survival and fatty acids profile of Macrobrachium rosenbergii larvae through Moina micrura enrichment

A study was carried out to determine the effect of tocopherol acetate along with cod liver oil astaxanthin enriched Moina micrura (MC- control, Ml- tocopherol acetate enriched, M2-tocopherol acetate combined with cod liver oil (CLO) enriched and M3- tocopherol acetate combined with astaxanthin enriched) on growth, survival and fatty acid composition of M. rosenbergii (de Man) larvae (TC- unenriched Moina fed larvae, Tl- tocopherol acetate enriched Moina fed larvae, T2- tocopherol acetate + CLO enriched Moina fed larvae to T3 – tocopherol acetate+ astaxanthin enriched Moina fed larvae). Growth was expressed as the time taken in to the settlement of 95% post larvae. Maximum growth i.e., the lowest time taken to the 95% PL settlement (40 days) and the maximum survival percentage (61%) was observed in both T2 and T3 treatments fed with M2 and M3 Moina respectively. Minimum growth and survival was observed in unenriched Moina fed larvae (TC). In larval treatments T2, (larvae fed with (M2) vitamin E + CLO enriched Moina), showed a higher percentage of EPA, DHA and higher HUFA level than other treatments.

Survival, growth and production of Penaeus monodon and P. indicus at different density combinations with milkfish

Penaeus monodon and P. indicus juveniles were stocked and reared for about 3 months in earthen ponds at different density combinations with Chanos chanos. The presence of either Penaeus species at any density ratio did not affect significantly the C. chanos survival. Survival rates of the penaeids indicated that intraspecific and interspecific competition occurred and were reduced with the reduction in stocking rate. It is concluded that further studies on higher density ratios and feeding and economic consideration would be of help to the development of this kind of fishpond management system.

Supply of Astaxanthin and its combinations through live feed (Moina micrura) enrichment affects the growth, survival and fatty acid profile of Macrobrachium rosenbergii larvae

A study was carried out with three replicates to determine the effects of feeding Moina micrura enriched with astaxanthin alone (M1) or astaxanthin in combination with either vitamin E (M2), vitamin D (M3) or Cod Liver oil (M4) on the growth, survival and fatty acid composition of giant fresh water prawn Macrobrachium rosenbergii (de Man) larvae. Growth rate was expressed as the time taken to the settlement of 95% post larvae. Maximum growth, the lowest time taken to the 95% PL settlement (38.5±0.50 days), was observed in larvae fed with M3 Moina. The highest survival rate (66.0±1.00%) was observed in those fed with M4 Moina and the second highest survival (61.0±1.00%) and growth rates (40.0±0.00 days) were shown with M2 Moina. The minimum values for both growth (42.5±0.50 days) and survival (33.0±1.50%) were observed in the group fed un-enriched Moina. Results also showed that the survival of prawn larvae increased as the quantities of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) increased in the dietary Moina. The highest levels of EPA (5.57±0.21%), DHA (3.50±0.21%) and highest total Highly Unsaturated Fatty Acids (HUFA) (13.87±0.68%) were seen in the Moina fed on astaxanthin and Cod Liver Oil (CLO). The results of the study showed that the nutritive quality of Moina, with respect to important fatty acids, can be increased by enrichment and will influence the growth, survival and the fatty acid composition of fresh water prawn larvae fed on them.