Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes

The highly modular nature of protein kinases generates diverse functional roles mediated by evolutionary events such as domain recombination, insertion and deletion of domains. Usually domain architecture of a kinase is related to the subfamily to which the kinase catalytic domain belongs. However outlier kinases with unusual domain architectures serve in the expansion of the functional space of the protein kinase family. For example, Src kinases are made-up of SH2 and SH3 domains in addition to the kinase catalytic domain. A kinase which lacks these two domains but retains sequence characteristics within the kinase catalytic domain is an outlier that is likely to have modes of regulation different from classical src kinases. This study defines two types of outlier kinases: hybrids and rogues depending on the nature of domain recombination. Hybrid kinases are those where the catalytic kinase domain belongs to a kinase subfamily but the domain architecture is typical of another kinase subfamily. Rogue kinases are those with kinase catalytic domain characteristic of a kinase subfamily but the domain architecture is typical of neither that subfamily nor any other kinase subfamily. This report provides a consolidated set of such hybrid and rogue kinases gleaned from six eukaryotic genomes-S. cerevisiae, D. melanogaster, C. elegans, M. musculus, T. rubripes and H. sapiens-and discusses their functions. The presence of such kinases necessitates a revisiting of the classification scheme of the protein kinase family using full length sequences apart from classical classification using solely the sequences of kinase catalytic domains. The study of these kinases provides a good insight in engineering signalling pathways for a desired output. Lastly, identification of hybrids and rogues in pathogenic protozoa such as P. falciparum sheds light on possible strategies in host-pathogen interactions.

Si-mediated fabrication of reduced graphene oxide and its hybrids for electrode materials

Here, we demonstrate a Si-mediated environmentally friendly reduction of graphene oxide (GO) and the fabrication of its hybrids with multiwall carbon nanotubes and nanofibers. The reduction of GO is facilitated by nascent hydrogen generated by the reaction between Si and KOH at similar to 60 degrees C. The overall process takes 5 to 7 minutes and 10 to 15 mu m of Si is consumed each time. We show that Si can be used multiple times and the rGO based hybrids can be used for electrode materials.

First-principles study of the influence of different interfaces and core types on the properties of CdSe/CdS core-shell nanocrystals

With the expanding field of nanoengineering and the production of nanocrystals (NCs) with higher quality and tunable size, having reliable theoretical calculations to complement the experimental results is very important. Here we present such a study of CdSe/CdS core-shell NCs using density functional theory, where we focus on dependence of the properties of these NCs on core types and interfaces between the core and the shell, as well as on the core/shell ratio. We show that the density of states and the absorption indices depend rather weakly on the type of interface and core type. We demonstrate that the HOMO wavefunction is mainly localised in the core of the nanocrystal, depending primarily on the core/shell ratio. On the other hand the LUMO wavefunction spreads more into the shell of the nanocrystal, where its confinement in the core is almost the same in each of the studied structural models. Furthermore, we show that the radiative lifetimes decrease with increasing core sizes due to changes in the dipolar overlap integral of the HOMO and LUMO wavefunctions. In addition, the electron-hole Coulomb interaction energies follow a similar pattern as the localisation of the wavefunctions, with the smaller NCs having higher Coulomb interaction energies.

Rapid synthesis of hybrids and hollow PdO nanostructures by controlled in situ dissolution of a ZnO nanorod template: insights into the formation mechanism and thermal stability

Hollow nanomaterials have attracted a lot of interest by virtue of their wide range of applications that arise primarily due to their unique architecture. A common strategy to synthesize hollow nanomaterials is by nucleation of the shell material over a preformed core and subsequent dissolution of the core in the second step. Herein an ultrafast, microwave route has been demonstrated, to synthesize PdO nanotubes in a single step using ZnO as a sacrificial template. The mechanism of the nanotube formation has been investigated in detail using control experiments. By tuning the starting ratio of PdCl2 : ZnO, hollow to hybrid PdO nanostructures could be obtained using the same method. Conversion of the PdO to Pd nanotubes has been shown by simple NaBH4 treatment. The thermal stability of the PdO nanotubes has been studied. The insights presented here are general and applicable for the synthesis of hybrids/hollow structures in other systems as well.

Travellers' Types

This paper uses subjects’ self-reported justifications to explain discrepancies between observed heterogeneous behavior and the unique equilibrium prediction in a one-shot traveler’s dilemma experiment (TD). Principal components (PC) analysis suggests that iterative reasoning, aspiration levels, competitive behavior, attitudes towards risk and penalties and focal points may be behind different choices. Such reasons are coherent with same subjects’ behavior in other tests and experiments in which these particular issues are prominent. Overall, we identify types of subjects whose motivations are consistent across tasks.

Wetland Habitat Types of the Carmel River Lagoon.

This is a report delivered to California Department of Parks and Recreation. The purpose of this report is to document and describe the presence, location, and general characteristics for each of the wetland types currently found in the lagoon area. Comments are also made on the general use by different fauna. (Document contains 15 pages)

Assessing movements of three buoy line types using DSTmilli Loggers: Implications for entanglements of bottlenose dolphins in the crab pot fishery

A study was conducted in October 2006 in the Charleston, South Carolina area to test the movements of three different buoy line types to determine which produced a preferred profile that could reduce the risk of dolphin entanglement. Tests on diamond-braided nylon commonly used in the crab pot fishery were compared with stiffened line of Esterpro and calf types in both shallow and deep water environments using DSTmilli data loggers. Loggers were placed at intervals along the lines to record depth, and thus movements, over a 24 hour period. Three observers viewed video animations and charts created for each of the six trial days from the collected logger data and provided their opinions on the most desirable line type that fit set criteria. A quantitative analysis (ANCOVA) of the data was conducted taking into consideration daily tidal fluctuations and logger movements. Loggers tracking the tides had an r2 value approaching 1.00 and produced little movement other than with the tides. Conversely, r2 values approaching 0.00 were less affected by tidal movement and influenced by currents that cause more erratic movement. Results from this study showed that stiffened line, in particular the medium lay Esterpro type, produced the more desirable profiles that could reduce risk of dolphin entanglement. Combining the observer’s results with the ANCOVA results, Esterpro was chosen nearly 60% of the time as opposed to the nylon line which was only chosen 10% of the time. ANCOVA results showed that the stiffened lines performed better in both the shallow and deep water environments, while the nylon line only performed better during one trial in a deep water set, most probably due to the increased current velocities experienced that day. (58pp.)(PDF contains 68 pages)

Various types of canoe fishery in Ikot Abasi

Ikot Abasi, one of the six maritime local government areas in the Cross River State has a longstanding reputation as a fishing centre in Nigeria. Here various types of fishery are practiced. A description is given of 5 definitive areas, the criteria of which are either on the type of gear used, for example hook fishery or on the type of fish species landed e.g. Bonga. For a period of 12 months some detailed observations were registered on how they operate in 4 coastal fishing ports of Uta Ewa, Okoroeta, Iko and Kampa all on Atlantic coastline of Opobo

Nutrient digestibility and growth response of rainbow trout (Salmo gairdneri ) fed different carbohydrate types

Seven groups of fingerling rainbow trout (S. gairdneri ) were fed for 10 weeks on 0%, 10%, 20% and 30% of cassava or rice in isonitrogenous diets. Optimum growth and food utilization was at 20% dietary cassava. High fiber content of the control diet did not suppress protein digestibility in this group. Rather, at all levels, protein digestibility was good and remained between 84.4% and 90.1%. However, in the control group, carbohydrate digestibility was very poor. The cassava diets which had the highest digestible energy as carbohydrate produced the best growth performance, food utilization and protein sparing. At the levels studied, the dietary carbohydrates produced no hyperglycamic effect on the fish

Effects of different types of fertilizers on plankton productivity in earthen ponds

Three fertilizer types (NPK, Super-phosphate and cow dung) were applied at two levels (Low, 0.3 kg/25m super(2)/2weeks and High, 0.7kg/25 m super(2)/2weeks) to 12 ponds with two ponds serving as control. Each pond had an area of 25 m super(2). Application of fertilizers and monitoring of plankton productivity and water quality parameters continued fortnightly for 52 days. Results obtained were subjected to Statistical Variance Analysis. The abundance of phytoplankton was in the order: Chlorophyceae > Bacillariophyceae > Cyanophyceae > Desmideaceae. While that of zooplankton followed the order: Crustacean > Rotifer > Protozoan. Primary productivity showed a variation between treatments with lowest value of 5592 mg/O sub(2)/m super(3)/day obtained in the control and cow dung low application rates (1.5 kg/25 m super(2)/2weeks). The highest value for primary productivity was obtained at M sub(2) (0.7 kg/25 m super(2)/2weeks, N.P.K) with primary productivity value of 7200 mg/O sub(2)/m super(3)/day, closely followed by M sub(4) (0.7 kg/25 m super(2)/2weeks, super phosphate) with 6792 mg/O sub(2)/m super(3)/day.

Comparative growth and survival of fry of Clarias gariepinus (B), Clarias anguillaris (L), Heterobranchus bidorsalis (G), Heteroclarias, Clariabranchus and Clarias hybrids under outdoor nursery management system

Hybrids of Clariid catfishes; C. gariepinus (Netherlands), C. anguillaris, H. bidorsalis and their parental species were monitored for 8 weeks in 2 x 2 x 1m outdoor concrete tanks. The fry were fed NIFFR diet (40% crude protein) twice daily, 7 days of the week. Growth and survival records were taken weekly. The male HEB X female CLG hybrid showed an overall highest performance in growth rate while the lowest was recorded in male CLA X female CLG hybrid. The male HEB X female CLG hybrid grew at a faster rate than its reciprocal hybrid. In view or their growth rate, it is possible that the growth and survival rates or H. bidorsalis especially at the fry to fingerling stage could be improved through hybridization. The hybrid have potential as commercial food fish

Gene enrichment using antibodies to DNA/RNA hybrids : mapping the ribosomal DNA of slime mold and rat

A novel method for gene enrichment has been developed and applied to mapping the rRNA genes of two eucaryotic organisms. The method makes use of antibodies to DNA/RNA hybrids prepared by injecting rabbits with the synthetic hybrid poly(rA)•poly(dT). Antibodies which cross-react with non-hybrid nucleic acids were removed from the purified IgG fraction by adsorption on columns of DNA-Sepharose, oligo(dT)-cellulose, and poly(rA)-Sepharose. Subsequent purification of the specific DNA/RNA hybrid antibody was carried out on a column of oligo(dT)-cellulose to which poly(rA) was hybridized. Attachment of these antibodies to CNBr-activated Sepharose produced an affinity resin which specifically binds DNA/RNA hybrids.

In order to map the rDNA of the slime mold Dictyostelium discoideum, R-loops were formed using unsheared nuclear DNA and the 178 and 268 rRNAs of this organism. This mixture was passed through a column containing the affinity resin, and bound molecules containing R- loops were eluted by high salt. This purified rDN A was observed directly in the electron microscope. Evidence was obtained that there is a physical end to Dictyostelium rDN A molecules approximately 10 kilobase pairs (kbp) from the region which codes for the 268 rRNA. This finding is consistent with reports of other investigators that the rRNA genes exist as inverse repeats on extra-chromosomal molecules of DNA unattached to the remainder of the nuclear DNA in this organism.

The same general procedure was used to map the rRNA genes of the rat. Molecules of DNA which contained R-loops formed with the 188 and 288 rRNAs were enriched approximately 150- fold from total genomal rat DNA by two cycles of purification on the affinity column. Electron microscopic measurements of these molecules enabled the construction of an R-loop map of rat rDNA. Eleven of the observed molecules contained three or four R-loops or else two R-loops separated by a long spacer. These observations indicated that the rat rRNA genes are arranged as tandem repeats. The mean length of the repeating units was 37.2 kbp with a standard deviation of 1.3 kbp. These eleven molecules may represent repeating units of exactly the same length within the errors of the measurements, although a certain degree of length heterogeneity cannot be ruled out. If significantly shorter or longer repeating units exist, they are probably much less common than the 37.2 kbp unit.

The last section of the thesis describes the production of antibodies to non-histone chromosomal proteins which have been exposed to the ionic detergent sodium dodecyl sulfate (SDS). The presence of low concentrations of SDS did not seem to affect either production of antibodies or their general specificity. Also, a technique is described for the in situ immunofluorescent detection of protein antigens in polyacrylamide gels.