Structural and functional characteristics of homing endonucleases

Mobile genetic elements constitute a remarkably diverse group of nonessential selfish genes that provide no apparent function to the host. These selfish genes have been implicated in host extinction, speciation and architecture of genetic systems. Homing endonucleases, encoded by the open reading frames embedded in introns or inteins of mobile genetic elements, possess double-stranded DNA-specific endonuclease activity. They inflict sequence-specific double-strand breaks at or near the homing site in intron- or intein-less allele. Subsequently, through nonreciprocal exchange the insertion sequence (intron or intein) is transferred from an intein- or intron-containing allele to an intein- or intron-less allele. The components of host double-strand break repair pathway are thought to finish the "homing" process. Several lines of evidence suggest that homing endonucleases are capable of promoting transposition into ectopic sites within or across genomes for their survival as well as dispersal in natural populations. The occurrence of inteins at high frequencies serves as instructive models for understanding the mechanistic aspects of the process of homing and its evolution. This review focuses on genetic, biochemical, structural, and phylogenetic aspects of homing endonucleases, and their comparison with restriction endonucleases.

Enhanced adsorption capacity of activated alumina by impregnation with alum for removal of As(V) from water

Alum-impregnated activated alumina (AIAA) was investigated in the present work as an adsorbent for the removal of As(V) from water by batch mode. Adsorption study at different pH values shows that the efficiency of AIAA is much higher than as such activated alumina and is suitable for treatment of drinking water. The adsorption isotherm experiments indicated that the uptake of As(V) increased with increasing As(V) concentration from 1 to 25 mg/l and followed Langmuir-type adsorption isotherm. Speciation diagram shows that in the pH range of 2.8–11.5, arsenate predominantly exists as H2AsO4− and HAsO42− species and hence it is presumed that these are the major species being adsorbed on the surface of AIAA. Intraparticle diffusion and kinetic studies revealed that adsorption of As(V) was due to physical adsorption as well as through intraparticle diffusion. Effect of interfering ions revealed that As(V) sorption is strongly influenced by the presence of phosphate ion. The presence of arsenic on AIAA is depicted from zeta potential measurement, scanning electron microscopy (SEM) and energy-dispersive analysis of X-ray (EDAX) mapping study. Alum-impregnated activated alumina successfully removed As(V) to below 40 ppb (within the permissible limit set by WHO) from water, when the initial concentration of As(V) is 10 mg/l.

Karyotype instability in the ponerine ant genus Diacamma

The queenless ponerine ant Diacamma ceylonense and a population of Diacamma from the Nilgiri hills which we refer to as `nilgiri', exhibit interesting similarities as well as dissimilarities. Molecular phylogenetic study of these morphologically almost similar taxa has shown that D ceylonense is closely related to `nilgiri' and indicates that `nilgiri' is a recent diversion in the Diacamma phylogenetic tree. However, there is a striking behavioural difference in the way reproductive monopoly is maintained by the respective gamergates (mated egg laying workers), and there is evidence that they are genetically differentiated, suggesting a lack of gene flow To develop a better understanding of the mechanism involved in speciation of Diacamma, we have analysed karyotypes of D. ceylonense and `nilgiri' In both, we found surprising inter-individual and intra-individual karyotypic mosaicism. The observed numerical variability, both at intra-individual and inter-individual levels, does not appear to have hampered the sustainability of the chromosomal diversity in each population under study Since the related D. indicum, displays no such intra-individual or inter-Individual variability whatsoever under identical experimental conditions, these results are unlikely to he artifacts. Although no known mechanisms can account for the observed karyotypic variability of this nature, we believe that the present findings on the ants under study would provide opportunities for exciting new discoveries concerning the origin, maintenance and significance of intra-individual and inter-individual karyotypic mosaicism.

A Numerical-Simulation Of The Gneiss-Charnockite Transformations In Southern India

This paper presents a numerical simulation of the well-documented, fluid-controlled Kabbal and Ponmudi type gneiss-chamockite transformations in southern India using a free energy minimization method. The computations have considered all the major solid phases and important fluid species in the rock - C-O-H and rock - C-O-H-N systems. Appropriate activity-composition relations for the solid solutions and equations of state for the fluids have been included in order to evaluate the mineral-fluid equilibria attending the incipient chamockite development in the gneisses. The C-O-H fluid speciation pattern in both the Kabbal and Ponmudi type systems indicates that CO2 and H2O make up the bulk of the fluid phase with CO, CH4, H-2 and O2 as minor constituents. In the graphite-buffered Ponmudi-system, the abundance of CO, CH4 and H-2 is orders of magnitude higher than that in the graphite-free Kabbal system. Simulation with C-O-H-N fluids of varying composition demonstrates the complementary role of CO2 and N2 as rather inert dilutants of H2O in the fluid phase. The simulation, carried out on available whole-rock data, has demonstrated the dependence of the transformation X(H2O) on P,T, and phase and chemical composition of the precursor gneiss.

Mismatch repair genes of eukaryotes

Mismatches that arise during replication or genetic recombination or owing to damage to DNA by chemical agents are recognized by mismatch repair systems. The pathway has been characterized in detail in Escherichia coli. Several homologues of the genes encoding the proteins of this pathway have been identified in the yeast Saccharomyces cerevisiae and in human cells. Mutations in the human genes hMSH2, hMLH1, hPMS1 and hPMS2 have been linked to hereditary nonpolyposis colon cancer (HNPCC) and to some sporadic tumours. Mismatch repair also plays an antirecombinogenic role and is implicated in speciation.

Thermo-physical and structural studies of sodium zinc borovanadate glasses in the region of high concentration of modifier oxides

This paper reports investigation of Na2O and ZnO modified borovanadate glasses in the highly modified regime of compositions. These glasses have been prepared by microwave route. Ultraviolet (UV) and visible, infrared (IR), Magic Angle Spinning Nuclear Magnetic Resonance (MAS NMR) and Electron Paramagnetic Resonance (EPR) spectroscopies have been used to characterize the speciation in the glasses. Together with the variation of properties such as molar volume and glass transition temperatures, spectroscopic data indicate that at high levels of modification, ZnO tends to behave like network former. It is proposed that the observed variation of all the properties can be reasonably well understood with a structural model. The model considers that the modification and speciation in glasses are strongly determined by the hierarchy of group electronegativities. Further, it is proposed that the width of the transitions of glasses obtained under same condition reflects the fragility of the glasses. An empirical expression has been suggested to quantify fragility on the basis of width of the transition regions. (C) 2012 Elsevier Ltd. All rights reserved.

A phylogeny of the only ground-dwelling radiation of Cyrtodactylus (Squamata, Gekkonidae): diversification of Geckoella across peninsular India and Sri Lanka

The subgenus Geckoella, the only ground-dwelling radiation within Cyrtodactylus, closely overlaps in distribution with brookii group Hemidactylus in peninsular India and Sri Lanka. Both groups have Oligocene origins, the latter with over thrice as many described species. The striking difference in species richness led us to believe that Geckoella diversity is underestimated, and we sampled for Geckoella across peninsular India. A multi-locus phylogeny reveals Geckoella diversity is hugely underestimated, with at least seven undescribed species, doubling previously known richness. Strikingly, the new species correspond to cryptic lineages within described Indian species (complexes); a number of these endemic lineages from the hills of peninsular India outside the Western Ghats, highlighting the undocumented diversity of the Indian dry zone. The Geckoella phylogeny demonstrates deep splits between the Indian species and Sri Lankan G. triedrus, and between Indian dry and wet zone clades, dating back to the late Oligocene. Geckoella and brookii group Hemidactylus show contrasting diversification patterns. Geckoella shows signals of niche conservatism and appears to have retained its ancestral forest habitat. The late Miocene burst in speciation in Geckoella may be linked to the expansion of rain forests during the mid-Miocene climatic optimum and subsequent fragmentation with increasing late Miocene aridification. (C) 2014 Elsevier Inc. All rights reserved.