Evolution of sequence specificity in a restriction endonuclease by a point mutation

Restriction endonucleases (REases) protect bacteria from invading foreign DNAs and are endowed with exquisite sequence specificity. REases have originated from the ancestral proteins and evolved new sequence specificities by genetic recombination, gene duplication, replication slippage, and transpositional events. They are also speculated to have evolved from nonspecific endonucleases, attaining a high degree of sequence specificity through point mutations. We describe here an example of generation of exquisitely site-specific REase from a highly-promiscuous one by a single point mutation.

Evolution of nanocrystalline BaBi2Nb2O9 in Li2B4O7 BaO-Bi(2)O3-Nb2O5 glass system

Transparent glasses and glass nano crystal composites (GNCs) of various compositions in the system (100 - x)Li2B4O7-x (BaO-Bi2O3-Nb2O5) (where x = 10, 20, and 30 in molar ratio) were fabricated via splat-quenching technique. The glassy nature of the as quenched samples was established by differential thermal analyses. X-ray powder diffraction and transmission electron microscopic (TEM) studies confirmed the formation of layered perovskite BBN via a fluorite like phase. TEM studies revealed the presence of 10 nm sized spherical crystallites of fluorite like BaBi2Nb2O9 phase in the glassy matrix of Li2B4O7 (LBO). The influence of composition on the dielectric and the optical properties (transmission, optical band gap) of these samples has been investigated. (c) 2007 Elsevier B.V. All rights reserved.

Evolution of isolated streamwise vortices in the late stages of boundary layer transition

Experiments were conducted with two, smooth hills, lying well within the boundary layer over a flat plate mounted in a wind tunnel. One hill was shallow, with peak height 1.5 mm and width 50 mm; the other, steep, 3 mm high and 30 mm wide. Since the hills occupied one-half of the tunnel span, streamwise vorticity formed near the hills' edge. At a freestream speed of 3.5 m/s, streaks formed with inflectional wall-normal and spanwise velocity profiles but without effecting transition. Transition, observed at 7.5 m/s, took different routes with the two hills. With the steep hill, streamwise velocity signals exhibited the passage of a wave packet which intensified before breakdown to turbulence. With the shallow hill there was a broad range of frequencies present immediately downstream of the hill. These fluctuations grew continuously and transition occurred within a shorter distance. Since the size of the streamwise vorticity generated at the hill edge is of the order of the hill height, the shallow hill generates vorticity closer to the wall and supports an earlier transition, whereas the steep hill creates a thicker vortex and associated streaks which exhibit oscillations due to their own instability as an additional precursor stage before transition.

Evolution of domain combinations in protein kinases and its implications for functional diversity

Protein kinases phosphorylating Ser/Thr/Tyr residues in several cellular proteins exert tight control over their biological functions. They constitute the largest protein family in most eukaryotic species. Protein kinases classified based on sequence similarity in their catalytic domains, cluster into subfamilies, which share gross functional properties. Many protein kinases are associated or tethered covalently to domains that serve as adapter or regulatory modules,naiding substrate recruitment, specificity, and also serve as scaffolds. Hence the modular organisation of the protein kinases serves as guidelines to their functional and molecular properties. Analysis of genomic repertoires of protein kinases in eukaryotes have revealed wide spectrum of domain organisation across various subfamilies of kinases. Occurrence of organism-specific novel domain combinations suggests functional diversity achieved by protein kinases in order to regulate variety of biological processes. In addition, domain architecture of protein kinases revealed existence of hybrid protein kinase subfamilies and their emerging roles in the signaling of eukaryotic organisms. In this review we discuss the repertoire of non-kinase domains tethered to multi-domain kinases in the metazoans. Similarities and differences in the domain architectures of protein kinases in these organisms indicate conserved and unique features that are critical to functional specialization. (C) 2009 Elsevier Ltd. All rights reserved.

Microstructural evolution during laser resolidification of Fe-25 atom percent Ge alloy

The microstructural evolution of concentrated alloys is relatively less understood both in terms of experiments as well as theory. Laser resolidification represents a powerful technique to study the solidification behavior under controlled growth conditions. This technique has been utilized in the current study to probe experimentally microstructural selection during rapid solidification of concentrated Fe-25 atom pct Ge alloy. Under the equilibrium solidification condition, the alloy undergoes a peritectic reaction between ordered alpha(2) (B2) and its liquid, leading to the formation of ordered hexagonal intermetallic phase epsilon (DO19). In general, the as-cast microstructure consists of epsilon phase and e-p eutectic and alpha(2) that forms as a result of an incomplete peritectic reaction. With increasing laser scanning velocity, the solidification front undergoes a number of morphological transitions leading to the selection of the microstructure corresponding to metastable alpha(2)/beta eutectic to alpha(2) dendrite + alpha(2)/beta eutectic to alpha(2) dendrite. The transition velocities as obtained from the experiments are well characterized. The microstructural selection is discussed using competitive growth kinetics.

Unraveling the packing pattern leading to gelation using SS NMR and X-ray diffraction: direct observation of the evolution of self-assembled fibers

A detailed understanding of the mode of packing patterns that leads to the gelation of low molecular mass gelators derived from bile acid esters was carried out using solid state NMR along with complementary techniques such as powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and polarizing optical microscopy (POM). Solid state C-13{H-1} cross polarization (CP) magic angle spinning (MAS) NMR of the low molecularmass gel in its native state was recorded for the first time. A close resemblance in the packing patterns of the gel, xerogel and bulk solid states was revealed upon comparing their C-13{H-1} CPMAS NMR spectral pattern. A doublet resonance pattern of C-13 signals in C-13{H-1}CPMAS NMR spectra were observed for the gelator molecules, whereas the non-gelators showed simple singlet resonance or resulted inthe formation of inclusion complexes/solvates. PXRD patterns revealed a close isomorphous nature of the gelators indicating the similarity in the mode of the packing pattern in their solid state. Direct imaging of the evolution of nanofibers (sol-gel transition) was carried out using POM, which proved the presence of self-assembled fibrillar networks (SAFINs) in the gel. Finally powder X-ray structure determination revealed the presence of two non-equivalent molecules in an asymmetric unit which is responsible for the doublet resonance pattern in the solid state NMR spectra.

Joseph A. Schumpeter's Theory of Social and Economic Evolution : a Reconstruction and Critique

The book presents a reconstruction, interpretation and critical evaluation of the Schumpeterian theoretical approach to socio-economic change. The analysis focuses on the problem of social evolution, on the interpretation of the innovation process and business cycles and, finally, on Schumpeter s optimistic neglect of ecological-environmental conditions as possible factors influencing social-economic change. The author investigates how the Schumpeterian approach describes the process of social and economic evolution, and how the logic of transformations is described, explained and understood in the Schumpeterian theory. The material of the study includes Schumpeter s works written after 1925, a related part of the commentary literature on these works, and a selected part of the related literature on the innovation process, technological transformations and the problem of long waves. Concerning the period after 1925, the Schumpeterian oeuvre is conceived and analysed as a more or less homogenous corpus of texts. The book is divided into 9 chapters. Chapters 1-2 describe the research problems and methods. Chapter 3 is an effort to provide a systematic reconstruction of Schumpeter's ideas concerning social and economic evolution. Chapters 4 and 5 focus their analysis on the innovation process. In Chapters 6 and 7 Schumpeter's theory of business cycles is examined. Chapter 8 evaluates Schumpeter's views concerning his relative neglect of ecological-environmental conditions as possible factors influencing social-economic change. Finally, chapter 9 draws the main conclusions.

The Palu Metamorphic Complex, NW Sulawesi, Indonesia: Origin and evolution of a young metamorphic terrane with links to Gondwana and Sundaland

The Palu Metamorphic Complex (PMC) is exposed in a late Cenozoic orogenic belt in NW Sulawesi, Indonesia. It is a composite terrane comprising a gneiss unit of Gondwana origin, a schist unit composed of meta-sediments deposited along the SE Sundaland margin in the Late Cretaceous and Early Tertiary, and one or more slivers of amphibolite with oceanic crust characteristics. The gneiss unit forms part of the West Sulawesi block underlying the northern and central sections of the Western Sulawesi Province. The presence of Late Triassic granitoids and recycled Proterozoic zircons in this unit combined with its isotopic signature suggests that the West Sulawesi block has its origin in the New Guinea margin from which it rifted in the late Mesozoic. It docked with Sundaland sometime during the Late Cretaceous. U–Th–Pb dating results for monazite suggest that another continental fragment may have collided with the Sundaland margin in the earliest Miocene. High-pressure (HP) and ultrahigh-pressure (UHP) rocks (granulite, peridotite, eclogite) are found as tectonic slices within the PMC, mostly along the Palu–Koro Fault Zone, a major strike-slip fault that cuts the complex. Mineralogical and textural features suggest that some of these rocks resided at depths of 60–120 km during a part of their histories. Thermochronological data (U–Th–Pb zircon and 40Ar/39Ar) from the metamorphic rocks indicate a latest Miocene to mid-Pliocene metamorphic event, which was accompanied by widespread granitoid magmatism and took place in an extensional tectonic setting. It caused recrystallization of, and new overgrowths on, pre-existing zircon crystals, and produced andalusite–cordierite–sillimanite–staurolite assemblages in pelitic protoliths, indicating HT–LP (Buchan-type) metamorphism. The PMC was exhumed as a core complex at moderate rates (c. 0.7–1.0 mm/yr) accompanied by rapid cooling in the Plio-Pleistocene. Some of the UHP rocks were transported to the surface at significantly higher rates (⩾16 mm/yr). The results of our study do not support recent plate tectonic reconstructions that propose a NW Australia margin origin for the West Sulawesi block (e.g. Hall et al., 2009).

Not in their genes: phenotypic flexibility, behavioural traditions and cultural evolution in wild bonnet macaques

Phenotypic flexibility, or the within-genotype, context-dependent, variation in behaviour expressed by single reproductively mature individuals during their lifetimes, often impart a selective advantage to organisms and profoundly influence their survival and reproduction. Another phenomenon apparently not under direct genetic control is behavioural inheritance whereby higher animals are able to acquire information from the behaviour of others by social learning, and, through their own modified behaviour, transmit such information between individuals and across generations. Behavioural information transfer of this nature thus represents another form of inheritance that operates in many animals in tandem with the more basic genetic system. This paper examines the impact that phenotypic flexibility, behavioural inheritance and socially transmitted cultural traditions may have in shaping the structure and dynamics of a primate society--that of the bonnet macaque (Macaca radiata), a primate species endemic to peninsular India. Three principal issues are considered: the role of phenotypic flexibility in shaping social behaviour, the occurrence of individual behavioural traits leading to the establishment of social traditions, and the appearance of cultural evolution amidst such social traditions. Although more prolonged observations are required, these initial findings suggest that phenotypic plasticity, behavioural inheritance and cultural traditions may be much more widespread among primates than have previously been assumed but may have escaped attention due to a preoccupation with genetic inheritance in zoological thinking.

GMRT observations of the group Holmberg 124: Evolution by tidal forces and ram pressure?

We report new radio continuum and 21 cm HI observations using the Giant Metrewave Radio Telescope (GMRT) of the group Holmberg 124 ( Ho 124) comprising four late-type galaxies, namely NGC 2820, Mrk 108, NGC 2814 and NGC 2805. The three galaxies, NGC 2820, Mrk 108 and NGC 2814 which are closely located in the sky plane have clearly undergone tidal interactions as seen from the various morphological tidal signatures and debris. Moreover we note various features in the group members which we believe might be due to ram pressure. In this paper, we describe four interesting results emerging from our observations: a) detection of the tidal radio continuum bridge at 330 MHz connecting the galaxies NGC 2820+ Mrk 108 with NGC 2814. The radio bridge was discovered at 1465 MHz by van der Hulst & Hummel ( 1985, A& A, 150, 17). We find that the bridge has a fairly steep spectrum with a spectral index alpha(S proportional to nu(alpha)) of - 1.8(-0.2)(+0.3) which is much steeper than the - 0.8 quoted by van der Hulst & Hummel ( 1985); b) detection of other tidal features like the tilted HI and radio continuum disk of NGC 2814, a HI streamer and a radio continuum tail arising from the south of NGC 2814. We also report the detection of a possible tidal dwarf galaxy in HI; c) sharp truncation in the HI distribution in the south of NGC 2820 and in the HI and radio continuum distribution in the north of NGC 2814. The optical disks in both the cases look undisturbed. As pointed out by Davis et al. ( 1997, AJ, 114, 613), ram pressure affects different components of the interstellar medium to varying degrees. Simple estimates of pressure in different components of the interstellar medium ( radio continuum, Ha and HI) in NGC 2820 indicate that ram pressure will significantly influence HI; d) detection of a large one-sided HI loop to the north of NGC 2820. No radio continuum emission or Ha emission is associated with the HI loop. We discuss various scenarios for the origin of this loop including a central starburst, ram pressure stripping and tidal interaction. We do not support the central starburst scenario since the loop is not detected in ionized gas. Using the upper limit on X-ray luminosity of Ho 124 (Mulchaey et al. 2003, ApJS, 145, 39), we estimate an upper limit on the intragroup medium (IGrM) density of 8.8 x 10(-4) cm(-3). For half this electron density, we estimate the ram pressure force of the IGrM to be comparable to the gravitational pull of the disk of NGC 2820. Since tidal interaction has obviously influenced the group, we suggest that the loop could have formed by ram pressure stripping if tidal effects had reduced the surface density of HI in NGC 2820. From the complex observational picture of Ho 124 and the numerical estimates, we suggest that the evolution of the Ho 124 group may be governed by both tidal forces due to the interaction and the ram pressure due to motion of the member galaxies in the IGrM and that the IGrM densities should not be too low (i.e. >= 4 x 10(-4)). However this needs to be verified by further observations.

Evolution of the Neckeraceae (Bryophyta): resolving the backbone phylogeny

Earlier phylogenetic studies, including species belonging to the Neckeraceae, have indicated that this pleurocarpous moss family shares a strongly supported sister group relationship with the Lembophyllaceae, but the family delimitation of the former needs adjustment. To test the monophyly of the Neckeraceae, as well as to redefine the family circumscription and to pinpoint its phylogenetic position in a larger context, a phylogenetic study based on molecular data was carried out. Sequence data were compiled, combining data from all three genomes: nuclear ITS1 and 2, plastid trnS-rps4-trnT-trnL-trnF and rpl16, and mitochondrial nad5 intron. The Neckeraceae have sometimes been divided into the two families, Neckeraceae and Thamnobryaceae, a division rejected here. Both parsimony and Bayesian analyses of molecular data revealed that the family concept of the Neckeraceae needs several further adjustments, such as the exclusion of some individual species and smaller genera as well as the inclusion of the Leptodontaceae. Within the family three well-supported clades (A, B and C) can be distinguished. Members of clade A are mainly non-Asiatic and nontropical. Most species have a weak costa and immersed capsules with reduced peristomes (mainly Neckera spp.) and the teeth at the leaf margins are usually unicellular. Clade B members are also mainly non-Asiatic. They are typically fairly robust, distinctly stipilate, having a single, at least relatively strong costa, long setae (capsules exserted), and the peristomes are well developed or only somewhat reduced. Members of clade C are essentially Asiatic and tropical. The species of this clade usually have a strong costa and a long seta, the seta often being mammillose in its upper part. The peristome types in this clade are mixed, since both reduced and unreduced types are found. Several neckeraceous genera that were recognised on a morphological basis are polyphyletic (e.g. Neckera, Homalia, Thamnobryum, Porotrichum). Ancestral state reconstructions revealed that currently used diagnostic traits, such as the leaf asymmetry and costa strength are highly homoplastic. Similarly, the reconstructions revealed that the 'reduced' sporophyte features have evolved independently in each of the three clades.

Evolution, Homology Conservation, and Identification of Unique Sequence Signatures in GH19 Family Chitinases

The discovery of GH (Glycoside Hydrolase) 19 chitinases in Streptomyces sp. raises the possibility of the presence of these proteins in other bacterial species, since they were initially thought to be confined to higher plants. The present study mainly concentrates on the phylogenetic distribution and homology conservation in GH19 family chitinases. Extensive database searches are performed to identify the presence of GH19 family chitinases in the three major super kingdoms of life. Multiple sequence alignment of all the identified GH19 chitinase family members resulted in the identification of globally conserved residues. We further identified conserved sequence motifs across the major sub groups within the family. Estimation of evolutionary distance between the various bacterial and plant chitinases are carried out to better understand the pattern of evolution. Our study also supports the horizontal gene transfer theory, which states that GH19 chitinase genes are transferred from higher plants to bacteria. Further, the present study sheds light on the phylogenetic distribution and identifies unique sequence signatures that define GH19 chitinase family of proteins. The identified motifs could be used as markers to delineate uncharacterized GH19 family chitinases. The estimation of evolutionary distance between chitinase identified in plants and bacteria shows that the flowering plants are more related to chitinase in actinobacteria than that of identified in purple bacteria. We propose a model to elucidate the natural history of GH19 family chitinases.

Crystallographic Evolution, Dielectric, and Piezoelectric Properties of Bi4Ti3O12:W/Cr Ceramics

W/Cr codoped Bi4Ti3O12 ceramics, Bi4Ti3-xWxO12+x+0.2 wt%Cr2O3 (BITWC, x=0-0.15), were prepared using a solid-state reaction method. The crystallographic evolution and phase analysis were distinctly determined focusing on the X-ray diffraction peak changes in (020)/(200) and (220)/(1115) diffraction planes, by which the lattice parameters, a, b, and c can be refined. The thermal variations of permittivity, dielectric loss (tan delta), impedance, and electrical conductivity properties were characterized. A decrease in the values of Curie temperature from 675 degrees to 640 degrees C and an increase in the values of the dielectric constant due to an increase of W6+/Cr3+ content were observed. The highest piezoelectric constant, d(33) of 22 pC/N, was achieved with the composition of Bi4Ti2.975W0.025O12.025+0.2 wt% Cr2O3. Also, this composition had a lower electrical conductivity than the other investigated compositions.

Microstructural Evolution during Laser Resolidification of Fe-18 At. Pct Ge Alloy

The technique of laser resolidification has been used to study the rapid solidification behavior of concentrated Fe-18 at. pct Ge alloy. The microstructural evolution has been studied as a function of scanning rate of laser beam. Scanning electron microscopy (SEM) reveals the formation of a two-layer (designated as "A" and "B") microstructure in the remelted pool. The A layer shows a band consisting of a network of interconnected channels and walls, quite similar to cell walls. The B layer shows dendritic growth. Transmission electron microscopic observations reveal the formation of bcc alpha-FeGe in the B layer. Laser melting has been found to play an important role in formation of the A layer. Microstructural evolution in B has been analyzed using the competitive growth criterion, and formation of bcc alpha-FeGe has been rationalized in the remelted layers.