Mycobacterium tuberculosis Rho Is an NTPase with Distinct Kinetic Properties and a Novel RNA-Binding Subdomain

Two mechanisms - factor independent and dependent termination - ensure the completion of RNA synthesis in eubacteria. Factor-dependent mechanism relies on the Rho protein to terminate transcription by interacting with RNA polymerase. Although well studied in Escherichia coli, the properties of the Rho homologs from most bacteria are not known. The rho gene is unusually large in genus Mycobacterium and other members of actinobacteria, having,150 additional residues towards the amino terminal end. We describe the distinct properties of Rho from Mycobacterium tuberculosis. It is an NTPase with a preference for purine nucleoside triphosphates with kinetic properties different from E. coli homolog and an ability to use various RNA substrates. The N-terminal subdomain of MtbRho can bind to RNA by itself, and appears to contribute to the interaction of the termination factor with RNAs. Furthermore, the interaction with RNA induces changes in conformation and oligomerization of MtbRho.

In a hot bubble: why does superbubble feedback work, but isolated supernovae do not?

Using idealized one-dimensional Eulerian hydrodynamic simulations, we contrast the behaviour of isolated supernovae with the superbubbles driven by multiple, collocated supernovae. Continuous energy injection via successive supernovae exploding within the hot/dilute bubble maintains a strong termination shock. This strong shock keeps the superbubble over-pressured and drives the outer shock well after it becomes radiative. Isolated supernovae, in contrast, with no further energy injection, become radiative quite early (less than or similar to 0.1Myr, tens of pc), and stall at scales less than or similar to 100 pc. We show that isolated supernovae lose almost all of their mechanical energy by 1 Myr, but superbubbles can retain up to similar to 40 per cent of the input energy in the form of mechanical energy over the lifetime of the star cluster (a few tens of Myr). These conclusions hold even in the presence of realistic magnetic fields and thermal conduction. We also compare various methods for implementing supernova feedback in numerical simulations. For various feedback prescriptions, we derive the spatial scale below which the energy needs to be deposited in order for it to couple to the interstellar medium. We show that a steady thermal wind within the superbubble appears only for a large number (greater than or similar to 10(4)) of supernovae. For smaller clusters, we expect multiple internal shocks instead of a smooth, dense thermalized wind.

Sequence and conformational preferences at termini of alpha-helices in membrane proteins: Role of the helix environment

-helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These -helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze -helices in a high-resolution dataset of integral -helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. Proteins 2014; 82:3420-3436. (c) 2014 Wiley Periodicals, Inc.

Vaccination for pregnant women: Need to address

Pregnancy is a critically important state for any women in her life time. Administration of a vaccine to a pregnant woman is not a routine event and it is generally preferred to administer vaccines either prior to conception or in the postpartum period. Currently vaccination with inactivated vaccines are recommended due to potential risk to mother and fetus with live vaccines. Multiple factors determine the administration of the vaccines for example age, life style, medical conditions (e.g., asthma, diabetes etc.), type and location of travel and status of previous vaccination. If pregnant woman is exposed to these vaccines or if pregnancy occurs soon after vaccination, the women should be counselled regarding the risks to the fetus and vaccination should not be a reason to consider termination of pregnancy. Further research in vaccination among pregnancy is warranted for the safety of the pregnant women and their newborn for a healthy living and better life.

Seismotectonics of the April-May 2015 Nepal earthquakes: An assessment based on the aftershock patterns, surface effects and deformational characteristics

Occurrence of the April 25, 2015 (Mw 7.8) earthquake near Gorkha, central Nepal, and another one that followed on May 12 (Mw 7.3), located similar to 140 km to its east, provides an exceptional opportunity to understand some new facets of Himalayan earthquakes. Here we attempt to assess the seismotectonics of these earthquakes based on the deformational field generated by these events, along with the spatial and temporal characteristics of their aftershocks. When integrated with some of the post-earthquake field observations, including the localization of damage and surface deformation, it became obvious that although the mainshock slip was mostly limited to the Main Himalayan Thrust (MHT), the rupture did not propagate to the Main Frontal Thrust (MFT). Field evidence, supported by the available InSAR imagery of the deformation field, suggests that a component of slip could have emerged through a previously identified out-of-sequence thrust/active thrust in the region that parallels the Main Central Thrust (MCT), known in the literature as a co-linear physiographic transitional zone called PT2. Termination of the first rupture, triggering of the second large earthquake, and distribution of aftershocks are also spatially constrained by the eastern extremity of PT2. Mechanism of the 2015 sequence demonstrates that the out-of-sequence thrusts may accommodate part of the slip, an aspect that needs to be considered in the current understanding of the mechanism of earthquakes originating on the MHT. (c) 2015 Elsevier Ltd. All rights reserved.

Role of upward leaders in modifying the induced currents in solitary down-conductors during a nearby lightning strike to ground

Electromagnetic field produced by a lightning strike to ground causes significant induction to tall objects in the vicinity. The frequency of occurrence of such nearby ground strikes can be higher than the number of direct strikes. Therefore, a complete knowledge on these induced currents is of practical relevance. However, limited efforts towards the characterisation of such induced currents in tall down-conductors could be seen in the literature. Due to the intensification of the background field caused by the descending stepped leader, tall towers/down-conductors can launch upward leaders of significant length. The nonlinearity in the conductance of upward leader and the surrounding corona sheath can alter the characteristics of the induced currents. Preliminary aspects of this phenomenon have been studied by the author previously and the present work aims to perform a detailed investigation on the role of upward leaders in modifying the characteristics of the induced currents. A consistent model for the upward leader, which covers all the essential electrical aspects of the phenomena, is employed. A first order arc model for representing the conductance of upward leader and a field dependant quadratic conductivity model for the corona sheath is employed. The initial gradient in the upward leader and the field produced by the return stroke forms the excitation. The dynamic electromagnetic response is determined by solving the wave equation using thin-wire time-domain formulation. Simulations are carried out initially to ascertain the role of individual parameters, including the length of the upward leader. Based on the simulation results, it is shown that the upward leader enhances the induced current, and when significant in length, can alter the waveshape of induced current from bipolar oscillatory to unipolar. The duration of the induced current is governed by the length of upward leader, which in turn is dependant on the return stroke current and the effective length of the down-conductor. If the current during the upward leader developmental phase is considered along with that after the stroke termination to ground, it would present a bipolar current pulse. (C) 2015 Elsevier Ltd. All rights reserved.

Stalagmite growth perturbations from the Kumaun Himalaya as potential earthquake recorders

The central part of the Himalaya (Kumaun and Garhwal Provinces of India) is noted for its prolonged seismic quiescence, and therefore, developing a longer-term time series of past earthquakes to understand their recurrence pattern in this segment assumes importance. In addition to direct observations of offsets in stratigraphic exposures or other proxies like paleoliquefaction, deformation preserved within stalagmites (speleothems) in karst system can be analyzed to obtain continuous millennial scale time series of earthquakes. The Central Indian Himalaya hosts natural caves between major active thrusts forming potential storehouses for paleoseismological records. Here, we present results from the limestone caves in the Kumaun Himalaya and discuss the implications of growth perturbations identified in the stalagmites as possible earthquake recorders. This article focuses on three stalagmites from the Dharamjali Cave located in the eastern Kumaun Himalaya, although two other caves, one of them located in the foothills, were also examined for their suitability. The growth anomalies in stalagmites include abrupt tilting or rotation of growth axes, growth termination, and breakage followed by regrowth. The U-Th age data from three specimens allow us to constrain the intervals of growth anomalies, and these were dated at 4273 +/- 410 years BP (2673-1853 BC), 2782 +/- 79 years BP (851-693 BC), 2498 +/- 117 years BP (605-371 BC), 1503 +/- 245 years BP (262-752 AD), 1346 +/- 101 years BP (563-765 AD), and 687 +/- 147 years BP (1176-1470 AD). The dates may correspond to the timings of major/great earthquakes in the region and the youngest event (1176-1470 AD) shows chronological correspondence with either one of the great medieval earthquakes (1050-1250 and 1259-1433 AD) evident from trench excavations across the Himalayan Frontal Thrust.

Formation, Thermal Stability and Deformation Behavior of Graphite-Flakes Reinforced Cu-based Bulk Metallic Glass Matrix Composites

Graphite-flake reinforced Cu47Ti34Zr11 Ni-8 bulk metallic glass matrix composite was fabricated by water-cooled copper mould cast. Most of the graphite flakes still keep unreacted and distribute uniformly in the amorphous matrix except that some reactive wetting occurs by the formation of TiC particles around the flakes. It reveals that the presence of graphite flakes does not affect the onset of the glass transition temperature, crystallization reaction and liquidus of the metallic glass. The resulting material shows obvious serrated flow and higher fracture strength under room temperature compressive load, comparing with the monolithic bulk metallic glass (BMG). Three types of interaction between the shear bands and graphite flakes, namely, shear band termination, shear bands branching and new shear bands formation near the graphite flakes can be observed by quasi-static uniaxial compression test and bonded interface technique through Vickers indentation.

Flow properties of a dusty-gas point source in a supersonic free stream

By using Lagrangian method, the flow properties of a dusty-gas point source in a supersonic free stream were studied and the particle parameters in the near-symmetry-axis region were obtained. It is demonstrated that fairly inertial particles travel along oscillating and intersecting trajectories between the bow and termination shock waves. In this region,formation of "multi-layer structure" in particle distribution with alternating low- and highdensity layers is revealed. Moreover, sharp accumulation of particles occurs near the envelopes of particle trajectories.

The influence of stacks on flow patterns and stratification associated with natural ventilation

We investigate the steady state natural ventilation of an enclosed space in which vent A, located at height hA above the floor, is connected to a vertical stack with a termination at height H, while the second vent, B, at height hB above the floor, connects directly to the exterior. We first examine the flow regimes which develop with a distributed source of heating at the base of the space. If hBhB>hA, then two different flow regimes may develop. Either (i) there is inflow through vent B and outflow through vent A, or (ii) the flow reverses, with inflow down the stack into vent A and outflow through vent B. With inflow through vent A, the internal temperature and ventilation rate depend on the relative height of the two vents, A and B, while with inflow through vent B, they depend on the height of vent B relative to the height of the termination of the stack H. With a point source of heating, a similar transition occurs, with a unique flow regime when vent B is lower than vent A, and two possible regimes with vent B higher than vent A. In general, with a point source of buoyancy, each steady state is characterised by a two-layer density stratification. Depending on the relative heights of the two vents, in the case of outflow through vent A connected to the stack, the interface between these layers may lie above, at the same level as or below vent A, leading to discharge of either pure upper layer, a mixture of upper and lower layer, or pure lower layer fluid. In the case of inflow through vent A connected to the stack, the interface always lies below the outflow vent B. Also, in this case, if the inflow vent A lies above the interface, then the lower layer becomes of intermediate density between the upper layer and the external fluid, whereas if the interface lies above the inflow vent A, then the lower layer is composed purely of external fluid. We develop expressions to predict the transitions between these flow regimes, in terms of the heights and areas of the two vents and the stack, and we successfully test these with new laboratory experiments. We conclude with a discussion of the implications of our results for real buildings.

Supersonic dusty-gas flows with Knudsen effect in interphase momentum exchange

On the basis of the two-continuum model of dilute gas-solid suspensions, the dynamic behavior of inertial particles in supersonic dusty-gas flows past a blunt body is studied for moderate Reynolds numbers, when the Knudsen effect in the interphase momentum exchange is significant. The limits of the inertial particle deposition regime in the space of governing parameters are found numerically under the assumption of the slip and free-molecule flow regimes around particles. As a model problem, the flow structure is obtained for a supersonic dusty-gas point-source flow colliding with a hypersonic flow of pure gas. The calculations performed using the full Lagrangian approach for the near-symmetry-axis region and the free-molecular flow regime around the particles reveal a multi-layer structure of the dispersed-phase density with a sharp accumulation of the particles in some thin regions between the bow and termination shock waves.

Inhomogeneous isoparametric elements for stress analysis of composites

The concept of inhomogeneous element is proposed and the formulations of the inhomogeneous isoparametric elements for stress analysis of four kinds of problems are derived. As an example of applications of the inhomogeneous elements, the stress distribution in a cone-like composite syntheticrope termination is calculated.

Internationales Otolithen-Symposium in Australien

The Third International Symposium on Fish Otolith Research and Application in Townsville, Australia, from 11 to 16 July 2004, gathered around 300 scientists from 30 nations (http://www.otolith2004.com). Mayor topics were: structure of otoliths and function; micro-Chemitry and composition; determination of age and growth and their validation; de-termination of age in fish from tropical habitats; influence of climate, ecology and population biology; statistik and modelling; stock assessment and fishery management; quality control in institutions carrying out age determinations, and data processing; and development of technologies. The symposium was preceeded by a workshop at the James Cook University, Townsville, to enhance the knowledge and skill of participants in theoretrical and practical aspects for prearation of otoliths and interpretation of annuli; difficulties in interpreting age in tropical fish; daily increments as well as shape and image analysis.

Measurement of the band bending and surface dipole at chemically functionalized Si(111)/vacuum interfaces

The core-level energy shifts observed using X-ray photoelectron spectroscopy (XPS) have been used to determine the band bending at Si(111) surfaces terminated with Si-Br, Si-H, and Si-CH₃ groups, respectively. The surface termination influenced the band bending, with the Si 2p_3/2 binding energy affected more by the surface chemistry than by the dopant type. The highest binding energies were measured on Si(111)-Br (whose Fermi level was positioned near the conduction band at the surface), followed by Si(111)-H, followed by Si(111)-CH₃ (whose Fermi level was positioned near mid-gap at the surface). Si(111)-CH₃ surfaces exposed to Br₂(g) yielded the lowest binding energies, with the Fermi level positioned between mid-gap and the valence band. The Fermi level position of Br₂(g)-exposed Si(111)-CH₃ was consistent with the presence of negatively charged bromine-containing ions on such surfaces. The binding energies of all of the species detected on the surface (C, O, Br) shifted with the band bending, illustrating the importance of isolating the effects of band bending when measuring chemical shifts on semiconductor surfaces. The influence of band bending was confirmed by surface photovoltage (SPV) measurements, which showed that the core levels shifted toward their flat-band values upon illumination. Where applicable, the contribution from the X-ray source to the SPV was isolated and quantified. Work functions were measured by ultraviolet photoelectron spectroscopy (UPS), allowing for calculation of the sign and magnitude of the surface dipole in such systems. The values of the surface dipoles were in good agreement with previous measurements as well as with electronegativity considerations. The binding energies of the adventitious carbon signals were affected by band bending as well as by the surface dipole. A model of band bending in which charged surface states are located exterior to the surface dipole is consistent with the XPS and UPS behavior of the chemically functionalized Si(111) surfaces investigated herein.

Functional genomic studies of the structure and regulation of eukaryotic transcriptomes

The main focus of this thesis is the use of high-throughput sequencing technologies in functional genomics (in particular in the form of ChIP-seq, chromatin immunoprecipitation coupled with sequencing, and RNA-seq) and the study of the structure and regulation of transcriptomes. Some parts of it are of a more methodological nature while others describe the application of these functional genomic tools to address various biological problems. A significant part of the research presented here was conducted as part of the ENCODE (ENCyclopedia Of DNA Elements) Project.

The first part of the thesis focuses on the structure and diversity of the human transcriptome. Chapter 1 contains an analysis of the diversity of the human polyadenylated transcriptome based on RNA-seq data generated for the ENCODE Project. Chapter 2 presents a simulation-based examination of the performance of some of the most popular computational tools used to assemble and quantify transcriptomes. Chapter 3 includes a study of variation in gene expression, alternative splicing and allelic expression bias on the single-cell level and on a genome-wide scale in human lymphoblastoid cells; it also brings forward a number of critical to the practice of single-cell RNA-seq measurements methodological considerations.

The second part presents several studies applying functional genomic tools to the study of the regulatory biology of organellar genomes, primarily in mammals but also in plants. Chapter 5 contains an analysis of the occupancy of the human mitochondrial genome by TFAM, an important structural and regulatory protein in mitochondria, using ChIP-seq. In Chapter 6, the mitochondrial DNA occupancy of the TFB2M transcriptional regulator, the MTERF termination factor, and the mitochondrial RNA and DNA polymerases is characterized. Chapter 7 consists of an investigation into the curious phenomenon of the physical association of nuclear transcription factors with mitochondrial DNA, based on the diverse collections of transcription factor ChIP-seq datasets generated by the ENCODE, mouseENCODE and modENCODE consortia. In Chapter 8 this line of research is further extended to existing publicly available ChIP-seq datasets in plants and their mitochondrial and plastid genomes.

The third part is dedicated to the analytical and experimental practice of ChIP-seq. As part of the ENCODE Project, a set of metrics for assessing the quality of ChIP-seq experiments was developed, and the results of this activity are presented in Chapter 9. These metrics were later used to carry out a global analysis of ChIP-seq quality in the published literature (Chapter 10). In Chapter 11, the development and initial application of an automated robotic ChIP-seq (in which these metrics also played a major role) is presented.

The fourth part presents the results of some additional projects the author has been involved in, including the study of the role of the Piwi protein in the transcriptional regulation of transposon expression in Drosophila (Chapter 12), and the use of single-cell RNA-seq to characterize the heterogeneity of gene expression during cellular reprogramming (Chapter 13).

The last part of the thesis provides a review of the results of the ENCODE Project and the interpretation of the complexity of the biochemical activity exhibited by mammalian genomes that they have revealed (Chapters 15 and 16), an overview of the expected in the near future technical developments and their impact on the field of functional genomics (Chapter 14), and a discussion of some so far insufficiently explored research areas, the future study of which will, in the opinion of the author, provide deep insights into many fundamental but not yet completely answered questions about the transcriptional biology of eukaryotes and its regulation.