Implications of a viscosity bound on black hole accretion

Motivated by the viscosity bound in gauge/gravity duality, we consider the ratio of shear viscosity (eta) to entropy density (s) in black hole accretion flows. We use both an ideal gas equation of state and the QCD equation of state obtained from lattice for the fluid accreting onto a Kerr black hole. The QCD equation of state is considered since the temperature of accreting matter is expected to approach 10(12) K in certain hot flows. We find that in both the cases eta/s is small only for primordial black holes and several orders of magnitude larger than any known fluid for stellar and supermassive black holes. We show that a lower bound on the mass of primordial black holes leads to a lower bound on eta/s and vice versa. Finally we speculate that the Shakura-Sunyaev viscosity parameter should decrease with increasing density and/or temperatures. (C) 2012 Elsevier B.V. All rights reserved.

On the Presumed Kinetic Consequences of Pre-equilibrium. Implications for the Michaelis-Menten Equation

The overall rate equation for a reaction sequence consisting of a pre-equilibrium and rate-determining steps should not be derived on the basis of the concentration of the intermediate product (X). This is apparently indicated by transition state theory (as the path followed to reach the highest energy transition state is irrelevant), but also proved by a straight-forward mathematical approach. The thesis is further supported by the equations of concurrent reactions as applied to the partitioning of X between the two competing routes (reversal of the pre-equilibrium and formation of product). The rate equation may only be derived rigorously on the basis of the law of mass action. It is proposed that the reactants acquire the overall activation energy prior to the pre-equilibrium, thus forming X in a high-energy state en route to the rate-determining transition state. (It is argued that conventional energy profile diagrams are misleading and need to be reinterpreted.) Also, these arguments invalidate the Michaelis-Menten equation of enzyme kinetics, and necessitate a fundamental revision of our present understanding of enzyme catalysis. (The observed ``saturation kinetics'' possibly arises from weak binding of a second molecule of substrate at the active site; analogous conclusions apply to reactions at surfaces).

Deforestation and forest degradation in India - implications for REDD+

Reducing emissions from deforestation and forest degradation (REDD+) is considered as an important mechanism under the UNFCCC aimed at mitigating climate change. The Cancun Agreement on REDD mechanism has paved the way for designing and implementation of REDD+ activities, to assist countries experiencing large-scale deforestation and forest degradation. Contrary to the general perception, the present analysis shows that India is currently experiencing deforestation and forest degradation. According to the latest assessment of the Forest Survey of India, the net annual loss of forests is estimated to be 99,850 ha during the period 2007-2009, even though the total area under forests has increased. The REDD+ mechanism aims to provide financial incentives for reducing deforestation and forest degradation. India, despite having robust legislations, policies and remote sensing capabilities, is not ready to benefit from the emerging REDD+ mechanism, with potential flow of large financial benefits to rural and forest-dependent communities from international financial sources.

Distinct mechanisms of DNA repair in mycobacteria and their implications in attenuation of the pathogen growth

About a third of the human population is estimated to be infected with Mycobacterium tuberculosis. Emergence of drug resistant strains and the protracted treatment strategies have compelled the scientific community to identify newer drug targets, and to develop newer vaccines. In the host macrophages, the bacterium survives within an environment rich in reactive nitrogen and oxygen species capable of damaging its genome. Therefore, for its successful persistence in the host, the pathogen must need robust DNA repair mechanisms. Analysis of M. tuberculosis genome sequence revealed that it lacks mismatch repair pathway suggesting a greater role for other DNA repair pathways such as the nucleotide excision repair, and base excision repair pathways. In this article, we summarize the outcome of research involving these two repair pathways in mycobacteria focusing primarily on our own efforts. Our findings, using Mycobacterium smegmatis model, suggest that deficiency of various DNA repair functions in single or in combinations severely compromises their DNA repair capacity and attenuates their growth under conditions typically encountered in macrophages. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

Simulated water resource impacts and livelihood implications of stakeholder-developed scenarios in the Jaldhaka Basin, India

This paper shows how multidisciplinary research can help policy makers develop policies for sustainable agricultural water management interventions by supporting a dialogue between government departments that are in charge of different aspects of agricultural development. In the Jaldhaka Basin in West Bengal, India, a stakeholder dialogue helped identify potential water resource impacts and livelihood implications of an agricultural water management rural electrification scenario. Hydrologic modelling demonstrated that the expansion of irrigation is possible with only a localized effect on groundwater levels, but cascading effects such as declining soil fertility and negative impacts from agrochemicals will need to be addressed.

Peraluminous sapphirine-cordierite pods in Mg-rich orthopyroxene granulite from southern India: Implications for lower crustal processes

Sapphirine-cordierite intergrowths occur as pods within garnet-absent, high-Mg orthopyroxene-granulite xenoliths in the Kambam valley, Madurai Block, southern India. Whereas the cores of the pods are composed of sapphirine (X-Mg = 0.871-0.897) - cordierite (X-Mg = 0.892-0.931) intergrowth along with rutile, zircon and monazite, the rims are characterized by cordierite, apatite, plagioclase, K-feldspar, quartz and minor calcite. The surrounding matrix comprises orthopyroxene (maximum Al2O3 4.1 wt.%, X-Mg 0.848-0.850), plagioclase, biotite and quartz, similar to the assemblage in the surrounding charnockites. Sapphirine in the Kambam rocks is characterized by high Al contents with an end-member composition in the range of 7:9:3 and 3:5:1. The occurrence of peraluminous sapphirine in association with cordierite and in the absence of phases such as sillimanite and garnet is distinct from ultrahigh-temperature assemblages in other localities within the Madurai Block. The peraluminous composition of the pods suggests that these domains could represent cryptic pathways through which aluminous melts migrated. The reaction of such peraluminous melts with Mg-rich orthopyroxene in the host granulite at temperatures of 1025 degrees C and pressures around 8 kbar as computed from phase equilibria modeling followed by an isobaric cooling is inferred to have generated the sapphirine-cordierite pods. The unusual high-Mg orthopyroxene granulite suggests interaction of supracrustal rocks with mafic magmas, which probably acted as the heat source for the partial melting of lower crust and UHT metamorphism.

A LOWER INITIAL ABUNDANCE OF SHORT-LIVED Ca-41 IN THE EARLY SOLAR SYSTEM AND ITS IMPLICATIONS FOR SOLAR SYSTEM FORMATION

The short-lived radionuclide Ca-41 plays an important role in constraining the immediate astrophysical environment and the formation timescale of the nascent solar system due to its extremely short half-life (0.1 Myr). Nearly 20 years ago, the initial ratio of Ca-41/Ca-40 in the solar system was determined to be (1.41 +/- 0.14) x 10(-8), primarily based on two Ca-Al-rich Inclusions (CAIs) from the CV chondrite Efremovka. With an advanced analytical technique for isotopic measurements, we reanalyzed the potassium isotopic compositions of the two Efremovka CAIs and inferred the initial ratios of Ca-41/Ca-40 to be (2.6 +/- 0.9) x 10(-9) and (1.4 +/- 0.6) x 10(-9) (2 sigma), a factor of 7-10 lower than the previously inferred value. Considering possible thermal processing that led to lower Al-26/Al-27 ratios in the two CAIs, we propose that the true solar system initial value of Ca-41/Ca-40 should have been similar to 4.2 x 10(-9). Synchronicity could have existed between Al-26 and Ca-41, indicating a uniform distribution of the two radionuclides at the time of CAI formation. The new initial Ca-41 abundance is 4-16 times lower than the calculated value for steady-state galactic nucleosynthesis. Therefore, Ca-41 could have originated as part of molecular cloud materials with a free decay time of 0.2-0.4 Myr. Alternative possibilities, such as a last-minute input from a stellar source and early solar system irradiation, could not be definitively ruled out. This underscores the need for more data from diverse CAIs to determine the true astrophysical origin of Ca-41.

Single-Molecule DNA Analysis Reveals That Yeast Hop1 Protein Promotes DNA Folding and Synapsis: Implications for Condensation of Meiotic Chromosomes

During meiosis, long-range interaction between homologous chromosomes is thought to be crucial for homology recognition, exchange of DNA strands, and production of normal haploid gametes. However, little is known about the identity of the proteins involved and the actual molecular mechanism(s) by which chromosomes recognize and recombine with their appropriate homologous partners. Single-molecule analyses have the potential to provide insights into our understanding of this fascinating and long-standing question. Using atomic force microscopy and magnetic tweezers techniques, we discovered that Hop1 protein, a key structural component of Saccharomyces cerevisiae synaptonemal complex, exhibits the ability to bridge noncontiguous DNA segments into intramolecular stem-loop structures in which the DNA segments appear to be fully synapsed within the filamentous protein stems. Additional evidence suggests that Hop1 folds DNA into rigid protein DNA filaments and higher-order nucleoprotein structures. Importantly, Hop1 promotes robust intra- and intermolecular synapsis between double-stranded DNA molecules, suggesting that juxtaposition of DNA sequences may assist in strand exchange between homologues by recombination-associated proteins. Finally, the evidence from ensemble experiments is consistent with the notion that Hop1 causes rigidification of DNA molecules. These results provide the first direct evidence for long-range protein-mediated DNA DNA synapsis, independent of crossover recombination, which is presumed to occur during meiotic recombination.

Oncogenic MicroRNA-155 Down-regulates Tumor Suppressor CDC73 and Promotes Oral Squamous Cell Carcinoma Cell Proliferation IMPLICATIONS FOR CANCER THERAPEUTICS

The CDC73 gene is mutationally inactivated in hereditary and sporadic parathyroid tumors. It negatively regulates beta-catenin, cyclin D1, and c-MYC. Down-regulation of CDC73 has been reported in breast, renal, and gastric carcinomas. However, the reports regarding the role of CDC73 in oral squamous cell carcinoma (OSCC) are lacking. In this study we show that CDC73 is down-regulated in a majority of OSCC samples. We further show that oncogenic microRNA-155 (miR-155) negatively regulates CDC73 expression. Our experiments show that the dramatic up-regulation of miR-155 is an exclusive mechanism for down-regulation of CDC73 in a panel of human cell lines and a subset of OSCC patient samples in the absence of loss of heterozygosity, mutations, and promoter methylation. Ectopic expression of miR-155 in HEK293 cells dramatically reduced CDC73 levels, enhanced cell viability, and decreased apoptosis. Conversely, the delivery of a miR-155 antagonist (antagomir-155) to KB cells overexpressing miR-155 resulted in increased CDC73 levels, decreased cell viability, increased apoptosis, and marked regression of xenografts in nude mice. Cotransfection of miR-155 with CDC73 in HEK293 cells abrogated its pro-oncogenic effect. Reduced cell proliferation and increased apoptosis of KB cells were dependent on the presence or absence of the 3'-UTR in CDC73. In summary, knockdown of CDC73 expression due to overexpression of miR-155 not only adds a novelty to the list of mechanisms responsible for its down-regulation in different tumors, but the restoration of CDC73 levels by the use of antagomir-155 may also have an important role in therapeutic intervention of cancers, including OSCC.

Intrinsically disordered proteins and conformational noise Implications in cancer

Intrinsically disordered proteins, IDPs, are proteins that lack a rigid 3D structure under physiological conditions, at least in vitro. Despite the lack of structure, IDPs play important roles in biological processes and transition from disorder to order upon binding to their targets. With multiple conformational states and rapid conformational dynamics, they engage in myriad and often ``promiscuous'' interactions. These stochastic interactions between IDPs and their partners, defined here as conformational noise, is an inherent characteristic of IDP interactions. The collective effect of conformational noise is an ensemble of protein network configurations, from which the most suitable can be explored in response to perturbations, conferring protein networks with remarkable flexibility and resilience. Moreover, the ubiquitous presence of IDPs as transcriptional factors and, more generally, as hubs in protein networks, is indicative of their role in propagation of transcriptional (genetic) noise. As effectors of transcriptional and conformational noise, IDPs rewire protein networks and unmask latent interactions in response to perturbations. Thus, noise-driven activation of latent pathways could underlie state-switching events such as cellular transformation in cancer. To test this hypothesis, we created a model of a protein network with the topological characteristics of a cancer protein network and tested its response to a perturbation in presence of IDP hubs and conformational noise. Because numerous IDPs are found to be epigenetic modifiers and chromatin remodelers, we hypothesize that they could further channel noise into stable, heritable genotypic changes.

Implications of program phase behavior on timing analysis

Knowledge about program worst case execution time (WCET) is essential in validating real-time systems and helps in effective scheduling. One popular approach used in industry is to measure execution time of program components on the target architecture and combine them using static analysis of the program. Measurements need to be taken in the least intrusive way in order to avoid affecting accuracy of estimated WCET. Several programs exhibit phase behavior, wherein program dynamic execution is observed to be composed of phases. Each phase being distinct from the other, exhibits homogeneous behavior with respect to cycles per instruction (CPI), data cache misses etc. In this paper, we show that phase behavior has important implications on timing analysis. We make use of the homogeneity of a phase to reduce instrumentation overhead at the same time ensuring that accuracy of WCET is not largely affected. We propose a model for estimating WCET using static worst case instruction counts of individual phases and a function of measured average CPI. We describe a WCET analyzer built on this model which targets two different architectures. The WCET analyzer is observed to give safe estimates for most benchmarks considered in this paper. The tightness of the WCET estimates are observed to be improved for most benchmarks compared to Chronos, a well known static WCET analyzer.

Chromosomal translocations among the healthy human population: implications in oncogenesis

Chromosomal translocations are characteristic features of many cancers, especially lymphoma and leukemia. However, recent reports suggest that many chromosomal translocations can be found in healthy individuals, although the significance of this observation is still not clear. In this review, we summarize recent studies on chromosomal translocations in healthy individuals carried out in different geographical areas of the world and discuss the relevance of the observation with respect to oncogenesis.

Cavitation in materials with distributed weak zones: Implications on the origin of brittle fracture in metallic glasses

Several experimental studies have shown that fracture surfaces in brittle metallic glasses (MGs) generally exhibit nanoscale corrugations which may be attributed to the nucleation and coalescence of nanovoids during crack propagation. Recent atomistic simulations suggest that this phenomenon is due to large spatial fluctuations in material properties in a brittle MG, which leads to void nucleation in regions of low atomic density and then catastrophic fracture through void coalescence. To explain this behavior, we propose a model of a heterogeneous solid containing a distribution of weak zones to represent a brittle MG. Plane strain continuum finite element analysis of cavitation in such an elastic-plastic solid is performed with the weak zones idealized as periodically distributed regions having lower yield strength than the background material. It is found that the presence of weak zones can significantly reduce the critical hydrostatic stress for the onset of cavitation which is controlled uniquely by the local yield properties of these zones. Also, the presence of weak zones diminishes the sensitivity of the cavitation stress to the volume fraction of a preexisting void. These results provide plausible explanations for the observations reported in recent atomistic simulations of brittle MGs. An analytical solution for a composite, incompressible elastic-plastic solid with a weak inner core is used to investigate the effect of volume fraction and yield strength of the core on the nature of cavitation bifurcation. It is shown that snap-cavitation may occur, giving rise to sudden formation of voids with finite size, which does not happen in a homogeneous plastic solid. (c) 2012 Elsevier Ltd. All rights reserved.

Chromite-silicate chemistry of the Neoarchean Sittampundi Complex, southern India: Implications for subduction-related arc magmatism

The Neoarchean layered anorthositic complex at Sittampundi in southern India is known for its chromitite layers that are mostly associated with anorthosite (An(90-100)). The chromitites contain FeAl-rich chromites concentrated in layers between amphibole-rich layers with a dominant mineralogy of amphibole-spinel-plagiocase+/-sapphirine. The chromite-rich layers contain only amphibole and plagioclase. Mineral compositions illustrated by X-ray composition maps and profiles show subtle chemical differences. The chrome spinels are of refractory grade with Cr2O3 and Al2O3 contents varying between 34-40 wt.% and 23-28 wt.%. The chromite compositions are noticeably different from those in layered igneous intrusions of the Bushveld-Stillwater type. The existence of original highly calcic plagioclase, FeAl-rich chromite, and magmatic amphibole is consistent with derivation from a parental magma of hydrous tholeiitic composition that was most likely generated in a supra-subduction zone arc setting. In terms of mineralogy and field relations, the Sittampundi chromitites are remarkably similar to anorthosite-hosted chromitites in the Neoarchean Fiskensset anorthositic complex, Greenland. We propose that the Sittampundi chromitites formed by partial melting of unusually aluminous harzburgite in a hydrated mantle wedge above a subduction zone. This melting process produced hydrous, aluminous basalt, which fractionated at depth to give rise to a variety of high-alumina basalt compositions from which the anorthositic complex with its cumulate chromite-rich and amphibole-rich layers formed within the magma chamber of a supra-subduction zone arc. (C) 2011 Elsevier B.V. All rights reserved.

Cytochrome P450-mediated metabolism in brain: functional roles and their implications

Introduction: Cytochromes P450 (P450) and associated monooxygenases are a family of heme proteins involved in metabolism of endogenous compounds (arachidonic acid, eicosanoids and prostaglandins) as also xenobiotics including drugs and environmental chemicals. Liver is the major organ involved in P450-mediated metabolism and hepatic enzymes have been characterized. Extrahepatic organs, such as lung, kidney and brain have the capability for biotransformation through P450 enzymes. Brain, including human brain, expresses P450 enzymes that metabolize xenobiotics and endogenous compounds. Areas covered: An overview of P450-mediated metabolism in brain is presented focusing on distinct differences seen in expression of P450 enzymes, generation of unique P450 enzymes in brain through alternate splicing and their consequences in terms of metabolism of psychoactive drugs and inflammatory prompts, such as leukotrienes, thus modulating inflammatory response. Expert opinion: The brain possesses unique P450s that metabolize drugs and endogenous compounds through pathways that are markedly different from that seen in liver indicating that extrapolation directly from liver to brain is not appropriate. It is therefore necessary to characterize the unique brain P450s and their ability to metabolize xenobiotics and endogenous compounds to better understand the functions of this important class of enzymes in brain, especially human brain.