Topological properties of the one dimensional exponential random geometric graph

In this article we study the one-dimensional random geometric (random interval) graph when the location of the nodes are independent and exponentially distributed. We derive exact results and limit theorems for the connectivity and other properties associated with this random graph. We show that the asymptotic properties of a graph with a truncated exponential distribution can be obtained using the exponential random geometric graph. © 2007 Wiley Periodicals, Inc. Random Struct. Alg., 2008.

Importance of the amino terminus in maintenance of oligomeric structure of sheep liver cytosolic serine hydroxymethyltransferase

The Role Of The Amino And Carboxyl-Terminal Regions Of Cytosolic Serine Hydroxymethyltransferase (SHMT) In Subunit Assembly And Catalysis Was Studied Using Sis Amino-Terminal (Lacking The First 6, 14, 30, 49, 58, And 75 Residues) And Two Carboxyl-Terminal (Lacking The Last 49 And 185 Residues) Deletion Mutants. These Mutants Were Constructed From A Full Length Cdna Clone Using Restriction Enzyme/PCR-Based Methods And Overexpressed In Escherichia Coli. The Overexpressed Proteins, Des-(A1-K6) SHMT And Des-(A1-W14)-SHMT Were Present In The Soluble Fraction And They Were Purified To Homogeneity. The Deletion Clones, For Des-(A1-V30)-SHMT And Des-(A1-L49)-SHMT Were Expressed At Very Low Levels, Whereas Des-(A1-R58)-SHMT, Des-/A1-G75)-SHMT, Des-(Q435-F483)-SHMT And Des-(L299-F483)-SHMT Mutant Proteins Were Not Soluble And Formed Inclusion Bodies. Des-(A1-K6)-SHMT And Des-(A1-W14)-SHMT Catalyzed Both The Tetrahydrofolate-Dependent And Tetrahydrofolate-Independent Reactions, Generating Characteristic Spectral Intermediates With Glycine And Tetrahydrofolate. The Two Mutants Had Similar Kinetic Parameters To That Of The Recombinant SHMT (Rshmt). However, At 55 Degrees C, The Des-(A1-W14)-SHMT Lost Almost All The Activity Within 5 Min, While At The Same Temperature Rshmt And Des-(A1-K6)-SHMT Retained 85% And 70% Activity, Respectively. Thermal Denaturation Studies Showed That Des-(A1-W14)-SHMT Had A Lower Apparent Melting Temperature (52 Degrees C) Compared To Rshmt (56 Degrees C) And Des-(A1-K6)-SHMT (55 Degrees C), Suggesting That N-Terminal Deletion Had Resulted In A Decrease In The Thermal Stability Of The Enzyme. Further Urea Induced Inactivation Of The Enzymes Revealed That 50% Inactivation Occurred At A Lower Urea Concentration (1.2+/-0.1 M) In The Case Of Des-(A1-W14)-SHMT Compared To Rshmt (1.8+/-0.1 M) And Des-(A1 -K6)-SHMT (1.7+/-0.1 M). The Apoenzyme Of Des-/A1-K6)-SHMT Was Present Predominantly In The Dimer Form, Whereas The Apoenzymes Of Rshmt And Des-(A1-K6)-SHMT Were A Mixture Of Tetramers (Approximate To 75% And Approximate To 65%, Respectively) And Dimers. While, Rshmt And Des-(A1-K6)-SHMT Apoenzymes Could Be Reconstituted Upon The Addition Of Pyridoxal-5'-Phosphate To 96% And 94% Enzyme Activity, Respectively Des-(A1-W14)-SHMT Apoenzyme Could Be Reconstituted Only Upto 22%. The Percentage Activity Refined Correlated With The Appearance Of Visible CD At 425 Nm And With The Amount Of Enzyme Present In The Tetrameric Form Upon Reconstitution As Monitored By Gel Filtration. These Results Demonstrate That, In Addition To The Cofactor, The N-Terminal Arm Plays An Important Role In Stabilizing The Tetrameric Structure Of SHMT.

Ranking of Prospective New Generation Location for a Power Network in a Deregulated System

In developing countries high rate of growth in demand of electric energy is felt, and so the addition of new generating units becomes necessary. In deregulated power systems private generating stations are encouraged to add new generations. Finding the appropriate location of new generator to be installed can be obtained by running repeated power flows, carrying system studies like analyzing the voltage profile, voltage stability, loss analysis etc. In this paper a new methodology is proposed which will mainly consider the existing network topology into account. A concept of T-index is introduced in this paper, which considers the electrical distances between generator and load nodes.This index is used for ranking significant new generation expansion locations and also indicates the amount of permissible generations that can be installed at these new locations. This concept facilitates for the medium and long term planning of power generation expansions within the available transmission corridors. Studies carried out on a sample 7-bus system, EHV equivalent 24-bus system and IEEE 39 bus system are presented for illustration purpose.

X-ray Crystallographic Analysis of the Complexes of Enoyl Acyl Carrier Protein Reductase of Plasmodium falciparum with Triclosan Variants to Elucidate the Importance of Different Functional Groups in Enzyme Inhibition

Triclosan, a well-known inhibitor of Enoyl Acyl Carrier Protein Reductase (ENR) from several pathogenic organisms, is a promising lead compound to design effective drugs. We have solved the X-ray crystal structures of Plasmodium falciparum ENR in complex with triclosan variants having different substituted and unsubstituted groups at different key functional locations. The structures revealed that 4 and 2' substituted compounds have more interactions with the protein, cofactor, and solvents when compared with triclosan. New water molecules were found to interact with some of these inhibitors. Substitution at the 2' position of triclosan caused the relocation of a conserved water molecule, leading to an additional hydrogen bond with the inhibitor. This observation can help in conserved water-based inhibitor design. 2' and 4' unsubstituted compounds showed a movement away from the hydrophobic pocket to compensate for the interactions made by the halogen groups of triclosan. This compound also makes additional interactions with the protein and cofactor which compensate for the lost interactions due to the unsubstitution at 2' and 4'. In cell culture, this inhibitor shows less potency, which indicates that the chlorines at 2' and 4' positions increase the ability of the inhibitor to cross multilayered membranes. This knowledge helps us to modify the different functional groups of triclosan to get more potent inhibitors. (C) 2010 IUBMB IUBMB Life, 62(6): 467-476.

The top 100 questions of importance to the future of global agriculture

Despite a significant growth in food production over the past half-century, one of the most important challenges facing society today is how to feed an expected population of some nine billion by the middle of the 20th century. To meet the expected demand for food without significant increases in prices, it has been estimated that we need to produce 70-100 per cent more food, in light of the growing impacts of climate change, concerns over energy security, regional dietary shifts and the Millennium Development target of halving world poverty and hunger by 2015. The goal for the agricultural sector is no longer simply to maximize productivity, but to optimize across a far more complex landscape of production, rural development, environmental, social justice and food consumption outcomes. However, there remain significant challenges to developing national and international policies that support the wide emergence of more sustainable forms of land use and efficient agricultural production. The lack of information flow between scientists, practitioners and policy makers is known to exacerbate the difficulties, despite increased emphasis upon evidence-based policy. In this paper, we seek to improve dialogue and understanding between agricultural research and policy by identifying the 100 most important questions for global agriculture. These have been compiled using a horizon-scanning approach with leading experts and representatives of major agricultural organizations worldwide. The aim is to use sound scientific evidence to inform decision making and guide policy makers in the future direction of agricultural research priorities and policy support. If addressed, we anticipate that these questions will have a significant impact on global agricultural practices worldwide, while improving the synergy between agricultural policy, practice and research. This research forms part of the UK Government's Foresight Global Food and Farming Futures project.

Establishment of the functional importance of thiamin carrier protein in pregnant rats by using monoclonal antibodies

Monoclonal antibodies (mAbs) to chicken thiamin carrier protein (TCP) have been produced by hybridoma technology to identify the crucial epitopes involved in bioneutralization of the vitamin carrier. The monoclonality of these mAbs (A4C4, F3H6, H8H3, C8C1 and G7H10) was sought to be confirmed by sub-class isotyping; they all belong to IgG1, k type. The epitopes recognized by all the five mAbs are conserved in TCP from the chicken to the rat as assessed by liquid phase RIA and immunoprecipitation of I-125-labelled proteins from pregnant rat serum. Among these mAbs, passive immunization of pregnant rats with the mAb C8C1 only on three consecutive days (day 10, 11 and 12) resulted in embryonic resorption. These results demonstrate the importance of epitopic structure specified by the mAb C8C1 on TCP during pregnancy in rats.

A kinetic study of the phase transformations in Al2O3 and Na2O · 6Al2O3 by a combined use of 27Al MAS NMR spectroscopy and x-ray diffraction: Importance of nucleation

Phase transformations of Al2O3 and Na2O · 6Al2O3 prepared by the gel route have been investigated for the first time by 27Al MAS NMR spectroscopy in combination with x-ray diffraction. Of particular interest in the study is the kinetics of the γ → α and γ → β transformations, respectively, in these two systems. Analysis of the kinetic data shows the important role of nucleation in both these transformations.

Infinite push: a new support vector ranking algorithm that directly optimizes accuracy at the absolute top of the list

Ranking problems have become increasingly important in machine learning and data mining in recent years, with applications ranging from information retrieval and recommender systems to computational biology and drug discovery. In this paper, we describe a new ranking algorithm that directly maximizes the number of relevant objects retrieved at the absolute top of the list. The algorithm is a support vector style algorithm, but due to the different objective, it no longer leads to a quadratic programming problem. Instead, the dual optimization problem involves l1, ∞ constraints; we solve this dual problem using the recent l1, ∞ projection method of Quattoni et al (2009). Our algorithm can be viewed as an l∞-norm extreme of the lp-norm based algorithm of Rudin (2009) (albeit in a support vector setting rather than a boosting setting); thus we refer to the algorithm as the ‘Infinite Push’. Experiments on real-world data sets confirm the algorithm’s focus on accuracy at the absolute top of the list.

Redox regulation of protein tyrosine phosphatase 1B (PTP1B): Importance of steric and electronic effects on the unusual cyclization of the sulfenic acid intermediate to a sulfenyl amide

The redox regulation of protein tyrosine phosphatase 1B (PTP1B) via the unusual transformation of its sulfenic acid (PTP1B-SOH) to a cyclic sulfenyl amide intermediate is studied by using small molecule chemical models. These studies suggest that the sulfenic acids derived from the H2O2-mediated reactions o-amido thiophenols do not efficiently cyclize to sulfenyl amides and the sulfenic acids produced in situ can be trapped by using methyl iodide. Theoretical calculations suggest that the most stable conformer of such sulfenic acids are stabilized by n(O) -> sigma* (S-OH) orbital interactions, which force the -OH group to adopt a position trans to the S center dot center dot center dot O interaction, leading to an almost linear arrangement of the O center dot center dot center dot S-O moiety and this may be the reason for the slow cyclization of such sulfenic acids to their corresponding sulfenyl amides. On the other hand, additional substituents at the 6-position of o-amido phenylsulfenic acids that can induce steric environment and alter the electronic properties around the sulfenic acid moiety by S center dot center dot center dot N or S center dot center dot center dot O nonbonded interactions destabilize the sulfenic acids by inducing strain in the molecule. This may lead to efficient the cyclization of such sulfenic acids. This model study suggests that the amino acid residues in the close proximity of the sulfenic acid moiety in PTP1B may play an important role in the cyclization of PTP1B-SOH to produce the corresponding sulfenyl amide.

Crystal structures of SCP2-thiolases of Trypanosomatidae, human pathogens causing widespread tropical diseases: the importance for catalysis of the cysteine of the unique HDCF loop

Thiolases are essential CoA-dependent enzymes in lipid metabolism. In the present study we report the crystal structures of trypanosomal and leishmanial SCP2 (sterol carrier protein, type-2)-thiolases. Trypanosomatidae cause various widespread devastating (sub)-tropical diseases, for which adequate treatment is lacking. The structures reveal the unique geometry of the active site of this poorly characterized subfamily of thiolases. The key catalytic residues of the classical thiolases are two cysteine residues, functioning as a nucleophile and an acid/base respectively. The latter cysteine residue is part of a CxG motif. Interestingly, this cysteine residue is not conserved in SCP2-thiolases. The structural comparisons now show that in SCP2-thiolases the catalytic acid/base is provided by the cysteine residue of the HDCF motif, which is unique for this thiolase subfamily. This HDCF cysteine residue is spatially equivalent to the CxG cysteine residue of classical thiolases. The HDCF cysteine residue is activated for acid/base catalysis by two main chain NH-atoms, instead of two water molecules, as present in the CxG active site. The structural results have been complemented with enzyme activity data, confirming the importance of the HDCF cysteine residue for catalysis. The data obtained suggest that these trypanosomatid SCP2-thiolases are biosynthetic thiolases. These findings provide promise for drug discovery as biosynthetic thiolases catalyse the first step of the sterol biosynthesis pathway that is essential in several of these parasites.

Photophysical, electrochemical and solid state properties of diketopyrrolopyrrole based molecular materials: importance of the donor group

Diketopyrrolopyrrole (DPP) based molecular semiconductors have emerged as promising materials for high performance active layers in organic solar cells. It is imperative to comprehend the origin of such a property by investigating the fundamental structure property correlation. In this report we have investigated the role of the donor group in DPP based donor-acceptor- donor (D-A-D) structure to govern the solid state, photophysical and electrochemical properties. We have prepared three derivatives of DPP with varying strengths of the donor groups, such as phenyl (PDPP-Hex), thiophene (TDPP-Hex) and selenophene (SeDPP-Hex). The influence of the donor units on the solid state packing was studied by single crystal X-ray diffraction. The photophysical, electrochemical and density functional theory ( DFT) results were combined to elucidate the structural and electronic properties of three DPP derivatives. We found that these DPP derivatives crystallized in the monoclinic space group P21/c and show herringbone packing in the crystal lattice. The derivatives exhibit weak p-p stacking interactions as two neighboring molecules slip away from each other with varied torsional angles at the donor units. The high torsional angle of 32 degrees ( PDPP-Hex) between the phenyl and lactam ring results in weak intramolecular interactions between the donor and acceptor, while TDPP-Hex and SeDPP-Hex show lower torsional angles of 9 degrees and 12 degrees with a strong overlap between the donor and acceptor units. The photophysical properties reveal that PDPP-Hex exhibits a high Stokes shift of 0.32 eV and SeDPP- Hex shows a high molar absorption co-efficient of 33 600 L mol -1 1 cm -1 1 with a low band gap of similar to 2.2 eV. The electrochemical studies of SeDPP- Hex indicate the pronounced effect of selenium in stabilizing the LUMO energy levels and this further emphasizes the importance of chalcogens in developing new n-type organic semiconductors for optoelectronic devices.

Electronic Properties of the Vortex State in Cuprate Superconductors

The superconducting state of the cuprates in the presence of a magnetic field has been investigated very actively in the past few years through measurements of electrical and thermal transport, ac conductivity, specific heat, and other quantities. The observed behavior is not well understood; it probes the nature of quasiparticies, vortices, and their interactions in a superconductor with nodes in the pair amplitude. We summarize here experimental results and our attempts to understand the phenomena.

Distribution of black nodes at various levels in a linear quadtree

The distribution of black leaf nodes at each level of a linear quadtree is of significant interest in the context of estimation of time and space complexities of linear quadtree based algorithms. The maximum number of black nodes of a given level that can be fitted in a square grid of size 2n × 2n can readily be estimated from the ratio of areas. We show that the actual value of the maximum number of nodes of a level is much less than the maximum obtained from the ratio of the areas. This is due to the fact that the number of nodes possible at a level k, 0≤k≤n − 1, should consider the sum of areas occupied by the actual number of nodes present at levels k + 1, k + 2, …, n − 1.

Novel role of the nitrite transporter NirC in Salmonella pathogenesis: SPI2-dependent suppression of inducible nitric oxide synthase in activated macrophages

Activation of macrophages by interferon gamma (IFN- ) and the subsequent production of nitric oxide (NO) are critical for the host defence against Salmonella enterica serovar Typhimurium infection. We report here the inhibition of IFN- -induced NO production in RAW264.7 macrophages infected with wild-type Salmonella. This phenomenon was shown to be dependent on the nirC gene, which encodes a potential nitrite transporter. We observed a higher NO output from IFN- -treated macrophages infected with a nirC mutant of Salmonella. The nirC mutant also showed significantly decreased intracellular proliferation in a NO-dependent manner in activated RAW264.7 macrophages and in liver, spleen and secondary lymph nodes of mice, which was restored by complementing the gene in trans. Under acidified nitrite stress, a twofold more pronounced NO-mediated repression of SPI2 was observed in the nirC knockout strain compared to the wild-type. This enhanced SPI2 repression in the nirC knockout led to a higher level of STAT-1 phosphorylation and inducible nitric oxide synthase (iNOS) expression than seen with the wild-type strain. In iNOS knockout mice, the organ load of the nirC knockout strain was similar to that of the wild-type strain, indicating that the mutant is exclusively sensitive to the host nitrosative stress. Taken together, these results reveal that intracellular Salmonella evade killing in activated macrophages by downregulating IFN- -induced NO production, and they highlight the critical role of nirC as a virulence gene.

Salmonella Typhimurium: Insight into the multi-faceted role of the LysR-type transcriptional regulators in Salmonella

The LysR-type transcriptional regulators (LTTRs) are widely distributed in various genera of prokaryotes LTTRs are DNA binding proteins that can positively or negatively regulate target gene expression and can also repress their own transcription Salmonella enterica comprises a group of Gram-negative bacteria capable of causing clinical syndromes that range from self-limiting diarrhoea to severe fibrinopurulent necrotizing enteritis and life threatening systemic disease. The survival and replication of Salmonella in macrophages and in infected host is brought about by the means of various two component regulatory systems, transporters and other virulence islands In Salmonella genome the existence of 44 LTTRs has been documented These LTTRs regulate bacterial stress response. systemic virulence in mice and also many virulence determinants in vitro. Here we focus on the findings that elucidate the structure and function of the LTTRs in Salmonella and discuss the importance of these LTTRs in making Salmonella a Successful pathogen...