Functional roles of N-terminal and C-terminal domains in the overall activity of a novel single-stranded DNA binding protein of Deinococcus radiodurans

Single-stranded DNA binding protein (Ssb) of Deinococcus radiodurans comprises N- and C-terminal oligonucleotide/oligosaccharide binding (OB) folds connected by a beta hairpin connector. To assign functional roles to the individual OB folds, we generated three Ssb variants: Ssb(N) (N-terminal without connector), Ssb(NC) (N-terminal with connector) and Ssb(C) (C-terminal), each harboring one OB fold. Both Ssb(N) and Ssb(NC) displayed weak single-stranded DNA (ssDNA) binding activity, compared to the full-length Ssb (Ssb(FL)). The level of ssDNA binding activity displayed by SsbC was intermediate between Ssb(FL) and Ssb(N). Ssb(C) and Ssb(FL) predominantly existed as homo-dimers while Ssb(NC)/Ssb(N) formed different oligomeric forms. In vitro, Ssb(NC) or Ssb(N) formed a binary complex with Ssb(C) that displayed enhanced ssDNA binding activity. Unlike Ssb(FL), Ssb variants were able to differentially modulate topoisomerase-I activity, but failed to stimulate Deinococcal RecA-promoted DNA strand exchange. The results suggest that the C-terminal OB fold is primarily responsible for ssDNA binding. The N-terminal OB fold binds weakly to ssDNA but is involved in multimerization. (C) 2015 The Authors. Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies. This is an open access article under the CC BY-NC-ND license.

Measuring the magnetic-field-dependent chemical potential of a low-density three-dimensional electron gas in n-GaAs and extracting its magnetic susceptibility

We report the magnetic-field-dependent shift of the electron chemical potential in bulk, n-type GaAs at room temperature. A transient voltage of similar to 100 mu V was measured across a Au-Al2O3-GaAs metal-oxide-semiconductor capacitor in a pulsed magnetic field of similar to 6 T. Several spurious voltages larger than the signal that had plagued earlier researchers performing similar experiments were carefully eliminated. The itinerant magnetic susceptibility of GaAs is extracted from the experimentally measured data for four different doping densities, including one as low as 5 x 10(15) cm(-3). Though the susceptibility in GaAs is dominated by Landau-Peierls diamagnetism, the experimental technique demonstrated can be a powerful tool for extracting the total free carrier magnetization of any electron system. The method is also virtually independent of the carrier concentration and is expected to work better in the nondegenerate limit. Such experiments had been successfully performed in two-dimensional electron gases at cryogenic temperatures. However, an unambiguous report on having observed this effect in any three-dimensional electron gas has been lacking. We highlight the 50 year old literature of various trials and discuss the key details of our experiment that were essential for its success. The technique can be used to unambiguously yield only the itinerant part of the magnetic susceptibility of complex materials such as magnetic semiconductors and hexaborides, and thus shed light on the origin of ferromagnetism in such systems.

Negative Cooperativity and High Affinity in Chitooligosaccharide Binding by a Mycobacterium smegmatis Protein Containing LysM and Lectin Domains

LysM domains have been recognized in bacteria and eukaryotes as carbohydrate-binding protein modules, but the mechanism of their binding to chitooligosaccharides has been underexplored. Binding of a Mycobacterium smegmatis protein containing a lectin (MSL) and one LysM domain to chitooligosaccharides has been studied using isothermal titration calorimetry and fluorescence titration that demonstrate the presence of two binding sites of nonidentical affinities per dimeric MSL-LysM molecule. The affinity of the molecule for chitooligosaccharides correlates with the length of the carbohydrate chain. Its binding to chitooligosaccharides is characterized by negative cooperativity in the interactions of the two domains. Apparently, the flexibility of the long linker that connects the LysM and MSL domains plays a facilitating role in this recognition. The LysM domain in the MSL-LysM molecule, like other bacterial domains but unlike plant LysM domains, recognizes equally well peptidoglycan fragments as well as chitin polymers. Interestingly, in the case presented here, two LysM domains are enough for binding to peptidoglycan in contrast to the three reportedly required by the LysM domains of Bacillus subtilis and Lactococcus lactis. Also, the affinity of the MSL-LysM molecule for chitooligosaccharides is higher than that of LysM-chitooligosaccharide interactions reported so far.

Mutations in the nucleotide binding and hydrolysis domains of Helicobacter pylori MutS2 lead to altered biochemical activities and inactivation of its in vivo function

Background: Helicobacter pylori MutS2 (HpMutS2), an inhibitor of recombination during transformation is a non-specific nuclease with two catalytic sites, both of which are essential for its anti-recombinase activity. Although HpMutS2 belongs to a highly conserved family of ABC transporter ATPases, the role of its ATP binding and hydrolysis activities remains elusive. Results: To explore the putative role of ATP binding and hydrolysis activities of HpMutS2 we specifically generated point mutations in the nucleotide-binding Walker-A (HpMutS2-G338R) and hydrolysis Walker-B (HpMutS2-E413A) domains of the protein. Compared to wild-type protein, HpMutS2-G338R exhibited similar to 2.5-fold lower affinity for both ATP and ADP while ATP hydrolysis was reduced by similar to 3-fold. Nucleotide binding efficiencies of HpMutS2-E413A were not significantly altered; however the ATP hydrolysis was reduced by similar to 10-fold. Although mutations in the Walker-A and Walker-B motifs of HpMutS2 only partially reduced its ability to bind and hydrolyze ATP, we demonstrate that these mutants not only exhibited alterations in the conformation, DNA binding and nuclease activities of the protein but failed to complement the hyper-recombinant phenotype displayed by mutS2-disrupted strain of H. pylori. In addition, we show that the nucleotide cofactor modulates the conformation, DNA binding and nuclease activities of HpMutS2. Conclusions: These data describe a strong crosstalk between the ATPase, DNA binding, and nuclease activities of HpMutS2. Furthermore these data show that both, ATP binding and hydrolysis activities of HpMutS2 are essential for the in vivo anti-recombinase function of the protein.

Archeal lectins: An identification through a genomic search

Forty-six lectin domains which have homologues among well established eukaryotic and bacterial lectins of known three-dimensional structure, have been identified through a search of 165 archeal genomes using a multipronged approach involving domain recognition, sequence search and analysis of binding sites. Twenty-one of them have the 7-bladed -propeller lectin fold while 16 have the -trefoil fold and 7 the legume lectin fold. The remainder assumes the C-type lectin, the -prism I and the tachylectin folds. Acceptable models of almost all of them could be generated using the appropriate lectins of known three-dimensional structure as templates, with binding sites at one or more expected locations. The work represents the first comprehensive bioinformatic study of archeal lectins. The presence of lectins with the same fold in all domains of life indicates their ancient origin well before the divergence of the three branches. Further work is necessary to identify archeal lectins which have no homologues among eukaryotic and bacterial species. Proteins 2016; 84:21-30. (c) 2015 Wiley Periodicals, Inc.

Identification of type and degree of railway ballast fouling using ground coupled GPR antennas

GPR is widely used for ballast fouling identification, however, there are no robust guidelines to find the degree and type of fouling quantitatively. In this study, GPR studies were carried out on model and actual railway tracks using three ground coupled antennas and considering three fouling materials. Three ground coupled antennas viz., 100 MHz, 500 MHz and 800 MHz antennas were used for the initial survey and it was found that the 800 MHz ground coupled antenna is an optimum one to get quality results. Three major fouling materials viz., screened/broken ballast, coal and iron ore were used to construct prototype model sections, which were 1/2 of the actual Indian broad-gauge railway track. A separate model section has been created for each degree and type of fouling and GPR surveys were carried out. GPR study shows that increasing the fouling content results in a decrease in the Electromagnetic Wave (EMW) velocity and an increase in the dielectric constant. EMW velocity of ballast fouled with screened ballast was found to be more than coal fouled ballast and iron ore fouled ballast at any degree of fouling and EMW velocity of iron ore fouled ballast was found to be less than coal and screen ballast fouled ballast. Dielectric constant of iron ore fouled ballast was found to be higher than coal and screen ballast fouled ballast for all degrees of fouling. Average slope of the trend line of screen ballast fouled section is low (25.6 degrees), coal fouled ballast is medium (27.8 degrees) and iron ore fouled ballast is high (47.6 degrees). (C) 2016 Elsevier B.V. All rights reserved.

COMPLEX GEODESICS, THEIR BOUNDARY REGULARITY, AND A HARDY-LITTLEWOOD-TYPE LEMMA

We begin by giving an example of a smoothly bounded convex domain that has complex geodesics that do not extend continuously up to partial derivative D. This example suggests that continuity at the boundary of the complex geodesics of a convex domain Omega (sic) C-n, n >= 2, is affected by the extent to which partial derivative Omega curves or bends at each boundary point. We provide a sufficient condition to this effect (on C-1-smoothly bounded convex domains), which admits domains having boundary points at which the boundary is infinitely flat. Along the way, we establish a Hardy-Littlewood-type lemma that might be of independent interest.

Insulin analog preparations and their use in children and adolescents with type 1 diabetes mellitus.

Standard or 'traditional' human insulin preparations such as regular soluble insulin and neutral protamine Hagedorn (NPH) insulin have shortcomings in terms of their pharmacokinetic and pharmacodynamic properties that limit their clinical efficacy. Structurally modified insulin molecules or insulin 'analogs' have been developed with the aim of delivering insulin replacement therapy in a more physiological manner. In the last 10 years, five insulin analog preparations have become commercially available for clinical use in patients with type 1 diabetes mellitus: three 'rapid' or fast-acting analogs (insulin lispro, aspart, and glulisine) and two long-acting analogs (insulin glargine and detemir). This review highlights the specific pharmacokinetic properties of these new insulin analog preparations and focuses on their potential clinical advantages and disadvantages when used in children and adolescents with type 1 diabetes mellitus. The fast-acting analogs specifically facilitate more flexible insulin injection timing with regard to meals and activities, whereas the long-acting analogs have a more predictable profile of action and lack a peak effect. To date, clinical trials in children and adolescents have been few in number, but the evidence available from these and from other studies carried out in adults with type 1 diabetes suggest that they offer significant benefits in terms of reduced frequency of nocturnal hypoglycemia, better postprandial blood glucose control, and improved quality of life when compared with traditional insulins. In addition, insulin detemir therapy is unique in that patients may benefit from reduced risk of excessive weight, particularly during adolescence. Evidence for sustained long-term improvements in glycosylated hemoglobin, on the other hand, is modest. Furthermore, alterations to insulin/insulin-like growth factor I receptor binding characteristics have also raised theoretical concerns that insulin analogs may have an increased mitogenic potential and risk of tumor development, although evidence from both in vitro and in vivo animal studies do not support this assertion. Long-term surveillance has been recommended and further carefully designed prospective studies are needed to evaluate the overall benefits and clinical efficacy of insulin analog therapy in children and adolescents with type 1 diabetes.

Structure of Vortex Dislocations in a Wake-type Flow

Structure and dynamical processes of vortex dislocations in a kind of wake-type flow are described clearly by vortex lines, which are directly constructed from data of three-dimensional direct numerical simulations of the flow evolution.

Low-Dimensional Dynamical Systems for a Wake-Type Shear Flow with Vortex Dislocations

Low-dimensional systems are constructed to investigate dynamics of vortex dislocations in a wake-type shear flow. High-resolution direct numerical simulations are employed to obtain flow snapshots from which the most energetic modes are extracted using proper orthogonal decomposition (POD). The first 10 modes are classified into two groups. One represents the general characteristics of two-dimensional wake-type shear flow, and the other is related to the three-dimensional properties or non-uniform characteristics along the span. Vortex dislocations are generated by these two kinds of coherent structures. The results from the first 20 three-dimensional POD modes show that the low- dimensional systems have captured the basic properties of the wake-type shear flow with vortex dislocation, such as two incommensurable frequencies and their beat frequency.

Numerical exploration of new features on three-dimensional transition of a cylinder wake

The three-dimensional transition of the wake flow behind a circular cylinder is studied in detail by direct numerical simulations using 3D incompressible N-S equations for Reynolds number ranging from 200 to 300. New features and vortex dynamics of the 3D transition of the wake are found and investigated. At Re = 200, the flow pattern is characterized by mode A instability. However, the spanwise characteristic length of the cylinder determines the transition features. Particularly for the specific spanwise characteristic length linear stable mode may dominate the wake in place of mode A and determine the spanwise phase difference of the primary vortices shedding. At Re = 250 and 300 it is found that the streamwise vortices evolve into a new type of mode - "dual vortex pair mode" downstream. The streamwise vortex structures switch among mode A, mode B and dual vortex pair mode from near wake to downstream wake. At Re = 250, an independent low frequency f(m) in addition to the vortex shedding frequency f(s) is identified. Frequency coupling between f(m) and f(s) occurs. These result in the irregularity of the temporal signals and become a key feature in the transition of the wake. Based on the formation analysis of the streamwise vorticity in the vicinity of cylinder, it is suggested that mode A is caused by the emergence of the spanwise velocity due to three dimensionality of the incoming flow past the cylinder. Energy distribution on various wave numbers and the frequency variation in the wake are also described.

Lattice type of fracture model for concrete

Concrete is usually described as a three-phase material, where matrix, aggregate and interface zones are distinguished. The beam lattice model has been applied widely by many investigators to simulate fracture processes in concrete. Due to the extremely large computational effort, however, the beam lattice model faces practical difficulties. In our investigation, a new lattice called generalized beam (GB) lattice is developed to reduce computational effort. Numerical experiments conducted on a panel subjected to uniaxial tension show that the GB lattice model can reproduce the load-displacement curves and crack patterns in agreement to what are observed in tests. Moreover, the effects of the particle overlay on the fracture process are discussed in detail. (C) 2007 Elsevier Ltd. All rights reserved.

Study of three elastic-plastic constitutive models by non-proportional finite deformations of OFHC copper

Experimental stress-strain data of OFHC copper first under torsion to 13% and then under torsion-tension to about 10% are used to study the characteristics of three elastic-plastic constitutive models: Chaboche's super-positional nonlinear model, Dafalias and Popov's two surface model and Watanabe and Atluri's version of the endochronic model. The three models, originally oriented for infinitesimal deformation, have been extended for finite deformation. The results show (a) the Mises-type yield surface used in the three models brings about significant departure of the predictions from the experimental data; (b) Chaboche's and Dafalias' models are easier than Watanabe and Atluri's model in determining the material parameters in them, and (c) Chaboche's and Watanabe & Atluri's models produce almost the same prediction to the data, while Dafalias' model cannot accurately predict the plastic deformations when a loading path changes in its direction. Copyright (C) 1996 Elsevier Science Ltd

Recommendation domains for pond aquaculture: country case study: development and status of freshwater aquaculture in Malawi

This monograph is a result of a 3-year project to produce a decision-support toolkit with supporting databases and case studies to help researchers, planners and extension agents working on freshwater pond aquaculture. The purpose of the work was to provide tools and information to help practitioners identify places and conditions where pond aquaculture can benefit the poor, both as producers and as consumers of fish. This monograph is the case study for Malawi. Written in three parts, it describes the historical background, practices, stakeholder profiles, production levels, economic and institutional environment, policy issues, and prospects for aquaculture in the country. First, it documents the history and current status of the aquaculture in the country. Second, it assesses the technologies and approaches that either succeeded or failed to foster aquaculture development and discusses why. Third, it identifies the key reasons for aquaculture adoption.

Recommendation domains for pond aquaculture: country case study: development and status of freshwater aquaculture in Cameroon

This report is an output of the project “Determination of high-potential aquaculture development areas and impact in Africa and Asia”. This monograph is the case study for Cameroon. Written in three parts, it describes the historical background, practices, stakeholder profiles, production levels, economic and institutional environment, policy issues, and prospects for aquaculture in the country. First, it documents the history and current status of the aquaculture in the country. Second, it assesses the technologies and approaches that either succeeded or failed to foster aquaculture development and discusses why. Third, it identifies the key reasons for aquaculture adoption.