Modeling harvest rates and numbers from age and sex ratios: A demonstration for elephant populations

Illegal harvest rates of wildlife populations are often unknown or difficult to estimate from field data due to under-reporting or incomplete detection of carcasses. This is especially true for elephants that are killed for ivory or in conflicts with people. We describe a method to infer harvest rates from coarse field data of three population parameters, namely, adult female to male ratio, male old-adult to young-adult ratio, and proportion of adult males in the population using Jensen's (2000) 2-sex, density-dependent Leslie matrix model. The specific combination of male and female harvest rates and numbers can be determined from the history of harvest and estimate of population size. We applied this technique to two populations of elephants for which data on age structure and records of mortality were available-a forest-dwelling population of the Asian elephant (at Nagarahole, India) and an African savannah elephant population (at Samburu, Kenya) that had experienced male-biased harvest regimes over 2-3 decades. For the Nagarahole population, the recorded numbers of male and female elephants killed illegally during 1981-2000 were 64% and 88% of the values predicted by the model, respectively, implying some non-detection or incomplete reporting while for the Samburu population the recorded and modeled numbers of harvest during 1990-1999 closely matched. This technique, applicable to any animal population following logistic growth model, can be especially useful for inferring illegal harvest numbers of forest elephants in Africa and Asia.

Synconset Waves and Chains: Spiking Onsets in Synchronous Populations Predict and Are Predicted by Network Structure

Synfire waves are propagating spike packets in synfire chains, which are feedforward chains embedded in random networks. Although synfire waves have proved to be effective quantification for network activity with clear relations to network structure, their utilities are largely limited to feedforward networks with low background activity. To overcome these shortcomings, we describe a novel generalisation of synfire waves, and define `synconset wave' as a cascade of first spikes within a synchronisation event. Synconset waves would occur in `synconset chains', which are feedforward chains embedded in possibly heavily recurrent networks with heavy background activity. We probed the utility of synconset waves using simulation of single compartment neuron network models with biophysically realistic conductances, and demonstrated that the spread of synconset waves directly follows from the network connectivity matrix and is modulated by top-down inputs and the resultant oscillations. Such synconset profiles lend intuitive insights into network organisation in terms of connection probabilities between various network regions rather than an adjacency matrix. To test this intuition, we develop a Bayesian likelihood function that quantifies the probability that an observed synfire wave was caused by a given network. Further, we demonstrate it's utility in the inverse problem of identifying the network that caused a given synfire wave. This method was effective even in highly subsampled networks where only a small subset of neurons were accessible, thus showing it's utility in experimental estimation of connectomes in real neuronal-networks. Together, we propose synconset chains/waves as an effective framework for understanding the impact of network structure on function, and as a step towards developing physiology-driven network identification methods. Finally, as synconset chains extend the utilities of synfire chains to arbitrary networks, we suggest utilities of our framework to several aspects of network physiology including cell assemblies, population codes, and oscillatory synchrony.

Structure constants of beta deformed super Yang-Mills

We study the structure constants of the N = 1 beta deformed theory perturbatively and at strong coupling. We show that the planar one loop corrections to the structure constants of single trace gauge invariant operators in the scalar sector is determined by the anomalous dimension Hamiltonian. This result implies that 3 point functions of the chiral primaries of the theory do not receive corrections at one loop. We then study the structure constants at strong coupling using the Lunin-Maldacena geometry. We explicitly construct the supergravity mode dual to the chiral primary with three equal U(1) R-charges in the Lunin-Maldacena geometry. We show that the 3 point function of this supergravity mode with semi-classical states representing two other similar chiral primary states but with large U(1) charges to be independent of the beta deformation and identical to that found in the AdS(5) x S-5 geometry. This together with the one-loop result indicate that these structure constants are protected by a non-renormalization theorem. We also show that three point function of U(1) R-currents with classical massive strings is proportional to the R-charge carried by the string solution. This is in accordance with the prediction of the R-symmetry Ward identity.

Structural Insights into Saccharomyces cerevisiae Msh4-Msh5 Complex Function Using Homology Modeling

The Msh4-Msh5 protein complex in eukaryotes is involved in stabilizing Holliday junctions and its progenitors to facilitate crossing over during Meiosis I. These functions of the Msh4-Msh5 complex are essential for proper chromosomal segregation during the first meiotic division. The Msh4/5 proteins are homologous to the bacterial mismatch repair protein MutS and other MutS homologs (Msh2, Msh3, Msh6). Saccharomyces cerevisiae msh4/5 point mutants were identified recently that show two fold reduction in crossing over, compared to wild-type without affecting chromosome segregation. Three distinct classes of msh4/5 point mutations could be sorted based on their meiotic phenotypes. These include msh4/5 mutations that have a) crossover and viability defects similar to msh4/5 null mutants; b) intermediate defects in crossing over and viability and c) defects only in crossing over. The absence of a crystal structure for the Msh4-Msh5 complex has hindered an understanding of the structural aspects of Msh4-Msh5 function as well as molecular explanation for the meiotic defects observed in msh4/5 mutations. To address this problem, we generated a structural model of the S. cerevisiae Msh4-Msh5 complex using homology modeling. Further, structural analysis tailored with evolutionary information is used to predict sites with potentially critical roles in Msh4-Msh5 complex formation, DNA binding and to explain asymmetry within the Msh4-Msh5 complex. We also provide a structural rationale for the meiotic defects observed in the msh4/5 point mutations. The mutations are likely to affect stability of the Msh4/5 proteins and/or interactions with DNA. The Msh4-Msh5 model will facilitate the design and interpretation of new mutational data as well as structural studies of this important complex involved in meiotic chromosome segregation.

Elastic thickness structure of the Andaman subduction zone: Implications for convergence of the Ninetyeast Ridge

We use the Bouguer coherence (Morlet isostatic response function) technique to compute the spatial variation of effective elastic thickness (T-e) of the Andaman subduction zone. The recovered T-e map resolves regional-scale features that correlate well with known surface structures of the subducting Indian plate and the overriding Burma plate. The major structure on the India plate, the Ninetyeast Ridge (NER), exhibits a weak mechanical strength, which is consistent with the expected signature of an oceanic ridge of hotspot origin. However, a markedly low strength (0< T-e <3 km) in that region, where the NER is close to the Andaman trench (north of 10 N), receives our main attention in this study. The subduction geometry derived from the Bouguer gravity forward modeling suggests that the NER has indented beneath the Andaman arc. We infer that the bending stresses of the viscous plate, which were reinforced within the subducting oceanic plate as a result of the partial subduction of the NER buoyant load, have reduced the lithospheric strength. The correlation, T-e < T-s (seismogenic thickness) reveals that the upper crust is actively deforming beneath the frontal arc Andaman region. The occurrence of normal-fault earthquakes in the frontal arc, low Te zone, is indicative of structural heterogeneities within the subducting plate. The fact that the NER along with its buoyant root is subducting under the Andaman region is inhibiting the subduction processes, as suggested by the changes in trench line, interrupted back-arc volcanism, variation in seismicity mechanism, slow subduction, etc. The low T-e and thinned crustal structure of the Andaman back-arc basin are attributed to a thermomechanically weakened lithosphere. The present study reveals that the ongoing back-arc spreading and strike-slip motion along the West Andaman Fault coupled with the ridge subduction exerts an important control on the frequency and magnitude of seismicity in the Andaman region. (C) 2013 Elsevier Ltd. All rights reserved.

mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet

The increasing number of available protein structures requires efficient tools for multiple structure comparison. Indeed, multiple structural alignments are essential for the analysis of function, evolution and architecture of protein structures. For this purpose, we proposed a new web server called multiple Protein Block Alignment (mulPBA). This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles. This sequence-like' representation enables the use of powerful sequence alignment methods for primary structure comparison, followed by an iterative refinement of the structural superposition. This approach yields alignments superior to most of the rigid-body alignment methods and highly comparable with the flexible structure comparison approaches. We implement this method in a web server designed to do multiple structure superimpositions from a set of structures given by the user. Outputs are given as both sequence alignment and superposed 3D structures visualized directly by static images generated by PyMol or through a Jmol applet allowing dynamic interaction. Multiple global quality measures are given. Relatedness between structures is indicated by a distance dendogram. Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at www.dsimb.inserm.fr/dsimb_tools/mulpba/.

Inactivation of the Bacterial RNA Polymerase Due to Acquisition of Secondary Structure by the omega Subunit

The widely conserved omega subunit encoded by rpoZ is the smallest subunit of Escherichia coli RNA polymerase (RNAP) but is dispensable for bacterial growth. Function of omega is known to be substituted by GroEL in omega-null strain, which thus does not exhibit a discernable phenotype. In this work, we report isolation of omega variants whose expression in vivo leads to a dominant lethal phenotype. Studies show that in contrast to omega, which is largely unstructured, omega mutants display substantial acquisition of secondary structure. By detailed study with one of the mutants, omega(6) bearing N60D substitution, the mechanism of lethality has been deciphered. Biochemical analysis reveals that omega(6) binds to beta ` subunit in vitro with greater affinity than that of omega. The reconstituted RNAP holoenzyme in the presence of omega(6) in vitro is defective in transcription initiation. Formation of a faulty RNAP in the presence of mutant omega results in death of the cell. Furthermore, lethality of omega(6) is relieved in cells expressing the rpoC2112 allele encoding beta ` (2112), a variant beta ` bearing Y457S substitution, immediately adjacent to the beta ` catalytic center. Our results suggest that the enhanced omega(6)-beta ` interaction may perturb the plasticity of the RNAP active center, implicating a role for omega and its flexible state.

Function of the Dufour's gland in solitary and social Hymenoptera

The poison gland and Dufour's gland are the two glands associated with the sting apparatus in female Apocrita (Hymenoptera). While the poison gland usually functions as an integral part of the venom delivery system, the Dufour's gland has been found to differ in its function in various hymenopteran groups. Like all exocrine glands, the function of the Dufour's gland is to secrete chemicals, but the nature and function of the secretions varies in different taxa. Functions of the Dufour's gland secretions range from serving as a component of material used in nest building, larval food, and pheromones involved in communicative functions that are important for both solitary and social species. This review summarizes the different functions reported for the Dufour's gland in hymenopterans, illustrating how the Dufour's gland secretions can be adapted to give rise to various functions in response to different challenges posed by the ways of life followed by different taxa. Aspects of development, structure, chemistry and the evolution of different functions are also touched upon briefly.

Multichannel-Emissive V-Shaped Boryl-BODIPY Dyads: Synthesis, Structure, and Remarkably Diverse Response toward Fluoride

Three new V-shaped boryl-BODIPY dyads (1-3) were synthesized and structurally characterized. Compounds 1-3 are structurally close molecular siblings differing only in the number of methyl substituents on the BODIPY moiety that were found to play a major role in determining their photophysical behavior. The dyads show rare forms of multiple-channel emission characteristics arising from different extents of electronic energy transfer (EET) processes between the two covalently linked fluorescent chromophores (borane and BODIPY units). Insights into the origin and nature of their emission behavior were gained from comparison with closely related model molecular systems and related photophysical investigations. Because of the presence of the Lewis acidic triarylborane moiety, the dyads function as highly selective and sensitive fluoride sensors with vastly different response behaviors. When fluoride binds to the tricoordinate borane center, dyad 1 shows gradual quenching of its BODIPY-dominated emission due to the ceasing of the (borane to BODIPY) EET process. Dyad 2 shows a ratiometric fluorescence response for fluoride ions. Dyad 3 forms fluoride-induced nanoaggregates that result in fast and effective quenching of its fluorescence intensity just for similar to 0.3 ppm of analyte (i.e., 0.1 equiv 0.26 ppm of fluoride). The small structural alterations in these three structurally close dyads (1 - 3) result in exceptionally versatile and unique photophysical behaviors and remarkably diverse responses toward a single analyte, i.e., fluoride ion.

Electronic band Structure and Photoemission Spectra of Graphene on Silicon Substrate

Synergizing graphene on silicon based nanostructures is pivotal in advancing nano-electronic device technology. A combination of molecular dynamics and density functional theory has been used to predict the electronic energy band structure and photo-emission spectrum for graphene-Si system with silicon as a substrate for graphene. The equilibrium geometry of the system after energy minimization is obtained from molecular dynamics simulations. For the stable geometry obtained, density functional theory calculations are employed to determine the energy band structure and dielectric constant of the system. Further the work function of the system which is a direct consequence of photoemission spectrum is calculated from the energy band structure using random phase approximations.

First-Principles Study of Structure, Vibrational, and Elastic Properties of Stoichiometric and Calcium-Deficient Hydroxyapatite

Hydroxyapatite (HAp), a primary constituent of human bone, is usually nonstoichiometric with varying Ca/P molar ratios, with the well-known fact that Ca deficiency can cause marked reductions in its mechanical properties. To gain insights into the mechanism of this degradation, we employ first-principles calculations based on density functional theory and determine the effects of Ca deficiency on structure, vibrational, and elastic properties of HAp. Our simulation results confirm a considerable reduction in the elastic constants of HAp due to Ca deficiency, which was experimentally reported earlier. Stress-induced transformation of the Ca-deficient defected structure into a metastable state upon the application of stress could be a reason for this. Local structural stability of HAp and Ca-deficient HAp structures is assessed with full phonon dispersion studies. Further, specific signatures in the computed vibrational spectra for Ca deficiency in HAp can be utilized in experimental characterization of different types of defected HAp.

FOLD TYPE II PYRIDOXAL 5 `-PHOSPHATE DEPENDENT ENZYMES: STRUCTURE, SUBSTRATE RECOGNITION AND CATALYSIS

Enzymes utilizing pyridoxal 5'-phosphate dependent mechanism for catalysis are observed in all cellular forms of living organisms. PLP-dependent enzymes catalyze a wide variety of reactions involving amino acid substrates and their analogs. Structurally, these ubiquitous enzymes have been classified into four major fold types. We have carried out investigations on the structure and function of fold type I enzymes serine hydroxymethyl transferase and acetylornithine amino transferase, fold type n enzymes catabolic threonine deaminase, D-serine deaminase, D-cysteine desulfhydrase and diaminopropionate ammonia lyase. This review summarizes the major findings of investigations on fold type II enzymes in the context of similar studies on other PLP-dependent enzymes. Fold type II enzymes participate in pathways of both degradation and synthesis of amino acids. Polypeptide folds of these enzymes, features of their active sites, nature of interactions between the cofactor and the polypeptide, oligomeric structure, catalytic activities with various ligands, origin of specificity and plausible regulation of activity are briefly described. Analysis of the available crystal structures of fold type II enzymes revealed five different classes. The dimeric interfaces found in these enzymes vary across the classes and probably have functional significance.

Microscopic description of the evolution of the local structure and an evaluation of the chemical pressure concept in a solid solution

Extended x-ray absorption fine-structure studies have been performed at the Zn K and Cd K edges for a series of solid solutions of wurtzite Zn1-xCdxS samples with x = 0.0, 0.1, 0.25, 0.5, 0.75, and 1.0, where the lattice parameter as a function of x evolves according to the well-known Vegard's law. In conjunction with extensive, large-scale first-principles electronic structure calculations with full geometry optimizations, these results establish that the percentage variation in the nearest-neighbor bond distances are lower by nearly an order of magnitude compared to what would be expected on the basis of lattice parameter variation, seriously undermining the chemical pressure concept. With experimental results that allow us to probe up to the third coordination shell distances, we provide a direct description of how the local structure, apparently inconsistent with the global structure, evolves very rapidly with interatomic distances to become consistent with it. We show that the basic features of this structural evolution with the composition can be visualized with nearly invariant Zn-S-4 and Cd-S-4 tetrahedral units retaining their structural integrity, while the tilts between these tetrahedral building blocks change with composition to conform to the changing lattice parameters according to the Vegard's law within a relatively short length scale. These results underline the limits of applicability of the chemical pressure concept that has been a favored tool of experimentalists to control physical properties of a large variety of condensed matter systems.

Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors

The nucleoid-associated protein HU plays an important role in maintenance of chromosomal architecture and in global regulation of DNA transactions in bacteria. Although HU is essential for growth in Mycobacterium tuberculosis (Mtb), there have been no reported attempts to perturb HU function with small molecules. Here we report the crystal structure of the N-terminal domain of HU from Mtb. We identify a core region within the HU-DNA interface that can be targeted using stilbene derivatives. These small molecules specifically inhibit HU-DNA binding, disrupt nucleoid architecture and reduce Mtb growth. The stilbene inhibitors induce gene expression changes in Mtb that resemble those induced by HU deficiency. Our results indicate that HU is a potential target for the development of therapies against tuberculosis.

A molecular dynamics study of ambient and high pressure phases of silica: Structure and enthalpy variation with molar volume

Extensive molecular dynamics studies of 13 different silica polymorphs are reported in the isothermal-isobaric ensemble with the Parrinello-Rahman variable shape simulation cell. The van Beest-Kramer-van Santen (BKS) potential is shown to predict lattice parameters for most phases within 2%-3% accuracy, as well as the relative stabilities of different polymorphs in agreement with experiment. Enthalpies of high-density polymorphs - CaCl2-type, alpha-PbO2-type, and pyrite-type for which no experimental data are available as yet, are predicted here. Further, the calculated enthalpies exhibit two distinct regimes as a function of molar volume-for low and medium-density polymorphs, it is almost independent of volume, while for high-pressure phases a steep dependence is seen. A detailed analysis indicates that the increased short-range contributions to enthalpy in the high-density phases arise not only from an increased coordination number of silicon but also shorter Si-O bond lengths. Our results indicate that amorphous phases of silica exhibit better optimization of short-range interactions than crystalline phases at the same density while the magnitude of Coulombic contributions is lower in the amorphous phase. (C) 2014 AIP Publishing LLC.