Molecular biogeography: towards an integrated framework for conserving pan-African biodiversity.

Directory of Open Access Journals (Sweden)

Yoshan Moodley

2007-05-01

Full Text Available Biogeographic models partition ecologically similar species assemblages into discrete ecoregions. However, the history, relationship and interactions between these regions and their assemblages have rarely been explored.Here we develop a taxon-based approach that explicitly utilises molecular information to compare ecoregion history and status, which we exemplify using a continentally distributed mammalian species: the African bushbuck (Tragelaphus scriptus. We reveal unprecedented levels of genetic diversity and structure in this species and show that ecoregion biogeographic history better explains the distribution of molecular variation than phenotypic similarity or geography. We extend these data to explore ecoregion connectivity, identify core habitats and infer ecological affinities from them.This analysis defines 28 key biogeographic regions for sub-Saharan Africa, and provides a valuable framework for the incorporation of genetic and biogeographic information into a more widely applicable model for the conservation of continental biodiversity.

Generation of monoclonal antibodies against highly conserved antigens.

Directory of Open Access Journals (Sweden)

Hongzhe Zhou

Full Text Available BACKGROUND: Therapeutic antibody development is one of the fastest growing areas of the pharmaceutical industry. Generating high-quality monoclonal antibodies against a given therapeutic target is very crucial for the success of the drug development. However, due to immune tolerance, some proteins that are highly conserved between mice and humans are not very immunogenic in mice, making it difficult to generate antibodies using a conventional approach. METHODOLOGY/PRINCIPAL FINDINGS: In this report, the impaired immune tolerance of NZB/W mice was exploited to generate monoclonal antibodies against highly conserved or self-antigens. Using two highly conserved human antigens (MIF and HMGB1 and one mouse self-antigen (TNF-alpha as examples, we demonstrate here that multiple clones of high affinity, highly specific antibodies with desired biological activities can be generated, using the NZB/W mouse as the immunization host and a T cell-specific tag fused to a recombinant antigen to stimulate the immune system. CONCLUSIONS/SIGNIFICANCE: We developed an efficient and universal method for generating surrogate or therapeutic antibodies against "difficult antigens" to facilitate the development of therapeutic antibodies.

Molecular identification of livestock breeds: a tool for modern conservation biology.

Science.gov (United States)

Yaro, Mohammed; Munyard, Kylie A; Stear, Michael J; Groth, David M

2017-05-01

Global livestock genetic diversity includes all of the species, breeds and strains of domestic animals, and their variations. Although a recent census indicated that there were 40 species and over 8000 breeds of domestic animals; for the purpose of conservation biology the diversity between and within breeds rather than species is regarded to be of crucial importance. This domestic animal genetic diversity has developed through three main evolutionary events, from speciation (about 3 million years ago) through domestication (about 12000 years ago) to specialised breeding (starting about 200 years ago). These events and their impacts on global animal genetic resources have been well documented in the literature. The key importance of global domestic animal resources in terms of economic, scientific and cultural heritage has also been addressed. In spite of their importance, there is a growing number of reports on the alarming erosion of domestic animal genetic resources. This erosion of is happening in spite of several global conservation initiatives designed to mitigate it. Herein we discuss these conservation interventions and highlight their strengths and weaknesses. However, pivotal to the success of these conservation initiatives is the reliability of the genetic assignment of individual members to a target breed. Finally, we discuss the prospect of using improved breed identification methodologies to develop a reliable breed-specific molecular identification tool that is easily applicable to populations of livestock breeds in various ecosystems. These identification tools, when developed, will not only facilitate the regular monitoring of threatened or endangered breed populations, but also enhance the development of more efficient and sustainable livestock production systems. © 2016 Cambridge Philosophical Society.

Widespread utility of highly informative AFLP molecular markers across divergent shark species.

Science.gov (United States)

Zenger, Kyall R; Stow, Adam J; Peddemors, Victor; Briscoe, David A; Harcourt, Robert G

2006-01-01

Population numbers of many shark species are declining rapidly around the world. Despite the commercial and conservation significance, little is known on even the most fundamental aspects of their population biology. Data collection that relies on direct observation can be logistically challenging with sharks. Consequently, molecular methods are becoming increasingly important to obtain knowledge that is critical for conservation and management. Here we describe an amplified fragment length polymorphism method that can be applied universally to sharks to identify highly informative genome-wide polymorphisms from 12 primer pairs. We demonstrate the value of our method on 15 divergent shark species within the superorder Galeomorphii, including endangered species which are notorious for low levels of genetic diversity. Both the endangered sand tiger shark (Carcharodon taurus, N = 18) and the great white shark (Carcharodon carcharias, N = 7) displayed relatively high levels of allelic diversity. A total of 59 polymorphic loci (H(e) = 0.373) and 78 polymorphic loci (H(e) = 0.316) were resolved in C. taurus and C. carcharias, respectively. Results from other sharks (e.g., Orectolobus ornatus, Orectolobus sp., and Galeocerdo cuvier) produced remarkably high numbers of polymorphic loci (106, 94, and 86, respectively) from a limited sample size of only 2. A major constraint to obtaining much needed genetic data from sharks is the time-consuming process of developing molecular markers. Here we demonstrate the general utility of a technique that provides large numbers of informative loci in sharks.

H2B ubiquitination: Conserved molecular mechanism, diverse physiologic functions of the E3 ligase during meiosis.

Science.gov (United States)

Wang, Liying; Cao, Chunwei; Wang, Fang; Zhao, Jianguo; Li, Wei

2017-09-03

RNF20/Bre1 mediated H2B ubiquitination (H2Bub) has various physiologic functions. Recently, we found that H2Bub participates in meiotic recombination by promoting chromatin relaxation during meiosis. We then analyzed the phylogenetic relationships among the E3 ligase for H2Bub, its E2 Rad6 and their partner WW domain-containing adaptor with a coiled-coil (WAC) or Lge1, and found that the molecular mechanism underlying H2Bub is evolutionarily conserved from yeast to mammals. However, RNF20 has diverse physiologic functions in different organisms, which might be caused by the evolutionary divergency of their domain/motif architectures. In the current extra view, we not only elucidate the evolutionarily conserved molecular mechanism underlying H2Bub, but also discuss the diverse physiologic functions of RNF20 during meiosis.

Molecular Tools For Biodiversity Conservation

Indian Academy of Sciences (India)

conservation in India. They are ... cuss these with case studies on some cat species in India. Introduction ... fallout since vital resources such as clean air, water, and food ... tion, climate change has become a much-dreaded catchword, and .... (Eastern. Mangroves Total and West- ern). /Inland wetlands. DNA extraction. 66.

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

Energy Technology Data Exchange (ETDEWEB)

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de [Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt (Germany)

2014-12-14

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

International Nuclear Information System (INIS)

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der

2014-01-01

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics

Molecular conservation of estrogen-response associated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines

Directory of Open Access Journals (Sweden)

Govindarajan Kunde R

2011-05-01

Full Text Available Abstract Background The zebrafish is recognized as a versatile cancer and drug screening model. However, it is not known whether the estrogen-responsive genes and signaling pathways that are involved in estrogen-dependent carcinogenesis and human cancer are operating in zebrafish. In order to determine the potential of zebrafish model for estrogen-related cancer research, we investigated the molecular conservation of estrogen responses operating in both zebrafish and human cancer cell lines. Methods Microarray experiment was performed on zebrafish exposed to estrogen (17β-estradiol; a classified carcinogen and an anti-estrogen (ICI 182,780. Zebrafish estrogen-responsive genes sensitive to both estrogen and anti-estrogen were identified and validated using real-time PCR. Human homolog mapping and knowledge-based data mining were performed on zebrafish estrogen responsive genes followed by estrogen receptor binding site analysis and comparative transcriptome analysis with estrogen-responsive human cancer cell lines (MCF7, T47D and Ishikawa. Results Our transcriptome analysis captured multiple estrogen-responsive genes and signaling pathways that increased cell proliferation, promoted DNA damage and genome instability, and decreased tumor suppressing effects, suggesting a common mechanism for estrogen-induced carcinogenesis. Comparative analysis revealed a core set of conserved estrogen-responsive genes that demonstrate enrichment of estrogen receptor binding sites and cell cycle signaling pathways. Knowledge-based and network analysis led us to propose that the mechanism involving estrogen-activated estrogen receptor mediated down-regulation of human homolog HES1 followed by up-regulation cell cycle-related genes (human homologs E2F4, CDK2, CCNA, CCNB, CCNE, is highly conserved, and this mechanism may involve novel crosstalk with basal AHR. We also identified mitotic roles of polo-like kinase as a conserved signaling pathway with multiple entry

Tilapia and human CLIC2 structures are highly conserved.

Science.gov (United States)

Zeng, Jiao; Li, Zhengjun; Lui, Eei Yin; Lam, Siew Hong; Swaminathan, Kunchithapadam

2018-01-08

Chloride intracellular channels (CLICs) exist in soluble and membrane bound forms. We have determined the crystal structure of soluble Clic2 from the euryhaline teleost fish Oreochromis mossambicus. Structural comparison of tilapia and human CLIC2 with other CLICs shows that these proteins are highly conserved. We have also compared the expression levels of clic2 in selected osmoregulatory organs of tilapia, acclimated to freshwater, seawater and hypersaline water. Structural conservation of vertebrate CLICs implies that they might play conserved roles. Also, tissue-specific responsiveness of clic2 suggests that it might be involved in iono-osmoregulation under extreme conditions in tilapia. Copyright © 2017 Elsevier Inc. All rights reserved.

Highly conserved non-coding sequences are associated with vertebrate development.

Directory of Open Access Journals (Sweden)

Adam Woolfe

2005-01-01

Full Text Available In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH, in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development

Novel cancer gene variants and gene fusions of triple-negative breast cancers (TNBCs) reveal their molecular diversity conserved in the patient-derived xenograft (PDX) model.

Science.gov (United States)

Jung, Jaeyun; Jang, Kiwon; Ju, Jung Min; Lee, Eunji; Lee, Jong Won; Kim, Hee Jung; Kim, Jisun; Lee, Sae Byul; Ko, Beom Seok; Son, Byung Ho; Lee, Hee Jin; Gong, Gyungyup; Ahn, Sei Yeon; Choi, Jung Kyoon; Singh, Shree Ram; Chang, Suhwan

2018-04-20

Despite the improved 5-year survival rate of breast cancer, triple-negative breast cancer (TNBC) remains a challenge due to lack of effective targeted therapy and higher recurrence and metastasis than other subtypes. To identify novel druggable targets and to understand its unique biology, we tried to implement 24 patient-derived xenografts (PDXs) of TNBC. The overall success rate of PDX implantation was 45%, much higher than estrogen receptor (ER)-positive cases. Immunohistochemical analysis revealed conserved ER/PR/Her2 negativity (with two exceptions) between the original and PDX tumors. Genomic analysis of 10 primary tumor-PDX pairs with Ion AmpliSeq CCP revealed high degree of variant conservation (85.0% to 96.9%) between primary and PDXs. Further analysis showed 44 rare variants with a predicted high impact in 36 genes including Trp53, Pten, Notch1, and Col1a1. Among them, we confirmed frequent Notch1 variant. Furthermore, RNA-seq analysis of 24 PDXs revealed 594 gene fusions, of which 163 were in-frame, including AZGP1-GJC3 and NF1-AARSD1. Finally, western blot analysis of oncogenic signaling proteins supporting molecular diversity of TNBC PDXs. Overall, our report provides a molecular basis for the usefulness of the TNBC PDX model in preclinical study. Copyright © 2018. Published by Elsevier B.V.

Breast Conservation Therapy: The Influence of Molecular Subtype and Margins

International Nuclear Information System (INIS)

Demirci, Senem; Broadwater, Gloria; Marks, Lawrence B.; Clough, Robert; Prosnitz, Leonard R.

2012-01-01

Purpose: To evaluate treatment results and prognostic factors, especially margin status and molecular subtype, in early-stage breast cancer patients treated with breast conservation therapy (BCT). Methods and Materials: The records of 1,058 Stage I or II breast cancer patients treated with BCT (surgical excision plus radiotherapy) at Duke University Medical Center, Durham, North Carolina, from 1985–2005 were retrospectively reviewed. Conventional receptor analyses were used as surrogate markers for molecular subtype classification (luminal A, luminal B, Her2 positive, and basal like). Actuarial estimates of overall survival (OS), cause-specific survival (CSS), failure-free survival, and locoregional control (LRC) were computed by use of Kaplan-Meier plots. We analyzed prognostic variables for significance using Cox proportional hazards univariate and multivariate analysis. The study was approved by the Duke University Medical Center Institutional Review Board. Results: The median age of the patients was 56 years (range, 18–89 years). Of the patients, 80% had T1 disease and 66% N0 disease pathologically. With a median follow-up of 9.8 years, an in-breast recurrence developed in 53 patients and 10 patients had nodal failure. For all patients, the 10-year CSS rate was 94%; LRC rate, 94%; and failure-free survival rate, 88%. Luminal A patients had a CSS rate of 95% and LRC rate of 99%. Basal-type patients appeared to do worse, with regard to both CSS rate (74%) and LRC rate (76%), but the numbers were small and the difference was not statistically significant. LRC rates of patients with negative margins (widely negative, close, and extent of margin not known) were virtually identical (93%, 96%, and 94%, respectively). Those with positive margins appeared to fare slightly worse based on LRC rate (88%), but again, the numbers were small and the difference was not statistically significant. Conclusions: BCT remains the treatment of choice for early-stage breast cancer

Breast Conservation Therapy: The Influence of Molecular Subtype and Margins

Energy Technology Data Exchange (ETDEWEB)

Demirci, Senem, E-mail: senem.demirci@ege.edu.tr [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Department of Radiation Oncology, Ege University Faculty of Medicine, Izmir (Turkey); Broadwater, Gloria [Department of Biostatistics and Bioinformatics, Duke Cancer Institute, Durham, NC (United States); Cancer and Leukemia Group B Statistical Center, Duke Cancer Institute, Durham, NC (United States); Marks, Lawrence B. [Department of Radiation Oncology, University of North Carolina School of Medicine, Chapel Hill, NC (United States); Clough, Robert; Prosnitz, Leonard R. [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States)

2012-07-01

Purpose: To evaluate treatment results and prognostic factors, especially margin status and molecular subtype, in early-stage breast cancer patients treated with breast conservation therapy (BCT). Methods and Materials: The records of 1,058 Stage I or II breast cancer patients treated with BCT (surgical excision plus radiotherapy) at Duke University Medical Center, Durham, North Carolina, from 1985-2005 were retrospectively reviewed. Conventional receptor analyses were used as surrogate markers for molecular subtype classification (luminal A, luminal B, Her2 positive, and basal like). Actuarial estimates of overall survival (OS), cause-specific survival (CSS), failure-free survival, and locoregional control (LRC) were computed by use of Kaplan-Meier plots. We analyzed prognostic variables for significance using Cox proportional hazards univariate and multivariate analysis. The study was approved by the Duke University Medical Center Institutional Review Board. Results: The median age of the patients was 56 years (range, 18-89 years). Of the patients, 80% had T1 disease and 66% N0 disease pathologically. With a median follow-up of 9.8 years, an in-breast recurrence developed in 53 patients and 10 patients had nodal failure. For all patients, the 10-year CSS rate was 94%; LRC rate, 94%; and failure-free survival rate, 88%. Luminal A patients had a CSS rate of 95% and LRC rate of 99%. Basal-type patients appeared to do worse, with regard to both CSS rate (74%) and LRC rate (76%), but the numbers were small and the difference was not statistically significant. LRC rates of patients with negative margins (widely negative, close, and extent of margin not known) were virtually identical (93%, 96%, and 94%, respectively). Those with positive margins appeared to fare slightly worse based on LRC rate (88%), but again, the numbers were small and the difference was not statistically significant. Conclusions: BCT remains the treatment of choice for early-stage breast cancer

Multi-scale coarse-graining of non-conservative interactions in molecular liquids

International Nuclear Information System (INIS)

Izvekov, Sergei; Rice, Betsy M.

2014-01-01

A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger

Multi-scale coarse-graining of non-conservative interactions in molecular liquids

Energy Technology Data Exchange (ETDEWEB)

Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M. [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States)

2014-03-14

A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger

GPU accelerated Discrete Element Method (DEM) molecular dynamics for conservative, faceted particle simulations

Energy Technology Data Exchange (ETDEWEB)

Spellings, Matthew [Chemical Engineering, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Marson, Ryan L. [Materials Science & Engineering, University of Michigan, 2300 Hayward St., Ann Arbor, MI 48109 (United States); Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Anderson, Joshua A. [Chemical Engineering, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Glotzer, Sharon C., E-mail: sglotzer@umich.edu [Chemical Engineering, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States); Materials Science & Engineering, University of Michigan, 2300 Hayward St., Ann Arbor, MI 48109 (United States); Biointerfaces Institute, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI 48109 (United States)

2017-04-01

Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging to model in these systems because they require detailed dynamical information at the individual particle level. Within the granular materials community the Discrete Element Method has been used extensively to model systems of anisotropic particles under gravity, with friction. We provide an implementation of this method intended for simulation of hard, faceted nanoparticles, with a conservative Weeks–Chandler–Andersen (WCA) interparticle potential, coupled to a thermodynamic ensemble. This method is a natural extension of classical molecular dynamics and enables rigorous thermodynamic calculations for faceted particles.

Conservation Biological Control of Pests in the Molecular Era: New Opportunities to Address Old Constraints

Science.gov (United States)

Gurr, Geoff M.; You, Minsheng

2016-01-01

Biological control has long been considered a potential alternative to pesticidal strategies for pest management but its impact and level of use globally remain modest and inconsistent. A rapidly expanding range of molecular – particularly DNA-related – techniques is currently revolutionizing many life sciences. This review identifies a series of constraints on the development and uptake of conservation biological control and considers the contemporary and likely future influence of molecular methods on these constraints. Molecular approaches are now often used to complement morphological taxonomic methods for the identification and study of biological control agents including microbes. A succession of molecular techniques has been applied to ‘who eats whom’ questions in food-web ecology. Polymerase chain reaction (PCR) approaches have largely superseded immunological approaches such as enzyme-linked immunosorbent assay (ELISA) and now – in turn – are being overtaken by next generation sequencing (NGS)-based approaches that offer unparalleled power at a rapidly diminishing cost. There is scope also to use molecular techniques to manipulate biological control agents, which will be accelerated with the advent of gene editing tools, the CRISPR/Cas9 system in particular. Gene editing tools also offer unparalleled power to both elucidate and manipulate plant defense mechanisms including those that involve natural enemy attraction to attacked plants. Rapid advances in technology will allow the development of still more novel pest management options for which uptake is likely to be limited chiefly by regulatory hurdles. PMID:26793225

A highly conserved amino acid in VP1 regulates maturation of enterovirus 71.

Directory of Open Access Journals (Sweden)

Yong-Xin Zhang

2017-09-01

Full Text Available Enterovirus 71 (EV71 is the major causative agent of hand, foot and mouth disease (HFMD in children, causing severe clinical outcomes and even death. Here, we report an important role of the highly conserved alanine residue at position 107 in the capsid protein VP1 (VP1A107 in the efficient replication of EV71. Substitutional mutations of VP1A107 significantly diminish viral growth kinetics without significant effect on viral entry, expression of viral genes and viral production. The results of mechanistic studies reveal that VP1A107 regulates the efficient cleavage of the VP0 precursor during EV71 assembly, which is required, in the next round of infection, for the transformation of the mature virion (160S into an intermediate or A-particle (135S, a key step of virus uncoating. Furthermore, the results of molecular dynamic simulations and hydrogen-bond networks analysis of VP1A107 suggest that flexibility of the VP1 BC loop or the region surrounding the VP1107 residue directly correlates with viral infectivity. It is possible that sufficient flexibility of the region surrounding the VP1107 residue favors VP0 conformational change that is required for the efficient cleavage of VP0 as well as subsequent viral uncoating and viral replication. Taken together, our data reveal the structural role of the highly conserved VP1A107 in regulating EV71 maturation. Characterization of this novel determinant of EV71 virulence would promote the study on pathogenesis of Enteroviruses.

High-resolution satellite imagery is an important yet underutilized resource in conservation biology.

Science.gov (United States)

Boyle, Sarah A; Kennedy, Christina M; Torres, Julio; Colman, Karen; Pérez-Estigarribia, Pastor E; de la Sancha, Noé U

2014-01-01

Technological advances and increasing availability of high-resolution satellite imagery offer the potential for more accurate land cover classifications and pattern analyses, which could greatly improve the detection and quantification of land cover change for conservation. Such remotely-sensed products, however, are often expensive and difficult to acquire, which prohibits or reduces their use. We tested whether imagery of high spatial resolution (≤5 m) differs from lower-resolution imagery (≥30 m) in performance and extent of use for conservation applications. To assess performance, we classified land cover in a heterogeneous region of Interior Atlantic Forest in Paraguay, which has undergone recent and dramatic human-induced habitat loss and fragmentation. We used 4 m multispectral IKONOS and 30 m multispectral Landsat imagery and determined the extent to which resolution influenced the delineation of land cover classes and patch-level metrics. Higher-resolution imagery more accurately delineated cover classes, identified smaller patches, retained patch shape, and detected narrower, linear patches. To assess extent of use, we surveyed three conservation journals (Biological Conservation, Biotropica, Conservation Biology) and found limited application of high-resolution imagery in research, with only 26.8% of land cover studies analyzing satellite imagery, and of these studies only 10.4% used imagery ≤5 m resolution. Our results suggest that high-resolution imagery is warranted yet under-utilized in conservation research, but is needed to adequately monitor and evaluate forest loss and conversion, and to delineate potentially important stepping-stone fragments that may serve as corridors in a human-modified landscape. Greater access to low-cost, multiband, high-resolution satellite imagery would therefore greatly facilitate conservation management and decision-making.

High sensitivity optical molecular imaging system

Science.gov (United States)

An, Yu; Yuan, Gao; Huang, Chao; Jiang, Shixin; Zhang, Peng; Wang, Kun; Tian, Jie

2018-02-01

Optical Molecular Imaging (OMI) has the advantages of high sensitivity, low cost and ease of use. By labeling the regions of interest with fluorescent or bioluminescence probes, OMI can noninvasively obtain the distribution of the probes in vivo, which play the key role in cancer research, pharmacokinetics and other biological studies. In preclinical and clinical application, the image depth, resolution and sensitivity are the key factors for researchers to use OMI. In this paper, we report a high sensitivity optical molecular imaging system developed by our group, which can improve the imaging depth in phantom to nearly 5cm, high resolution at 2cm depth, and high image sensitivity. To validate the performance of the system, special designed phantom experiments and weak light detection experiment were implemented. The results shows that cooperated with high performance electron-multiplying charge coupled device (EMCCD) camera, precision design of light path system and high efficient image techniques, our OMI system can simultaneously collect the light-emitted signals generated by fluorescence molecular imaging, bioluminescence imaging, Cherenkov luminance and other optical imaging modality, and observe the internal distribution of light-emitting agents fast and accurately.

The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains

Directory of Open Access Journals (Sweden)

Wang Yiguo

2008-10-01

Full Text Available Abstract Background Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs. Accurate prediction of SLiMs has been difficult because they are short (often Results Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. Conclusion The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains.

In Vitro Propagation and Conservation of Bacopa monnieri L.

Science.gov (United States)

Sharma, Neelam; Singh, Rakesh; Pandey, Ruchira

2016-01-01

Bacopa monnieri L. (common name brahmi) is a traditional and renowned Indian medicinal plant with high commercial value for its memory revitalizer potential. Demand for this herb has further escalated due to popularization of various brahmi-based drugs coupled with reported anticancer property. Insufficient seed availability and problems associated with seed propagation including short seed viability are the major constraints of seed conservation in the gene banks. In vitro clonal propagation, a prerequisite for in vitro conservation by enhanced axillary branching was standardized. We have developed a simple, single step protocol for in vitro establishment, propagation and medium-term conservation of B. monnieri. Single node explants, cultured on Murashige and Skoog's medium supplemented with BA (0.2 mg/L), exhibited shoot proliferation without callus formation. Rooting was achieved on the same medium. The in vitro raised plants were successfully transferred to soil with ~80 % survival. On the same medium, shoots could also be conserved for 12 months with high survival and genetic stability was maintained as revealed by molecular markers. The protocol optimized in the present study has been applied for culture establishment, shoot multiplication and medium-term conservation of several Bacopa germplasm, procured from different agro-ecological regions of India.

Evolution of star-bearing molecular clouds: the high-velocity HCO+ flow in NGC 2071

International Nuclear Information System (INIS)

Wootten, A.; Loren, R.B.; Sandqvist, A.; Friberg, P.; Hjalmarson, Aa.

1984-01-01

The J = 1-0 and J = 302 lines of HCO + and H 13 CO + have been observed in the molecular cloud NGC 2071, where they map the dense portions of a bidirectional molecular flow. The high resolution (42'') of our observations has enabled us to determine the distribution of mass, momentum , and energy in the flow as a function of projected distance from the cluster. Both momentum and energy diminish with distance from the central cluster of infrared sources. The highest velocities at a given intensity in this dense flow occur in a limited region coincident with an infrared cluster and the densest part of the molecular cloud. Higher resolution (33'') CO and 13 CO observations reveal that the extreme velocities in the flow occur in regions displaced on opposite sides of the cluster, suggesting that the flow only becomes visible in molecular line emission at distances approx.0.1 pc from its supposed source. Lower velocity material containing most of the mass of the flow is found over larger regions, as expected if the flow has decelerated as it has evolved. Assuming conservation of momentum, the historical rate of momentum injection is found to have been roughly constant over a period of 10 4 years, suggesting a constancy of the average luminosity of the central cluster over that time. The J = 3--2 HCO + profile does not show the absorption which is a prominent feature of the J = 1--0 profile, and the J = 3--2 line appears to be a useful probe of conditions specific to the dense cores of clouds. The high velocity HCO + emission correlates very well with spatial and velocity events of molecular hydrogen emission. The abundance of HCO + [X(HCO + )approx.10 -8 ], and by inference the electron density, is similar in material at all velocities

ABCE1 is a highly conserved RNA silencing suppressor.

Directory of Open Access Journals (Sweden)

Kairi Kärblane

Full Text Available ATP-binding cassette sub-family E member 1 (ABCE1 is a highly conserved protein among eukaryotes and archaea. Recent studies have identified ABCE1 as a ribosome-recycling factor important for translation termination in mammalian cells, yeast and also archaea. Here we report another conserved function of ABCE1. We have previously described AtRLI2, the homolog of ABCE1 in the plant Arabidopsis thaliana, as an endogenous suppressor of RNA silencing. In this study we show that this function is conserved: human ABCE1 is able to suppress RNA silencing in Nicotiana benthamiana plants, in mammalian HEK293 cells and in the worm Caenorhabditis elegans. Using co-immunoprecipitation and mass spectrometry, we found a number of potential ABCE1-interacting proteins that might support its function as an endogenous suppressor of RNA interference. The interactor candidates are associated with epigenetic regulation, transcription, RNA processing and mRNA surveillance. In addition, one of the identified proteins is translin, which together with its binding partner TRAX supports RNA interference.

Amino acid properties conserved in molecular evolution.

Directory of Open Access Journals (Sweden)

Witold R Rudnicki

Full Text Available That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts - one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications.

Homologous high-throughput expression and purification of highly conserved E coli proteins

Directory of Open Access Journals (Sweden)

Duchmann Rainer

2007-06-01

Full Text Available Abstract Background Genetic factors and a dysregulated immune response towards commensal bacteria contribute to the pathogenesis of Inflammatory Bowel Disease (IBD. Animal models demonstrated that the normal intestinal flora is crucial for the development of intestinal inflammation. However, due to the complexity of the intestinal flora, it has been difficult to design experiments for detection of proinflammatory bacterial antigen(s involved in the pathogenesis of the disease. Several studies indicated a potential association of E. coli with IBD. In addition, T cell clones of IBD patients were shown to cross react towards antigens from different enteric bacterial species and thus likely responded to conserved bacterial antigens. We therefore chose highly conserved E. coli proteins as candidate antigens for abnormal T cell responses in IBD and used high-throughput techniques for cloning, expression and purification under native conditions of a set of 271 conserved E. coli proteins for downstream immunologic studies. Results As a standardized procedure, genes were PCR amplified and cloned into the expression vector pQTEV2 in order to express proteins N-terminally fused to a seven-histidine-tag. Initial small-scale expression and purification under native conditions by metal chelate affinity chromatography indicated that the vast majority of target proteins were purified in high yields. Targets that revealed low yields after purification probably due to weak solubility were shuttled into Gateway (Invitrogen destination vectors in order to enhance solubility by N-terminal fusion of maltose binding protein (MBP, N-utilizing substance A (NusA, or glutathione S-transferase (GST to the target protein. In addition, recombinant proteins were treated with polymyxin B coated magnetic beads in order to remove lipopolysaccharide (LPS. Thus, 73% of the targeted proteins could be expressed and purified in large-scale to give soluble proteins in the range of 500

Enhancing Conservation with High Resolution Productivity Datasets for the Conterminous United States

Science.gov (United States)

Robinson, Nathaniel Paul

Human driven alteration of the earth's terrestrial surface is accelerating through land use changes, intensification of human activity, climate change, and other anthropogenic pressures. These changes occur at broad spatio-temporal scales, challenging our ability to effectively monitor and assess the impacts and subsequent conservation strategies. While satellite remote sensing (SRS) products enable monitoring of the earth's terrestrial surface continuously across space and time, the practical applications for conservation and management of these products are limited. Often the processes driving ecological change occur at fine spatial resolutions and are undetectable given the resolution of available datasets. Additionally, the links between SRS data and ecologically meaningful metrics are weak. Recent advances in cloud computing technology along with the growing record of high resolution SRS data enable the development of SRS products that quantify ecologically meaningful variables at relevant scales applicable for conservation and management. The focus of my dissertation is to improve the applicability of terrestrial gross and net primary productivity (GPP/NPP) datasets for the conterminous United States (CONUS). In chapter one, I develop a framework for creating high resolution datasets of vegetation dynamics. I use the entire archive of Landsat 5, 7, and 8 surface reflectance data and a novel gap filling approach to create spatially continuous 30 m, 16-day composites of the normalized difference vegetation index (NDVI) from 1986 to 2016. In chapter two, I integrate this with other high resolution datasets and the MOD17 algorithm to create the first high resolution GPP and NPP datasets for CONUS. I demonstrate the applicability of these products for conservation and management, showing the improvements beyond currently available products. In chapter three, I utilize this dataset to evaluate the relationships between land ownership and terrestrial production

Integrating conservation costs into sea level rise adaptive conservation prioritization

Directory of Open Access Journals (Sweden)

Mingjian Zhu

2015-07-01

Full Text Available Biodiversity conservation requires strategic investment as resources for conservation are often limited. As sea level rises, it is important and necessary to consider both sea level rise and costs in conservation decision making. In this study, we consider costs of conservation in an integrated modeling process that incorporates a geomorphological model (SLAMM, species habitat models, and conservation prioritization (Zonation to identify conservation priorities in the face of landscape dynamics due to sea level rise in the Matanzas River basin of northeast Florida. Compared to conservation priorities that do not consider land costs in the analysis process, conservation priorities that consider costs in the planning process change significantly. The comparison demonstrates that some areas with high conservation values might be identified as lower priorities when integrating economic costs in the planning process and some areas with low conservation values might be identified as high priorities when considering costs in the planning process. This research could help coastal resources managers make informed decisions about where and how to allocate conservation resources more wisely to facilitate biodiversity adaptation to sea level rise.

Molecular dynamics in high electric fields

International Nuclear Information System (INIS)

Apostol, M.; Cune, L.C.

2016-01-01

Highlights: • New method for rotation molecular spectra in high electric fields. • Parametric resonances – new features in spectra. • New elementary excitations in polar solids from dipolar interaction (“dipolons”). • Discussion about a possible origin of the ferroelectricity from dipolar interactions. - Abstract: Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called “dipolons”); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.

Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation

DEFF Research Database (Denmark)

Weinert, Brian T; Wagner, Sebastian A; Horn, Heiko

2011-01-01

Posttranslational modification of proteins by acetylation and phosphorylation regulates most cellular processes in living organisms. Surprisingly, the evolutionary conservation of phosphorylated serine and threonine residues is only marginally higher than that of unmodified serines and threonines....... With high-resolution mass spectrometry, we identified 1981 lysine acetylation sites in the proteome of Drosophila melanogaster. We used data sets of experimentally identified acetylation and phosphorylation sites in Drosophila and humans to analyze the evolutionary conservation of these modification sites...... between flies and humans. Site-level conservation analysis revealed that acetylation sites are highly conserved, significantly more so than phosphorylation sites. Furthermore, comparison of lysine conservation in Drosophila and humans with that in nematodes and zebrafish revealed that acetylated lysines...

High-resolution finite-difference algorithms for conservation laws

International Nuclear Information System (INIS)

Towers, J.D.

1987-01-01

A new class of Total Variation Decreasing (TVD) schemes for 2-dimensional scalar conservation laws is constructed using either flux-limited or slope-limited numerical fluxes. The schemes are proven to have formal second-order accuracy in regions where neither u/sub x/ nor y/sub y/ vanishes. A new class of high-resolution large-time-step TVD schemes is constructed by adding flux-limited correction terms to the first-order accurate large-time-step version of the Engquist-Osher scheme. The use of the transport-collapse operator in place of the exact solution operator for the construction of difference schemes is studied. The production of spurious extrema by difference schemes is studied. A simple condition guaranteeing the nonproduction of spurious extrema is derived. A sufficient class of entropy inequalities for a conservation law with a flux having a single inflection point is presented. Finite-difference schemes satisfying a discrete version of each entropy inequality are only first-order accurate

High Molecular Weight Polybenzimidazole Membranes for High Temperature PEMFC

DEFF Research Database (Denmark)

Yang, Jingshuai; Cleemann, Lars Nilausen; Steenberg, T.

2014-01-01

High temperature operation of proton exchange membrane fuel cells under ambient pressure has been achieved by using phosphoric acid doped polybenzimidazole (PBI) membranes. To optimize the membrane and fuel cells, high performance polymers were synthesized of molecular weights from 30 to 94 kDa w...

Conservative Management for Stable High Ankle Injuries in Professional Football Players.

Science.gov (United States)

Knapik, Derrick M; Trem, Anthony; Sheehan, Joseph; Salata, Michael J; Voos, James E

High ankle "syndesmosis" injuries are common in American football players relative to the general population. At the professional level, syndesmotic sprains represent a challenging and unique injury lacking a standardized rehabilitation protocol during conservative management. PubMed, Biosis Preview, SPORTDiscus, PEDro, and EMBASE databases were searched using the terms syndesmotic injuries, American football, conservative management, and rehabilitation. Clinical review. Level 3. When compared with lateral ankle sprains, syndesmosis injuries result in significantly prolonged recovery times and games lost. For stable syndesmotic injuries, conservative management features a brief period of immobilization and protected weightbearing followed by progressive strengthening exercises and running, and athletes can expect to return to competition in 2 to 6 weeks. Further research investigating the efficacy of dry needling and blood flow restriction therapy is necessary to evaluate the benefit of these techniques in the rehabilitation process. Successful conservative management of stable syndesmotic injuries in professional American football athletes requires a thorough understanding of the anatomy, injury mechanisms, diagnosis, and rehabilitation strategies utilized in elite athletes.

Spatial overlap between environmental policy instruments and areas of high conservation value in forest.

Science.gov (United States)

Sverdrup-Thygeson, Anne; Søgaard, Gunnhild; Rusch, Graciela M; Barton, David N

2014-01-01

In order to safeguard biodiversity in forest we need to know how forest policy instruments work. Here we use a nationwide network of 9400 plots in productive forest to analyze to what extent large-scale policy instruments, individually and together, target forest of high conservation value in Norway. We studied both instruments working through direct regulation; Strict Protection and Landscape Protection, and instruments working through management planning and voluntary schemes of forest certification; Wilderness Area and Mountain Forest. As forest of high conservation value (HCV-forest) we considered the extent of 12 Biodiversity Habitats and the extent of Old-Age Forest. We found that 22% of productive forest area contained Biodiversity Habitats. More than 70% of this area was not covered by any large-scale instruments. Mountain Forest covered 23%, while Strict Protection and Wilderness both covered 5% of the Biodiversity Habitat area. A total of 9% of productive forest area contained Old-Age Forest, and the relative coverage of the four instruments was similar as for Biodiversity Habitats. For all instruments, except Landscape Protection, the targeted areas contained significantly higher proportions of HCV-forest than areas not targeted by these instruments. Areas targeted by Strict Protection had higher proportions of HCV-forest than areas targeted by other instruments, except for areas targeted by Wilderness Area which showed similar proportions of Biodiversity Habitats. There was a substantial amount of spatial overlap between the policy tools, but no incremental conservation effect of overlapping instruments in terms of contributing to higher percentages of targeted HCV-forest. Our results reveal that although the current policy mix has an above average representation of forest of high conservation value, the targeting efficiency in terms of area overlap is limited. There is a need to improve forest conservation and a potential to cover this need by better

Conserved water-mediated H-bonding dynamics of catalytic Asn ...

Indian Academy of Sciences (India)

Prakash

Extensive energy minimization and molecular dynamics simulation studies up to 2 ns ... Conserved water in molecular recognition; MD simulation; plant cysteine protease ..... Mustata G and Briggs J M 2004 Cluster analysis of water molecules.

Usherin expression is highly conserved in mouse and human tissues.

Science.gov (United States)

Pearsall, Nicole; Bhattacharya, Gautam; Wisecarver, Jim; Adams, Joe; Cosgrove, Dominic; Kimberling, William

2002-12-01

Usher syndrome is an autosomal recessive disease that results in varying degrees of hearing loss and retinitis pigmentosa. Three types of Usher syndrome (I, II, and III) have been identified clinically with Usher type II being the most common of the three types. Usher type II has been localized to three different chromosomes 1q41, 3p, and 5q, corresponding to Usher type 2A, 2B, and 2C respectively. Usherin is a basement membrane protein encoded by the USH2A gene. Expression of usherin has been localized in the basement membrane of several tissues, however it is not ubiquitous. Immunohistochemistry detected usherin in the following human tissues: retina, cochlea, small and large intestine, pancreas, bladder, prostate, esophagus, trachea, thymus, salivary glands, placenta, ovary, fallopian tube, uterus, and testis. Usherin was absent in many other tissues such as heart, lung, liver, kidney, and brain. This distribution is consistent with the usherin distribution seen in the mouse. Conservation of usherin is also seen at the nucleotide and amino acid level when comparing the mouse and human gene sequences. Evolutionary conservation of usherin expression at the molecular level and in tissues unaffected by Usher 2a supports the important structural and functional role this protein plays in the human. In addition, we believe that these results could lead to a diagnostic procedure for the detection of Usher syndrome and those who carry an USH2A mutation.

High-Order Entropy Stable Finite Difference Schemes for Nonlinear Conservation Laws: Finite Domains

Science.gov (United States)

Fisher, Travis C.; Carpenter, Mark H.

2013-01-01

Developing stable and robust high-order finite difference schemes requires mathematical formalism and appropriate methods of analysis. In this work, nonlinear entropy stability is used to derive provably stable high-order finite difference methods with formal boundary closures for conservation laws. Particular emphasis is placed on the entropy stability of the compressible Navier-Stokes equations. A newly derived entropy stable weighted essentially non-oscillatory finite difference method is used to simulate problems with shocks and a conservative, entropy stable, narrow-stencil finite difference approach is used to approximate viscous terms.

Molecular characterization and population structure study of cambuci: strategy for conservation and genetic improvement.

Science.gov (United States)

Santos, D N; Nunes, C F; Setotaw, T A; Pio, R; Pasqual, M; Cançado, G M A

2016-12-19

Cambuci (Campomanesia phaea) belongs to the Myrtaceae family and is native to the Atlantic Forest of Brazil. It has ecological and social appeal but is exposed to problems associated with environmental degradation and expansion of agricultural activities in the region. Comprehensive studies on this species are rare, making its conservation and genetic improvement difficult. Thus, it is important to develop research activities to understand the current situation of the species as well as to make recommendations for its conservation and use. This study was performed to characterize the cambuci accessions found in the germplasm bank of Coordenadoria de Assistência Técnica Integral using inter-simple sequence repeat markers, with the goal of understanding the plant's population structure. The results showed the existence of some level of genetic diversity among the cambuci accessions that could be exploited for the genetic improvement of the species. Principal coordinate analysis and discriminant analysis clustered the 80 accessions into three groups, whereas Bayesian model-based clustering analysis clustered them into two groups. The formation of two cluster groups and the high membership coefficients within the groups pointed out the importance of further collection to cover more areas and more genetic variability within the species. The study also showed the lack of conservation activities; therefore, more attention from the appropriate organizations is needed to plan and implement natural and ex situ conservation activities.

Evolutionary growth process of highly conserved sequences in vertebrate genomes.

Science.gov (United States)

Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

2012-08-01

Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

Molecular basis and regulation of OTULIN-LUBAC interaction

DEFF Research Database (Denmark)

Elliott, Paul R.; Al-Saoudi, Sofie Vincents; Marco-Casanova, Paola

2014-01-01

Ub. Now, we show that OTULIN binds via a conserved PUB-interacting motif (PIM) to the PUB domain of the LUBAC component HOIP. Crystal structures and nuclear magnetic resonance experiments reveal the molecular basis for the high-affinity interaction and explain why OTULIN binds the HOIP PUB domain...

High- and low-molecular-mass microbial surfactants.

Science.gov (United States)

Rosenberg, E; Ron, E Z

1999-08-01

Microorganisms synthesize a wide variety of high- and low-molecular-mass bioemulsifiers. The low-molecular-mass bioemulsifiers are generally glycolipids, such as trehalose lipids, sophorolipids and rhamnolipids, or lipopeptides, such as surfactin, gramicidin S and polymyxin. The high-molecular-mass bioemulsifiers are amphipathic polysaccharides, proteins, lipopolysaccharides, lipoproteins or complex mixtures of these biopolymers. The low-molecular-mass bioemulsifiers lower surface and interfacial tensions, whereas the higher-molecular-mass bioemulsifiers are more effective at stabilizing oil-in-water emulsions. Three natural roles for bioemulsifiers have been proposed: (i) increasing the surface area of hydrophobic water-insoluble growth substrates; (ii) increasing the bioavailability of hydrophobic substrates by increasing their apparent solubility or desorbing them from surfaces; (iii) regulating the attachment and detachment of microorganisms to and from surfaces. Bioemulsifiers have several important advantages over chemical surfactants, which should allow them to become prominent in industrial and environmental applications. The potential commercial applications of bioemulsifiers include bioremediation of oil-polluted soil and water, enhanced oil recovery, replacement of chlorinated solvents used in cleaning-up oil-contaminated pipes, vessels and machinery, use in the detergent industry, formulations of herbicides and pesticides and formation of stable oil-in-water emulsions for the food and cosmetic industries.

High temperature and high resolution uv photoelectron spectroscopy using supersonic molecular beams

International Nuclear Information System (INIS)

Wang, Lai-Sheng; Reutt-Robey, J.E.; Niu, B.; Lee, Y.T.; Shirley, D.A.

1989-07-01

A high temperature molecular beam source with electron bombardment heating has been built for high resolution photoelectron spectroscopic studies of high temperature species and clusters. This source has the advantages of: producing an intense, continuous, seeded molecular beam, eliminating the interference of the heating mechanism from the photoelectron measurement. Coupling the source with our hemispherical electron energy analyzer, we can obtain very high resolution HeIα (584 angstrom) photoelectron spectra of high temperature species. Vibrationally-resolved photoelectron spectra of PbSe, As 2 , As 4 , and ZnCl 2 are shown to demonstrate the performance of the new source. 25 refs., 8 figs., 1 tab

Constrained dansyl derivatives reveal bacterial specificity of highly conserved thymidylate synthases.

Science.gov (United States)

Calò, Sanuele; Tondi, Donatella; Ferrari, Stefania; Venturelli, Alberto; Ghelli, Stefano; Costi, Maria Paola

2008-03-25

The elucidation of the structural/functional specificities of highly conserved enzymes remains a challenging area of investigation, and enzymes involved in cellular replication are important targets for functional studies and drug discovery. Thymidylate synthase (TS, ThyA) governs the synthesis of thymidylate for use in DNA synthesis. The present study focused on Lactobacillus casei TS (LcTS) and Escherichia coli TS (EcTS), which exhibit 50 % sequence identity and strong folding similarity. We have successfully designed and validated a chemical model in which linear, but not constrained, dansyl derivatives specifically complement the LcTS active site. Conversely, chemically constrained dansyl derivatives showed up to 1000-fold improved affinity for EcTS relative to the inhibitory activity of linear derivatives. This study demonstrates that the accurate design of small ligands can uncover functional features of highly conserved enzymes.

Development of radiation-resisting high molecular-weight materials

International Nuclear Information System (INIS)

Nakagawa, Tsutomu

1976-01-01

The excellent radiation-resisting polyvinyl chloride developed at the opportunity of the research on the relationships between the protection of living body and the polymer-technological protection from radiation is reviewed. The report is divided into four main parts, namely 1) the change in the molecular arrangement of market-available, high molecular-weight materials by gamma-ray irradiation, 2) the protection of high molecular-weight materials from radiation, 3) the relationships between the biological radiation-protective substances and the change to radiation-resisting property of synthesized high molecular-weight substances, and 4) the development of the radiation-resisting high molecular-weight materials as metal-collecting agents. Attention is paid to the polyvinyl chloride having N-methyl-dithio-carbamate radical (PMD), synthesized by the author et. al., that has excellent radiation-resisting property. PMD has some possibility to form thiol- and amino-radicals necessary to protect living things from radiation. It is believed that the protection effects of N-methyl-dithio-carbamate radical are caused by the relatively stable S radical produced by the energy transfer. PMD film is suitable for the irradiation of foods, because it hardly changes the permeability of oxygen and carbon dioxide. PMD produces mercaptide or chelate. A new metal-collecting agent (PSDC) having reactivity with the metallic ions with radiation-resisting property was developed, which is derived from polyvinyl chloride and sodium N-methyl-N-carboxy-methyl-dithio-carbamate. (Iwakiri, K.)

Molecular evolution, intracellular organization, and the quinary structure of proteins.

OpenAIRE

McConkey, E H

1982-01-01

High-resolution two-dimensional polyacrylamide gel electrophoresis shows that at least half of 370 denatured polypeptides from hamster cells and human cells are indistinguishable in terms of isoelectric points and molecular weights. Molecular evolution may have been more conservative for this set of proteins than sequence studies on soluble proteins have implied. This may be a consequence of complexities of intracellular organization and the numerous macromolecular interactions in which most ...

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

Directory of Open Access Journals (Sweden)

Mingyuan Xu

2018-05-01

Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

"Toward High School Biology": Helping Middle School Students Understand Chemical Reactions and Conservation of Mass in Nonliving and Living Systems

Science.gov (United States)

Herrmann-Abell, Cari F.; Koppal, Mary; Roseman, Jo Ellen

2016-01-01

Modern biology has become increasingly molecular in nature, requiring students to understand basic chemical concepts. Studies show, however, that many students fail to grasp ideas about atom rearrangement and conservation during chemical reactions or the application of these ideas to biological systems. To help provide students with a better…

Molecular forensics in avian conservation: a DNA-based approach for identifying mammalian predators of ground-nesting birds and eggs.

Science.gov (United States)

Hopken, Matthew W; Orning, Elizabeth K; Young, Julie K; Piaggio, Antoinette J

2016-01-07

The greater sage-grouse (Centrocercus urophasianus) is a ground-nesting bird from the Northern Rocky Mountains and a species at risk of extinction in in multiple U.S. states and Canada. Herein we report results from a proof of concept that mitochondrial and nuclear DNAs from mammalian predator saliva could be non-invasively collected from depredated greater sage-grouse eggshells and carcasses and used for predator species identification. Molecular forensic approaches have been applied to identify predators from depredated remains as one strategy to better understand predator-prey dynamics and guide management strategies. This can aid conservation efforts by correctly identifying predators most likely to impact threatened and endangered species. DNA isolated from non-invasive samples around nesting sites (e.g. fecal or hair samples) is one method that can increase the success and accuracy of predator species identification when compared to relying on nest remains alone. Predator saliva DNA was collected from depredated eggshells and carcasses using swabs. We sequenced two partial fragments of two mitochondrial genes and obtained microsatellite genotypes using canid specific primers for species and individual identification, respectively. Using this multilocus approach we were able to identify predators, at least down to family, from 11 out of 14 nests (79%) and three out of seven carcasses (47%). Predators detected most frequently were canids (86%), while other taxa included rodents, a striped skunk, and cattle. We attempted to match the genotypes of individual coyotes obtained from eggshells and carcasses with those obtained from fecal samples and coyotes collected in the areas, but no genotype matches were found. Predation is a main cause of nest failure in ground-nesting birds and can impact reproduction and recruitment. To inform predator management for ground-nesting bird conservation, accurate identification of predator species is necessary. Considering

A new world monkey microsatellite (ap74) highly conserved in primates

International Nuclear Information System (INIS)

Oklander, Luciana Ines; Steinberg, Eliana Ruth; Dolores Mudry, Marta

2012-01-01

Given their great variability, microsatellites or STRS became the most commonly used genetic markers over the last 15 years. The analysis of these markers requires minimum quantities of DNA, allowing the use of noninvasive samples, such as feces or hair. We amplified the microsatellite ap74 in blood and hair samples in order to analyze the levels of genomic conservation among a wide range of primates including: lemur catta, alouatta caraya, ateles belzebuth, ateles chamek, pan troglodytes, papio sp., and Homo sapiens. in all cases we obtained amplification products that exhibited similar size both in monkeys and human (oscillating between 126 and 176 bp), except in the lemur where the detected fragment presented a size of approximately 1000 bp. the analysis of the nucleotide sequences permitted the evaluation of the molecular modifications experienced during the evolutionary process in primates.

Identification of a highly conserved valine-glycine-phenylalanine amino acid triplet required for HIV-1 Nef function

Directory of Open Access Journals (Sweden)

Meuwissen Pieter J

2012-04-01

Full Text Available Abstract Background The Nef protein of HIV facilitates virus replication and disease progression in infected patients. This role as pathogenesis factor depends on several genetically separable Nef functions that are mediated by interactions of highly conserved protein-protein interaction motifs with different host cell proteins. By studying the functionality of a series of nef alleles from clinical isolates, we identified a dysfunctional HIV group O Nef in which a highly conserved valine-glycine-phenylalanine (VGF region, which links a preceding acidic cluster with the following proline-rich motif into an amphipathic surface was deleted. In this study, we aimed to study the functional importance of this VGF region. Results The dysfunctional HIV group O8 nef allele was restored to the consensus sequence, and mutants of canonical (NL4.3, NA-7, SF2 and non-canonical (B2 and C1422 HIV-1 group M nef alleles were generated in which the amino acids of the VGF region were changed into alanines (VGF→AAA and tested for their capacity to interfere with surface receptor trafficking, signal transduction and enhancement of viral replication and infectivity. We found the VGF motif, and each individual amino acid of this motif, to be critical for downregulation of MHC-I and CXCR4. Moreover, Nef’s association with the cellular p21-activated kinase 2 (PAK2, the resulting deregulation of cofilin and inhibition of host cell actin remodeling, and targeting of Lck kinase to the trans-golgi-network (TGN were affected as well. Of particular interest, VGF integrity was essential for Nef-mediated enhancement of HIV virion infectivity and HIV replication in peripheral blood lymphocytes. For targeting of Lck kinase to the TGN and viral infectivity, especially the phenylalanine of the triplet was essential. At the molecular level, the VGF motif was required for the physical interaction of the adjacent proline-rich motif with Hck. Conclusion Based on these findings, we

Molecular sexing of threatened Gyps vultures: an important strategy for conservation breeding and ecological studies.

Science.gov (United States)

Ghorpade, Prabhakar B; Gupta, Praveen K; Prakash, Vibhu; Cuthbert, Richard J; Kulkarni, Mandar; Prakash, Nikita; Das, Asit; Sharma, Anil K; Saini, Mohini

2012-12-01

During the last two decades populations of three resident species of Gyps vulture have declined dramatically and are now threatened with extinction in South Asia. Sex identification of vultures is of key importance for the purpose of conservation breeding as it is desirable to have an equal sex ratio in these monogamous species which are housed together in large colony aviaries. Because vultures are monomorphic, with no differences in external morphology or plumage colour between the sexes, other methods are required for sex identification. Molecular methods for sex identification in birds rely on allelic length or nucleotide sequence discrimination of the chromohelicase-DNA binding (CHD) gene located on male and female chromosomes ZZ and ZW, respectively. We characterized the partial sequences of CHD alleles from Gyps indicus, Gyps bengalensis, Gyps himalayensis and Aegypius monachus and analysed the applicability of five molecular methods of sex identification of 46 individual vultures including 26 known-sex G. bengalensis and G. indicus. The results revealed that W-specific PCR in combination with ZW-common PCR is a quick, accurate and simple method, and is ideal for sex identification of vultures. The method is also suitable to augment ecological studies for identifying sex of these endangered birds during necropsy examinations especially when gonads are not apparent, possibly due to regression during non-breeding seasons.

Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants.

Science.gov (United States)

Li, Xinguo; Wu, Harry X; Southerton, Simon G

2010-06-21

Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution.

A conserved aromatic lock for the tryptophan rotameric switch in TM-VI of seven-transmembrane receptors

DEFF Research Database (Denmark)

Holst, Birgitte; Nygaard, Rie; Hansen, Louise Valentin

2010-01-01

simulations in rhodopsin demonstrated that rotation around the chi1 torsion angle of Trp-VI:13 brings its side chain close to the equally highly conserved Phe-V:13 (Phe-5.47) in TM-V. In the ghrelin receptor, engineering of high affinity metal-ion sites between these positions confirmed their close spatial...... degree as observed in the constructs where Trp-VI:13 itself was mutated, but again without affecting agonist potency. In a proposed active receptor conformation generated by molecular simulations, where the extracellular segment of TM-VI is tilted inwards in the main ligand-binding pocket, Trp-VI:13......The conserved tryptophan in position 13 of TM-VI (Trp-VI:13 or Trp-6.48) of the CWXP motif located at the bottom of the main ligand-binding pocket in TM-VI is believed to function as a rotameric microswitch in the activation process of seven-transmembrane (7TM) receptors. Molecular dynamics...

Molecular gas in dusty high-redshift galaxies

Science.gov (United States)

Sharon, Chelsea Electra

2013-12-01

We present high-resolution observations of carbon monoxide (CO) emission lines for three high-redshift galaxies in order to determine their molecular gas and star formation properties. These galaxies (SMM J14011+0252, SMM J00266+1708, and SDSS J0901+1814) have large infrared luminosities, which imply high dust enshrouded star formation rates and substantial molecular gas masses. We observed these sources using the Robert C. Byrd Green Bank Telescope, the Karl G. Jansky Very Large Array, the Plateau de Bure Interferometer, and the Submillimeter Array in order to obtain measurements of multiple CO spectral lines, allowing us to determine the physical conditions of the molecular gas. Our high resolution and multi-line CO mapping of SMM J00266+1708 reveals that it is a pair of merging galaxies, whose two components have different gas excitation conditions and different gas kinematics. For SMM J14011+0252 (J14011), we find a near-unity CO(3--2)/CO(1--0) intensity ratio, consistent with a single phase (i.e., a single temperature and density) of molecular gas and different from the average population value for dusty galaxies selected at submillimeter wavelengths. Our radiative transfer modeling (using the large velocity gradient approximation) indicates that converting the CO line luminosity to molecular gas mass requires a Galactic (disk-like) scale factor rather than the typical conversion factor assumed for starbursts. Despite this choice of conversion factor, J14011 falls in the same region of star formation rate surface density and gas mass surface density (the Schmidt-Kennicutt relation) as other starburst galaxies. SDSS J0901+1814 (J0901) was initially selected as a star-forming galaxy at ultraviolet wavelengths, but also has a large infrared luminosity. We use the magnification provided by the strong gravitational lensing affecting this system to examine the spatial variation of the CO excitation within J0901. We find that the CO(3--2)/CO(1--0) line ratio is

Telomeric expression sites are highly conserved in Trypanosoma brucei.

Directory of Open Access Journals (Sweden)

Christiane Hertz-Fowler

Full Text Available Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs. The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology.

Sintering of ultra high molecular weight polyethylene

Indian Academy of Sciences (India)

Abstract. Ultra high molecular weight polyethylene (UHMWPE) is a high performance polymer having low coefficient of friction, good abrasion resistance, good chemical ... In this study, we report our results on compaction and sintering behaviour of two grades of UHMWPE with reference to the powder morphology, sintering ...

Technical evaluation on high aging, and performance conditions on long-term conservation program

International Nuclear Information System (INIS)

Yamashita, Atsushi

2001-01-01

In order to secure safety and safe operation of power plants, in every nuclear power plants, conservation actions based on preventive conservation are performed. They contain operative condition monitoring, patrolling inspection, and periodical tests on important systems and apparatus by operators under plant operation and condition monitoring by maintenance workers, and so on, and when finding out their abnormal conditions, their detailed survey is performed to adopt adequate countermeasures such as recovery, exchange, and so on. And, to equipments for nuclear power generation periodical conditions were obliged by legal examinations and by independent inspections. As a result of these conservation actions, even on a plant elapsed about 30 years since beginning of its operation it was thought that the plant was aged with elapsing time even if not recognizing any indication on its aged deterioration at that time. Therefore, for its concrete countermeasure, by supposing long-term operation of a plant with longer operation history, some technical evaluation on aged phenomena were carried out, to investigate on reflection of the obtained results to present conservation actions. Here were described on efforts on the high aging countermeasures, and performing conditions of long-term conservation in the Tsuruga Unit No. 1 Nuclear Power Station. (G.K.)

Molecular dissection of a contiguous gene syndrome: Frequent submicroscopic deletions, evolutionarily conserved sequences, and a hypomethylated island in the Miller-Dieker chromosome region

International Nuclear Information System (INIS)

Ledbetter, D.H.; Ledbetter, S.A.; vanTuinen, P.

1989-01-01

The Miller-Dieker syndrome (MDS), composed of characteristic facial abnormalities and a severe neuronal migration disorder affecting the cerebral cortex, is caused by visible or submicroscopic deletions of chromosome band 17p13. Twelve anonymous DNA markers were tested against a panel of somatic cell hybrids containing 17p deletions from seven MDS patients. All patients, including three with normal karyotypes, are deleted for a variable set of 5-12 markers. Two highly polymorphic VNTR (variable number of tandem repeats) probes, YNZ22 and YNH37, are codeleted in all patients tested and make molecular diagnosis for this disorder feasible. By pulsed-field gel electrophoresis, YNZ22 and YNH37 were shown to be within 30 kilobases (kb) of each other. Cosmid clones containing both VNTR sequences were identified, and restriction mapping showed them to be 100 kb were completely deleted in all patients, providing a minimum estimate of the size of the MDS critical region. A hypomethylated island and evolutionarily conserved sequences were identified within this 100-kb region, indications of the presence of one or more expressed sequences potentially involved in the pathophysiology of this disorder. The conserved sequences were mapped to mouse chromosome 11 by using mouse-rat somatic cell hybrids, extending the remarkable homology between human chromosome 17 and mouse chromosome 11 by 30 centimorgans, into the 17p telomere region

Prospects for Parity Non-conservation Experiments with Highly Charged Heavy Ions

OpenAIRE

Maul, M.; Schäfer, A.; Greiner, W.; Indelicato, P.

1996-01-01

We discuss the prospects for parity non-conservation experiments with highly charged heavy ions. Energy levels and parity mixing for heavy ions with two to five electrons are calculated. We investigate two-photon-transitions and the possibility to observe interference effects between weak-matrix elements and Stark matrix elements for periodic electric field configurations.

Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi.

Science.gov (United States)

Subramanian, Sankar; Huynen, Leon; Millar, Craig D; Lambert, David M

2010-12-15

Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.

Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi

Directory of Open Access Journals (Sweden)

Huynen Leon

2010-12-01

Full Text Available Abstract Background Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. Results Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. Conclusions The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.

Multispecies genetic objectives in spatial conservation planning.

Science.gov (United States)

Nielsen, Erica S; Beger, Maria; Henriques, Romina; Selkoe, Kimberly A; von der Heyden, Sophie

2017-08-01

Growing threats to biodiversity and global alteration of habitats and species distributions make it increasingly necessary to consider evolutionary patterns in conservation decision making. Yet, there is no clear-cut guidance on how genetic features can be incorporated into conservation-planning processes, despite multiple molecular markers and several genetic metrics for each marker type to choose from. Genetic patterns differ between species, but the potential tradeoffs among genetic objectives for multiple species in conservation planning are currently understudied. We compared spatial conservation prioritizations derived from 2 metrics of genetic diversity (nucleotide and haplotype diversity) and 2 metrics of genetic isolation (private haplotypes and local genetic differentiation) in mitochondrial DNA of 5 marine species. We compared outcomes of conservation plans based only on habitat representation with plans based on genetic data and habitat representation. Fewer priority areas were selected for conservation plans based solely on habitat representation than on plans that included habitat and genetic data. All 4 genetic metrics selected approximately similar conservation-priority areas, which is likely a result of prioritizing genetic patterns across a genetically diverse array of species. Largely, our results suggest that multispecies genetic conservation objectives are vital to creating protected-area networks that appropriately preserve community-level evolutionary patterns. © 2016 Society for Conservation Biology.

Adaptation to high salt concentrations in halotolerant/ halophilic fungi: a molecular perspective

Directory of Open Access Journals (Sweden)

Ana ePlemenitas

2014-05-01

Full Text Available Molecular studies of salt tolerance of eukaryotic microorganisms have until recently been limited to the baker’s yeast Saccharomyces cerevisiae and a few other moderately halotolerant yeast. Discovery of the extremely halotolerant and adaptable fungus Hortaea werneckii and the obligate halophile Wallemia ichthyophaga introduced two new model organisms into studies on the mechanisms of salt tolerance in eukaryotes. H. werneckii is unique in its adaptability to fluctuations in salt concentrations, as it can grow without NaCl as well as in the presence of up to 5 M NaCl. On the other hand, W. ichthyophaga requires at least 1.5 M NaCl for growth, but also grows in up to 5 M NaCl. Our studies have revealed the novel and intricate molecular mechanisms used by these fungi to combat high salt concentrations, which differ in many aspects between the extremely halotolerant H. werneckii and the halophilic W. ichthyophaga. Specifically, the high osmolarity glycerol signalling pathway that is important for sensing and responding to increased salt concentrations is here compared between H. werneckii and W. ichthyophaga. In both of these fungi, the key signalling components are conserved, but there are structural and regulation differences between these pathways in H. werneckii and W. ichthyophaga. We also address differences that have been revealed from analysis of their newly sequenced genomes. The most striking characteristics associated with H. werneckii are the large genetic redundancy, the expansion of genes encoding metal cation transporters, and a relatively recent whole genome duplication. In contrast, the genome of W. ichthyophaga is very compact, as only 4,884 protein-coding genes are predicted, which cover almost three quarters of the sequence. Importantly, there has been a significant increase in their hydrophobins, cell-wall proteins that have multiple cellular functions.

Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

Directory of Open Access Journals (Sweden)

Ahmad A. Malik

2017-05-01

Full Text Available Dehydrins, a large family of abiotic stress proteins, are defined by the presence of a mostly conserved motif known as the K-segment, and may also contain two other conserved motifs known as the Y-segment and S-segment. Using the dehydrin literature, we developed a sequence motif definition of the K-segment, which we used to create a large dataset of dehydrin sequences by searching the Pfam00257 dehydrin dataset and the Phytozome 10 sequences of vascular plants. A comprehensive analysis of these sequences reveals that lysine residues are highly conserved in the K-segment, while the amino acid type is often conserved at other positions. Despite the Y-segment name, the central tyrosine is somewhat conserved, but can be substituted with two other small aromatic amino acids (phenylalanine or histidine. The S-segment contains a series of serine residues, but in some proteins is also preceded by a conserved LHR sequence. In many dehydrins containing all three of these motifs the S-segment is linked to the K-segment by a GXGGRRKK motif (where X can be any amino acid, suggesting a functional linkage between these two motifs. An analysis of the sequences shows that the dehydrin architecture and several biochemical properties (isoelectric point, molecular mass, and hydrophobicity score are dependent on each other, and that some dehydrin architectures are overexpressed during certain abiotic stress, suggesting that they may be optimized for a specific abiotic stress while others are involved in all forms of dehydration stress (drought, cold, and salinity.

MXene molecular sieving membranes for highly efficient gas separation.

Science.gov (United States)

Ding, Li; Wei, Yanying; Li, Libo; Zhang, Tao; Wang, Haihui; Xue, Jian; Ding, Liang-Xin; Wang, Suqing; Caro, Jürgen; Gogotsi, Yury

2018-01-11

Molecular sieving membranes with sufficient and uniform nanochannels that break the permeability-selectivity trade-off are desirable for energy-efficient gas separation, and the arising two-dimensional (2D) materials provide new routes for membrane development. However, for 2D lamellar membranes, disordered interlayer nanochannels for mass transport are usually formed between randomly stacked neighboring nanosheets, which is obstructive for highly efficient separation. Therefore, manufacturing lamellar membranes with highly ordered nanochannel structures for fast and precise molecular sieving is still challenging. Here, we report on lamellar stacked MXene membranes with aligned and regular subnanometer channels, taking advantage of the abundant surface-terminating groups on the MXene nanosheets, which exhibit excellent gas separation performance with H 2 permeability >2200 Barrer and H 2 /CO 2 selectivity >160, superior to the state-of-the-art membranes. The results of molecular dynamics simulations quantitatively support the experiments, confirming the subnanometer interlayer spacing between the neighboring MXene nanosheets as molecular sieving channels for gas separation.

Swertia chirayta, a Threatened High-Value Medicinal Herb: Microhabitats and Conservation Challenges in Sikkim Himalaya, India

Directory of Open Access Journals (Sweden)

Bharat Kumar Pradhan

2015-11-01

Full Text Available Assessing the impact of threats, identifying favorable growing conditions, and predicting future population scenarios are vital for the conservation and management of threatened species. This study investigated the availability, microhabitat characteristics, threat status, and community associations of Swertia chirayta, a highly threatened Himalayan medicinal herb, in 22 populations in Sikkim, India, using the vertical belt transect method. Of the 14 microhabitats identified, open grassy slope emerged as the most favorable and wet grassy slope as the least favorable for S. chirayta. The species was dominant in 8 of the 10 major plant communities identified. Among 9 major types of disturbance identified, human movement and collection of non-timber forest products appeared as the biggest threats to S. chirayta. Disturbances significantly affected the availability of the species. S. chirayta, though under high anthropogenic threat, maintains high microhabitat pliability, which is vital for its conservation and management, provided immediate conservation measures are taken.

Western blotting of high and low molecular weight proteins using heat.

Science.gov (United States)

Kurien, Biji T; Scofield, R Hal

2015-01-01

A method for the electrophoretic transfer of high and low molecular weight proteins to nitrocellulose membranes following sodium dodecyl sulfate (SDS) polyacrylamide gel is described here. The transfer was performed with heated (70-75 °C) normal transfer buffer from which methanol had been omitted. Complete transfer of high and low molecular weight antigens (molecular weight protein standards, a purified protein, and proteins from a human tissue extract) could be carried out in 10 min for a 7 % (0.75 mm) SDS polyacrylamide gel. For 10 and 12.5 % gels (0.75 mm) the corresponding time was 15 min. A complete transfer could be carried out in 20 min for 7, 10, and 12.5 % gels (1.5 mm gels). The permeability of the gel is increased by heat, such that the proteins trapped in the polyacrylamide gel matrix can be easily transferred to the membrane. The heat mediated transfer method was compared with a conventional transfer protocol, under similar conditions. The conventional method transferred minimal low molecular weight proteins while retaining most of the high molecular weight proteins in the gel. In summary, this procedure is particularly useful for the transfer of high molecular weight proteins, very rapid, and avoids the use of methanol.

Clinical and molecular features of high-grade osteosarcoma

NARCIS (Netherlands)

Anninga, Jakob Klaas

2013-01-01

It can be concluded from this thesis that high-grade osteosarcoma is at clinical, pathological and molecular level a heterogeneous disease. To treat high-grade osteosarcoma, neo-adjuvant chemotherapy should be combined with radical surgery, irrespective the localization. There are only 4 effective

Towards high-throughput molecular detection of Plasmodium: new approaches and molecular markers

Directory of Open Access Journals (Sweden)

Rogier Christophe

2009-04-01

Full Text Available Abstract Background Several strategies are currently deployed in many countries in the tropics to strengthen malaria control toward malaria elimination. To measure the impact of any intervention, there is a need to detect malaria properly. Mostly, decisions still rely on microscopy diagnosis. But sensitive diagnosis tools enabling to deal with a large number of samples are needed. The molecular detection approach offers a much higher sensitivity, and the flexibility to be automated and upgraded. Methods Two new molecular methods were developed: dot18S, a Plasmodium-specific nested PCR based on the 18S rRNA gene followed by dot-blot detection of species by using species-specific probes and CYTB, a Plasmodium-specific nested PCR based on cytochrome b gene followed by species detection using SNP analysis. The results were compared to those obtained with microscopic examination and the "standard" 18S rRNA gene based nested PCR using species specific primers. 337 samples were diagnosed. Results Compared to the microscopy the three molecular methods were more sensitive, greatly increasing the estimated prevalence of Plasmodium infection, including P. malariae and P. ovale. A high rate of mixed infections was uncovered with about one third of the villagers infected with more than one malaria parasite species. Dot18S and CYTB sensitivity outranged the "standard" nested PCR method, CYTB being the most sensitive. As a consequence, compared to the "standard" nested PCR method for the detection of Plasmodium spp., the sensitivity of dot18S and CYTB was respectively 95.3% and 97.3%. Consistent detection of Plasmodium spp. by the three molecular methods was obtained for 83% of tested isolates. Contradictory results were mostly related to detection of Plasmodium malariae and Plasmodium ovale in mixed infections, due to an "all-or-none" detection effect at low-level parasitaemia. Conclusion A large reservoir of asymptomatic infections was uncovered using the

Molecular Characterization of a Catalase from Hydra vulgaris

Science.gov (United States)

Dash, Bhagirathi; Phillips, Timothy D.

2012-01-01

Catalase, an antioxidant and hydroperoxidase enzyme protects the cellular environment from harmful effects of hydrogen peroxide by facilitating its degradation to oxygen and water. Molecular information on a cnidarian catalase and/or peroxidase is, however, limited. In this work an apparent full length cDNA sequence coding for a catalase (HvCatalase) was isolated from Hydra vulgaris using 3’- and 5’- (RLM) RACE approaches. The 1859 bp HvCatalase cDNA included an open reading frame of 1518 bp encoding a putative protein of 505 amino acids with a predicted molecular mass of 57.44 kDa. The deduced amino acid sequence of HvCatalase contained several highly conserved motifs including the heme-ligand signature sequence RLFSYGDTH and the active site signature FXRERIPERVVHAKGXGA. A comparative analysis showed the presence of conserved catalytic amino acids [His(71), Asn(145), and Tyr(354)] in HvCatalase as well. Homology modeling indicated the presence of the conserved features of mammalian catalase fold. Hydrae exposed to thermal, starvation, metal and oxidative stress responded by regulating its catalase mRNA transcription. These results indicated that the HvCatalase gene is involved in the cellular stress response and (anti)oxidative processes triggered by stressor and contaminant exposure. PMID:22521743

Geometric and electronic structures of molecular ions from high energy collisions

International Nuclear Information System (INIS)

Groeneveld, K.O.

1983-01-01

This chapter examines the characteristics of heavy ion collision and of beam foil spectroscopy. It discusses the kinematic consequences of the high energies and presents results from ''Coulomb explosion'' and structure determination of molecular ions. It demonstrates that studies of molecular ions with accelerators can provide electronic and geometric structure information of molecules or molecular ions and points out that the understanding of the microscopic processes at such high energies is incomplete and needs further experimental and theoretical efforts

High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae

DEFF Research Database (Denmark)

Rukov, Jakob Lewin; Irimia, Manuel; Mørk, Søren

2007-01-01

Alternative splicing (AS) is an important contributor to proteome diversity and is regarded as an explanatory factor for the relatively low number of human genes compared with less complex animals. To assess the evolutionary conservation of AS and its developmental regulation, we have investigated...... the qualitative and quantitative expression of 21 orthologous alternative splice events through the development of 2 nematode species separated by 85-110 Myr of evolutionary time. We demonstrate that most of these alternative splice events present in Caenorhabditis elegans are conserved in Caenorhabditis briggsae....... Moreover, we find that relative isoform expression levels vary significantly during development for 78% of the AS events and that this quantitative variation is highly conserved between the 2 species. Our results suggest that AS is generally tightly regulated through development and that the regulatory...

Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

Energy Technology Data Exchange (ETDEWEB)

Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

2014-10-15

The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

High Molecular Weight Melanoidins from Coffee Brew

NARCIS (Netherlands)

Bekedam, E.K.; Schols, H.A.; Boekel, van T.; Smit, G.

2006-01-01

The composition of high molecular weight (HMw) coffee melanoidin populations, obtained after ethanol precipitation, was studied. The specific extinction coefficient (Kmix) at 280, 325, 405 nm, sugar composition, phenolic group content, nitrogen content, amino acid composition, and non-protein

Entropy Viscosity Method for High-Order Approximations of Conservation Laws

KAUST Repository

Guermond, J. L.

2010-09-17

A stabilization technique for conservation laws is presented. It introduces in the governing equations a nonlinear dissipation function of the residual of the associated entropy equation and bounded from above by a first order viscous term. Different two-dimensional test cases are simulated - a 2D Burgers problem, the "KPP rotating wave" and the Euler system - using high order methods: spectral elements or Fourier expansions. Details on the tuning of the parameters controlling the entropy viscosity are given. © 2011 Springer.

Entropy Viscosity Method for High-Order Approximations of Conservation Laws

KAUST Repository

Guermond, J. L.; Pasquetti, R.

2010-01-01

A stabilization technique for conservation laws is presented. It introduces in the governing equations a nonlinear dissipation function of the residual of the associated entropy equation and bounded from above by a first order viscous term. Different two-dimensional test cases are simulated - a 2D Burgers problem, the "KPP rotating wave" and the Euler system - using high order methods: spectral elements or Fourier expansions. Details on the tuning of the parameters controlling the entropy viscosity are given. © 2011 Springer.

Molecular modeling: An open invitation for applied mathematics

Science.gov (United States)

Mezey, Paul G.

2013-10-01

Molecular modeling methods provide a very wide range of challenges for innovative mathematical and computational techniques, where often high dimensionality, large sets of data, and complicated interrelations imply a multitude of iterative approximations. The physical and chemical basis of these methodologies involves quantum mechanics with several non-intuitive aspects, where classical interpretation and classical analogies are often misleading or outright wrong. Hence, instead of the everyday, common sense approaches which work so well in engineering, in molecular modeling one often needs to rely on rather abstract mathematical constraints and conditions, again emphasizing the high level of reliance on applied mathematics. Yet, the interdisciplinary aspects of the field of molecular modeling also generates some inertia and perhaps too conservative reliance on tried and tested methodologies, that is at least partially caused by the less than up-to-date involvement in the newest developments in applied mathematics. It is expected that as more applied mathematicians take up the challenge of employing the latest advances of their field in molecular modeling, important breakthroughs may follow. In this presentation some of the current challenges of molecular modeling are discussed.

Genomic resources for the conservation and management of the harpy eagle (Harpia harpyja, Falconiformes, Accipitridae

Directory of Open Access Journals (Sweden)

Aureo Banhos

2008-01-01

Full Text Available We report the characterization and optimization of 45 heterologous microsatellite loci, and the development of a new set of molecular sex markers for the conservation and management of the Neotropical harpy eagle (Harpia harpyja L. 1758. Of the 45 microsatellites tested, 24 were polymorphic, six monomorphic, 10 uncharacterizable due to multiple bands and five did not amplify. The observed gene diversity of the analyzed sample of H. harpyja was low and similar to that of other threatened Falconiformes. While a high proportion of the microsatellite markers were highly variable, individuals of H. harpyja could be differentiated by a joint analysis of just three (p = 2.79 x 10-4 or four markers (p = 2.89 x 10-5. Paternity could be rejected with 95.23% and 97.83% probabilities using the same three and four markers, respectively. The sex determination markers easily and consistently differentiated males from females even with highly degraded DNA extracted from naturally shed feathers. The markers reported in this study potentially provide an excellent set of molecular tools for the conservation and management of wild and captive H. harpyja and they may also prove useful for the enigmatic Neotropical crested eagle (Morphnus guianensis Daudin 1800.

Radiation polymerization of acrylamide with super-high molecular weight in inverse emulsion

International Nuclear Information System (INIS)

Ye Qiang; Ge Xuewu; Xu Xiangling; Zhang Zhicheng

1998-01-01

The inverse emulsion polymerization of acrylamide has been studied with γ-ray initiation. Polyacrylamide with super high molecular weight over ten million (11 x 10 6 ), which is very important in application as flocculant, is obtained. In this work, some methods are taken to enhance the molecular weight as follows: (1) In order to prepare soluble polyacrylamide with super high molecular weight, the better conditions are: the emulsifier content is about 2% and the monomer concentration is about 20%∼24% in the composition of monomer emulsion, and the absorbed dose is about 500∼600 Gy. (2) Initiating with high dose rate and polymerizing with low dose rate can not only enhance the molecular weight of product, but also curtail the polymerizing time. (3) Stopping radiation when the conversion gets to about 10% and post-polymerizing outside the radiation source until the conversion gets to 82% can obtain polyacrylamide with super high molecular weight, and shorten the irradiation time as well

Genetic approaches refine ex situ lowland tapir (Tapirus terrestris) conservation.

Science.gov (United States)

Gonçalves da Silva, Anders; Lalonde, Danielle R; Quse, Viviana; Shoemaker, Alan; Russello, Michael A

2010-01-01

Ex situ conservation management remains an important tool in the face of continued habitat loss and global environmental change. Here, we use microsatellite marker variation to evaluate conventional assumptions of pedigree-based ex situ population management and directly inform a captive lowland tapir breeding program within a range country. We found relatively high levels of genetic variation (N(total) = 41; mean H(E) = 0.67 across 10 variable loci) and little evidence for relatedness among founder individuals (N(founders) = 10; mean relatedness = -0.05). Seven of 29 putative parent-offspring relationships were excluded by parentage analysis based on allele sharing, and we identified 2 individuals of high genetic value to the population (mk highly related led to overestimates of mean kinship and inbreeding, and underestimates of gene diversity, when compared with values found when genetic markers were used to inform kinship. We discuss our results within the context of recent studies that have assessed the utility of neutral molecular markers for ex situ conservation.

Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays

Science.gov (United States)

Brand, Luise H.; Fischer, Nina M.; Harter, Klaus; Kohlbacher, Oliver; Wanke, Dierk

2013-01-01

WRKY transcription factors constitute a large protein family in plants that is involved in the regulation of developmental processes and responses to biotic or abiotic stimuli. The question arises how stimulus-specific responses are mediated given that the highly conserved WRKY DNA-binding domain (DBD) exclusively recognizes the ‘TTGACY’ W-box consensus. We speculated that the W-box consensus might be more degenerate and yet undetected differences in the W-box consensus of WRKYs of different evolutionary descent exist. The phylogenetic analysis of WRKY DBDs suggests that they evolved from an ancestral group IIc-like WRKY early in the eukaryote lineage. A direct descent of group IIc WRKYs supports a monophyletic origin of all other group II and III WRKYs from group I by loss of an N-terminal DBD. Group I WRKYs are of paraphyletic descent and evolved multiple times independently. By homology modeling, molecular dynamics simulations and in vitro DNA–protein interaction-enzyme-linked immunosorbent assay with AtWRKY50 (IIc), AtWRKY33 (I) and AtWRKY11 (IId) DBDs, we revealed differences in DNA-binding specificities. Our data imply that other components are essentially required besides the W-box-specific binding to DNA to facilitate a stimulus-specific WRKY function. PMID:23975197

Habitat Re-Creation (Ecological Restoration) as a Strategy for Conserving Insect Communities in Highly Fragmented Landscapes.

Science.gov (United States)

Shuey, John A

2013-12-05

Because of their vast diversity, measured by both numbers of species as well as life history traits, insects defy comprehensive conservation planning. Thus, almost all insect conservation efforts target individual species. However, serious insect conservation requires goals that are set at the faunal level and conservation success requires strategies that conserve intact communities. This task is complicated in agricultural landscapes by high levels of habitat fragmentation and isolation. In many regions, once widespread insect communities are now functionally trapped on islands of ecosystem remnants and subject to a variety of stressors associated with isolation, small population sizes and artificial population fragmentation. In fragmented landscapes ecological restoration can be an effective strategy for reducing localized insect extinction rates, but insects are seldom included in restoration design criteria. It is possible to incorporate a few simple conservation criteria into restoration designs that enhance impacts to entire insect communities. Restoration can be used as a strategy to address fragmentation threats to isolated insect communities if insect communities are incorporated at the onset of restoration planning. Fully incorporating insect communities into restoration designs may increase the cost of restoration two- to three-fold, but the benefits to biodiversity conservation and the ecological services provided by intact insect communities justify the cost.

In situ conservation and landscape genetics in forest species

Directory of Open Access Journals (Sweden)

Martín L.M.

2012-03-01

Full Text Available Conservation of forest genetic resources is essential for sustaining the environmental and productive values of forests. One of the environmental values is the conservation of the diversity that is assessed through the amount of genetic diversity stored by forests, their structure and dynamics. The current need for forest conservation and management has driven a rapid expansion of landscape genetics discipline that combines tools from molecular genetics, landscape ecology and spatial statistics and is decisive for improving not only ecological knowledge but also for properly managing population genetic resources. The objective of this study is to show the way to establish the safeguard of genetic diversity through this approach using the results obtained in sweet chestnut (Castanea sativa Mill. that has provided a better understanding on the species genetic resources. In this respect, we will show how the information provided by different types of molecular markers (genomic and genic offer more accurate indication on the distribution of the genetic diversity among and within populations assuming different evolutionary drivers.

Impact of local empowerment on conservation practices in a highly developed country

OpenAIRE

Engen, Sigrid; Hausner, Vera Helene

2017-01-01

Source at http://dx.doi.org/10.1111/conl.12369 Community-based conservation, where local decision makers are responsible for balancing conservation and development, is often preferred to exclusion- ary conservation that prioritizes use-limitation through strict regulation. Un- raveling the evidence for conservation impact of different governance regimes is challenging. Focusing on conservation practices before and after a reform can provide an early indication of behaviora...

Development and evaluation of a bioinformatics approach for designing molecular assays for viral detection.

Directory of Open Access Journals (Sweden)

Pierre H H Schneeberger

Full Text Available Viruses belonging to the Flaviviridae and Bunyaviridae families show considerable genetic diversity. However, this diversity is not necessarily taken into account when developing diagnostic assays, which are often based on the pairwise alignment of a limited number of sequences. Our objective was to develop and evaluate a bioinformatics workflow addressing two recurrent issues of molecular assay design: (i the high intraspecies genetic diversity in viruses and (ii the potential for cross-reactivity with close relatives.The workflow developed herein was based on two consecutive BLASTn steps; the first was utilized to select highly conserved regions among the viral taxon of interest, and the second was employed to assess the degree of similarity of these highly-conserved regions to close relatives. Subsequently, the workflow was tested on a set of eight viral species, including various strains from the Flaviviridae and Bunyaviridae families.The genetic diversity ranges from as low as 0.45% variable sites over the complete genome of the Japanese encephalitis virus to more than 16% of variable sites on segment L of the Crimean-Congo hemorrhagic fever virus. Our proposed bioinformatics workflow allowed the selection-based on computing scores-of the best target for a diagnostic molecular assay for the eight viral species investigated.Our bioinformatics workflow allowed rapid selection of highly conserved and specific genomic fragments among the investigated viruses, while considering up to several hundred complete genomic sequences. The pertinence of this workflow will increase in parallel to the number of sequences made publicly available. We hypothesize that our workflow might be utilized to select diagnostic molecular markers for higher organisms with more complex genomes, provided the sequences are made available.

78 FR 51463 - Energy Conservation Program: Energy Conservation Standards for Metal Halide Lamp Fixtures

Science.gov (United States)

2013-08-20

... merging the metal halide lamp fixture and the high-intensity discharge (HID) lamp rulemakings. This NOPR... Conservation Program: Energy Conservation Standards for Metal Halide Lamp Fixtures; Proposed Rule #0;#0;Federal...: Energy Conservation Standards for Metal Halide Lamp Fixtures AGENCY: Office of Energy Efficiency and...

Some AFLP amplicons are highly conserved DNA sequences mapping to the same linkage groups in two F2 populations of carrot

Directory of Open Access Journals (Sweden)

Santos Carlos A.F.

2002-01-01

Full Text Available Amplified fragment length polymorphism (AFLP is a fast and reliable tool to generate a large number of DNA markers. In two unrelated F2 populations of carrot (Daucus carota L., Brasilia x HCM and B493 x QAL (wild carrot, it was hypothesized that DNA 1 digested with the same restriction endonuclease enzymes and amplified with the same primer combination and 2 sharing the same position in polyacrylamide gels should be conserved sequences. To test this hypothesis AFLP fragments from polyacrylamide gels were eluted, reamplified, separated in agarose gels, purified, cloned and sequenced. Among thirty-one paired fragments from each F2 population, twenty-six had identity greater than 91% and five presented identity of 24% to 44%. Among the twenty-six conserved AFLPs only one mapped to different linkage groups in the two populations while four of the five less-conserved bands mapped to different linkage groups. Of eight SCAR (sequence characterized amplified regions primers tested, one conserved AFLP resulted in co-dominant markers in both populations. Screening among 14 carrot inbreds or cultivars with three AFLP-SCAR primers revealed clear and polymorphic PCR products, with similar molecular sizes on agarose gels. The development of co-dominant markers based on conserved AFLP fragments will be useful to detect seed mixtures among hybrids, to improve and to merge linkage maps and to study diversity and phylogenetic relationships.

Laser-induced blurring of molecular structure information in high harmonic spectroscopy

DEFF Research Database (Denmark)

Risoud, Francois; Leveque, Camille; Labeye, Marie

2017-01-01

High harmonic spectroscopy gives access to molecular structure with Angstrom resolution. Such information is encoded in the destructive interferences occurring between the harmonic emissions from the different parts of the molecule. By solving the time-dependent Schrodinger equation, either....... These findings have important consequences for molecular imaging and orbital tomography using high harmonic spectroscopy....

Computation of Dielectric Response in Molecular Solids for High Capacitance Organic Dielectrics.

Science.gov (United States)

Heitzer, Henry M; Marks, Tobin J; Ratner, Mark A

2016-09-20

The dielectric response of a material is central to numerous processes spanning the fields of chemistry, materials science, biology, and physics. Despite this broad importance across these disciplines, describing the dielectric environment of a molecular system at the level of first-principles theory and computation remains a great challenge and is of importance to understand the behavior of existing systems as well as to guide the design and synthetic realization of new ones. Furthermore, with recent advances in molecular electronics, nanotechnology, and molecular biology, it has become necessary to predict the dielectric properties of molecular systems that are often difficult or impossible to measure experimentally. In these scenarios, it is would be highly desirable to be able to determine dielectric response through efficient, accurate, and chemically informative calculations. A good example of where theoretical modeling of dielectric response would be valuable is in the development of high-capacitance organic gate dielectrics for unconventional electronics such as those that could be fabricated by high-throughput printing techniques. Gate dielectrics are fundamental components of all transistor-based logic circuitry, and the combination high dielectric constant and nanoscopic thickness (i.e., high capacitance) is essential to achieving high switching speeds and low power consumption. Molecule-based dielectrics offer the promise of cheap, flexible, and mass producible electronics when used in conjunction with unconventional organic or inorganic semiconducting materials to fabricate organic field effect transistors (OFETs). The molecular dielectrics developed to date typically have limited dielectric response, which results in low capacitances, translating into poor performance of the resulting OFETs. Furthermore, the development of better performing dielectric materials has been hindered by the current highly empirical and labor-intensive pace of synthetic

High-latitude molecular clouds and infrared cirrus

International Nuclear Information System (INIS)

Vries, H.W. de.

1988-01-01

The high-latitude infrared cirrus detected by IRAS is identified with atomic and molecular clouds. These clouds are small (usually less than 1 sq. deg.) and show weak CO emission. On the basis of a distance of 100 pc they are characterized by a mass of a few solar masses and a radius of about 1 pc. Thermal radiation by dust as a results of heating by the diffuse interstellar radiation field is the most-plausible origin of the cirrus emission at far-infrared wavelengths. On the basis of plausible assumptions regarding the uniformity of both the gas-to-dust ratio and the heating and cooling of the dust, the flux density at 100 μm from regions with low visual extinction should be a good tracer of the gas column density. Indeed, the data show an approximately linear proportionality between N(HI), obtained from 21-cm observations, and I 100 (HI), the flux density from dust associated with HI. If the ratio of column density to flux density in high-latitude molecular clouds is equal to the corresponding relation in atomic ones, a value for the ratio of H 2 column density to CO velocity-integrated radiation temperature may be obtained. Although low-mass clouds may be large in number, the fraction of the Galactic molecular mass in the form of these clouds is probably no more than 1%

Molecular Characterization and Immune Protection of a New Conserved Hypothetical Protein of Eimeria tenella.

Directory of Open Access Journals (Sweden)

Qi Zhai

Full Text Available The genome sequences of Eimeria tenella have been sequenced, but >70% of these genes are currently categorized as having an unknown function or annotated as conserved hypothetical proteins, and few of them have been studied. In the present study, a conserved hypothetical protein gene of E. tenella, designated EtCHP559, was cloned using rapid amplification of cDNA 5'-ends (5'RACE based on the expressed sequence tag (EST. The 1746-bp full-length cDNA of EtCHP559 contained a 1224-bp open reading frame (ORF that encoded a 407-amino acid polypeptide with the predicted molecular weight of 46.04 kDa. Real-time quantitative PCR analysis revealed that EtCHP559 was expressed at higher levels in sporozoites than in the other developmental stages (unsporulated oocysts, sporulated oocysts and second generation merozoites. The ORF was inserted into pCold-TF to produce recombinant EtCHP559. Using western blotting, the recombinant protein was successfully recognized by rabbit serum against E. tenella sporozoites. Immunolocalization by using EtCHP559 antibody showed that EtCHP559 was mainly distributed on the parasite surface in free sporozoites and became concentrated in the anterior region after sporozoites were incubated in complete medium. The EtCHP559 became uniformly dispersed in immature and mature schizonts. Inhibition of EtCHP559 function using anti-rEtCHP559 polyclonal antibody reduced the ability of E. tenella sporozoites to invade host cells by >70%. Animal challenge experiments demonstrated that the recombinant EtCHP559 significantly increased the average body weight gain, reduced the oocyst outputs, alleviated cecal lesions of the infected chickens, and resulted in anticoccidial index >160 against E. tenella. These results suggest that EtCHP559 plays an important role in sporozoite invasion and could be an effective candidate for the development of a new vaccine against E. tenella.

DNA analysis indicates that Asian elephants are native to Borneo and are therefore a high priority for conservation.

Directory of Open Access Journals (Sweden)

Prithiviraj Fernando

2003-10-01

Full Text Available The origin of Borneo's elephants is controversial. Two competing hypotheses argue that they are either indigenous, tracing back to the Pleistocene, or were introduced, descending from elephants imported in the 16th-18th centuries. Taxonomically, they have either been classified as a unique subspecies or placed under the Indian or Sumatran subspecies. If shown to be a unique indigenous population, this would extend the natural species range of the Asian elephant by 1300 km, and therefore Borneo elephants would have much greater conservation importance than if they were a feral population. We compared DNA of Borneo elephants to that of elephants from across the range of the Asian elephant, using a fragment of mitochondrial DNA, including part of the hypervariable d-loop, and five autosomal microsatellite loci. We find that Borneo's elephants are genetically distinct, with molecular divergence indicative of a Pleistocene colonisation of Borneo and subsequent isolation. We reject the hypothesis that Borneo's elephants were introduced. The genetic divergence of Borneo elephants warrants their recognition as a separate evolutionary significant unit. Thus, interbreeding Borneo elephants with those from other populations would be contraindicated in ex situ conservation, and their genetic distinctiveness makes them one of the highest priority populations for Asian elephant conservation.

Molecular studies of Callithrix pygmaea (Primates, Platyrrhini based on transferrin intronic and ND1 regions: implications for taxonomy and conservation

Directory of Open Access Journals (Sweden)

Tagliaro Claudia Helena

2000-01-01

Full Text Available Traditional classifications of Platyrrhini monkeys, based mainly on morphological features, are being contested by recent molecular data. The subfamily Callitrichinae (Platyrrhini, Primates consists of a diverse group of species, many of them considered endangered. Our analysis of two DNA regions, a mtDNA gene (ND1 and a nuclear gene (intronic regions of the transferrin gene, suggests that Callithrix pygmaea may have sufficient variability to justify the existence of subspecies or even separate species. Phylogenetic dendrograms based on the ND1 region show that this species is more closely related to Amazonian than to Atlantic forest marmosets. These results reopen the discussion about diversity and conservation programs based exclusively on traditional classifications.

Conserved water-mediated hydrogen bond network between TM-I, -II, -VI, and -VII in 7TM receptor activation

DEFF Research Database (Denmark)

Nygaard, Rie; Hansen, Louise Valentin; Mokrosinski, Jacek

2010-01-01

Five highly conserved polar residues connected by a number of structural water molecules together with two rotamer micro-switches, TrpVI:13 and TyrVII:20, constitute an extended hydrogen bond network between the intracellular segments of TM-I, -II, -VI, and -VII of 7TM receptors. Molecular dynamics...... to apparently function as a catching trap for water molecules. Mutational analysis of the beta2-adrenergic receptor demonstrated that the highly conserved polar residues of the hydrogen bond network were all important for receptor signaling but served different functions, some dampening constitutive activity...... (AsnI:18, AspII:10, and AsnVII:13), whereas others (AsnVII:12 and AsnVII:16) located one helical turn apart and sharing a water molecule were shown to be essential for agonist-induced signaling. It is concluded that the conserved water hydrogen bond network of 7TM receptors constitutes an extended...

High molecular somatostatin, an interfering factor in radioimmunoassay

International Nuclear Information System (INIS)

Diel, F.; Schneider, E.; Baumann, H.

1977-01-01

Cyclic Tyr 1 -somatostatin (Tyr 1 -SRIF) is radioiodinated by the lactoperoxidase method. Purification is achieved by Sephadex G-25 adsorption chromatography. Specific anti-SRIF serum (FA1) has been raised in rabbits. A dose response curve is obtained in the range of 5 - 5,000 pg per tube using an antiserum dilution of 1:2,000. There is little cross-reaction with linear somatostatin and none with ocytocin, (lys-, arg-) vasopressin, valinomycin, polymyxin, insulin, glucagon, human growth hormone (hGH), and thyrotropin-releasing hormone (TRH). For recovery tests, extraction procedures are necessary. Thin-layer chromatography (TLC) and polyacrylamide-disc-electrophoresis (Disc-PAGE) are performed to identify the presumed high molecular 125 I-Tyr 1 -SRIF associate. This high molecular associate may represent an interfering factor in the radioimmunoassay for cyclic SRIF. (orig./AJ) [de

Outer Membrane Protein A Conservation among Orientia tsutsugamushi Isolates Suggests Its Potential as a Protective Antigen and Diagnostic Target

Directory of Open Access Journals (Sweden)

Sean M. Evans

2018-06-01

Full Text Available Scrub typhus threatens one billion people in the Asia-Pacific area and cases have emerged outside this region. It is caused by infection with any of the multitude of strains of the bacterium Orientia tsutsugamushi. A vaccine that affords heterologous protection and a commercially-available molecular diagnostic assay are lacking. Herein, we determined that the nucleotide and translated amino acid sequences of outer membrane protein A (OmpA are highly conserved among 51 O. tsutsugamushi isolates. Molecular modeling revealed the predicted tertiary structure of O. tsutsugamushi OmpA to be very similar to that of the phylogenetically-related pathogen, Anaplasma phagocytophilum, including the location of a helix that contains residues functionally essential for A. phagocytophilum infection. PCR primers were developed that amplified ompA DNA from all O. tsutsugamushi strains, but not from negative control bacteria. Using these primers in quantitative PCR enabled sensitive detection and quantitation of O. tsutsugamushi ompA DNA from organs and blood of mice that had been experimentally infected with the Karp or Gilliam strains. The high degree of OmpA conservation among O. tsutsugamushi strains evidences its potential to serve as a molecular diagnostic target and justifies its consideration as a candidate for developing a broadly-protective scrub typhus vaccine.

Balancing forest-regeneration probabilities and maintenance costs in dry grasslands of high conservation priority

Science.gov (United States)

Bolliger, Janine; Edwards, Thomas C.; Eggenberg, Stefan; Ismail, Sascha; Seidl, Irmi; Kienast, Felix

2011-01-01

Abandonment of agricultural land has resulted in forest regeneration in species-rich dry grasslands across European mountain regions and threatens conservation efforts in this vegetation type. To support national conservation strategies, we used a site-selection algorithm (MARXAN) to find optimum sets of floristic regions (reporting units) that contain grasslands of high conservation priority. We sought optimum sets that would accommodate 136 important dry-grassland species and that would minimize forest regeneration and costs of management needed to forestall predicted forest regeneration. We did not consider other conservation elements of dry grasslands, such as animal species richness, cultural heritage, and changes due to climate change. Optimal sets that included 95–100% of the dry grassland species encompassed an average of 56–59 floristic regions (standard deviation, SD 5). This is about 15% of approximately 400 floristic regions that contain dry-grassland sites and translates to 4800–5300 ha of dry grassland out of a total of approximately 23,000 ha for the entire study area. Projected costs to manage the grasslands in these optimum sets ranged from CHF (Swiss francs) 5.2 to 6.0 million/year. This is only 15–20% of the current total estimated cost of approximately CHF30–45 million/year required if all dry grasslands were to be protected. The grasslands of the optimal sets may be viewed as core sites in a national conservation strategy.

Histidine 114 Is Critical for ATP Hydrolysis by the Universally Conserved ATPase YchF.

Science.gov (United States)

Rosler, Kirsten S; Mercier, Evan; Andrews, Ian C; Wieden, Hans-Joachim

2015-07-24

GTPases perform a wide range of functions, ranging from protein synthesis to cell signaling. Of all known GTPases, only eight are conserved across all three domains of life. YchF is one of these eight universally conserved GTPases; however, its cellular function and enzymatic properties are poorly understood. YchF differs from the classical GTPases in that it has a higher affinity for ATP than for GTP and is a functional ATPase. As a hydrophobic amino acid-substituted ATPase, YchF does not possess the canonical catalytic Gln required for nucleotide hydrolysis. To elucidate the catalytic mechanism of ATP hydrolysis by YchF, we have taken a two-pronged approach combining classical biochemical and in silico techniques. The use of molecular dynamics simulations allowed us to complement our biochemical findings with information about the structural dynamics of YchF. We have thereby identified the highly conserved His-114 as critical for the ATPase activity of YchF from Escherichia coli. His-114 is located in a flexible loop of the G-domain, which undergoes nucleotide-dependent conformational changes. The use of a catalytic His is also observed in the hydrophobic amino acid-substituted GTPase RbgA and is an identifier of the translational GTPase family. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Planning tiger recovery: Understanding intraspecific variation for effective conservation

Science.gov (United States)

Wilting, Andreas; Courtiol, Alexandre; Christiansen, Per; Niedballa, Jürgen; Scharf, Anne K.; Orlando, Ludovic; Balkenhol, Niko; Hofer, Heribert; Kramer-Schadt, Stephanie; Fickel, Jörns; Kitchener, Andrew C.

2015-01-01

Although significantly more money is spent on the conservation of tigers than on any other threatened species, today only 3200 to 3600 tigers roam the forests of Asia, occupying only 7% of their historical range. Despite the global significance of and interest in tiger conservation, global approaches to plan tiger recovery are partly impeded by the lack of a consensus on the number of tiger subspecies or management units, because a comprehensive analysis of tiger variation is lacking. We analyzed variation among all nine putative tiger subspecies, using extensive data sets of several traits [morphological (craniodental and pelage), ecological, molecular]. Our analyses revealed little variation and large overlaps in each trait among putative subspecies, and molecular data showed extremely low diversity because of a severe Late Pleistocene population decline. Our results support recognition of only two subspecies: the Sunda tiger, Panthera tigris sondaica, and the continental tiger, Panthera tigris tigris, which consists of two (northern and southern) management units. Conservation management programs, such as captive breeding, reintroduction initiatives, or trans-boundary projects, rely on a durable, consistent characterization of subspecies as taxonomic units, defined by robust multiple lines of scientific evidence rather than single traits or ad hoc descriptions of one or few specimens. Our multiple-trait data set supports a fundamental rethinking of the conventional tiger taxonomy paradigm, which will have profound implications for the management of in situ and ex situ tiger populations and boost conservation efforts by facilitating a pragmatic approach to tiger conservation management worldwide. PMID:26601191

Planning tiger recovery: Understanding intraspecific variation for effective conservation.

Science.gov (United States)

Wilting, Andreas; Courtiol, Alexandre; Christiansen, Per; Niedballa, Jürgen; Scharf, Anne K; Orlando, Ludovic; Balkenhol, Niko; Hofer, Heribert; Kramer-Schadt, Stephanie; Fickel, Jörns; Kitchener, Andrew C

2015-06-01

Although significantly more money is spent on the conservation of tigers than on any other threatened species, today only 3200 to 3600 tigers roam the forests of Asia, occupying only 7% of their historical range. Despite the global significance of and interest in tiger conservation, global approaches to plan tiger recovery are partly impeded by the lack of a consensus on the number of tiger subspecies or management units, because a comprehensive analysis of tiger variation is lacking. We analyzed variation among all nine putative tiger subspecies, using extensive data sets of several traits [morphological (craniodental and pelage), ecological, molecular]. Our analyses revealed little variation and large overlaps in each trait among putative subspecies, and molecular data showed extremely low diversity because of a severe Late Pleistocene population decline. Our results support recognition of only two subspecies: the Sunda tiger, Panthera tigris sondaica, and the continental tiger, Panthera tigris tigris, which consists of two (northern and southern) management units. Conservation management programs, such as captive breeding, reintroduction initiatives, or trans-boundary projects, rely on a durable, consistent characterization of subspecies as taxonomic units, defined by robust multiple lines of scientific evidence rather than single traits or ad hoc descriptions of one or few specimens. Our multiple-trait data set supports a fundamental rethinking of the conventional tiger taxonomy paradigm, which will have profound implications for the management of in situ and ex situ tiger populations and boost conservation efforts by facilitating a pragmatic approach to tiger conservation management worldwide.

Development and use of molecular markers: past and present.

Science.gov (United States)

Grover, Atul; Sharma, P C

2016-01-01

Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications.

Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor

Energy Technology Data Exchange (ETDEWEB)

Zeymer, Cathleen, E-mail: cathleen.zeymer@mpimf-heidelberg.mpg.de; Barends, Thomas R. M.; Werbeck, Nicolas D.; Schlichting, Ilme; Reinstein, Jochen, E-mail: cathleen.zeymer@mpimf-heidelberg.mpg.de [Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)

2014-02-01

High-resolution crystal structures together with mutational analysis and transient kinetics experiments were utilized to understand nucleotide sensing and the regulation of the ATPase cycle in an AAA+ molecular motor. ATPases of the AAA+ superfamily are large oligomeric molecular machines that remodel their substrates by converting the energy from ATP hydrolysis into mechanical force. This study focuses on the molecular chaperone ClpB, the bacterial homologue of Hsp104, which reactivates aggregated proteins under cellular stress conditions. Based on high-resolution crystal structures in different nucleotide states, mutational analysis and nucleotide-binding kinetics experiments, the ATPase cycle of the C-terminal nucleotide-binding domain (NBD2), one of the motor subunits of this AAA+ disaggregation machine, is dissected mechanistically. The results provide insights into nucleotide sensing, explaining how the conserved sensor 2 motif contributes to the discrimination between ADP and ATP binding. Furthermore, the role of a conserved active-site arginine (Arg621), which controls binding of the essential Mg{sup 2+} ion, is described. Finally, a hypothesis is presented as to how the ATPase activity is regulated by a conformational switch that involves the essential Walker A lysine. In the proposed model, an unusual side-chain conformation of this highly conserved residue stabilizes a catalytically inactive state, thereby avoiding unnecessary ATP hydrolysis.

Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor

International Nuclear Information System (INIS)

Zeymer, Cathleen; Barends, Thomas R. M.; Werbeck, Nicolas D.; Schlichting, Ilme; Reinstein, Jochen

2014-01-01

High-resolution crystal structures together with mutational analysis and transient kinetics experiments were utilized to understand nucleotide sensing and the regulation of the ATPase cycle in an AAA+ molecular motor. ATPases of the AAA+ superfamily are large oligomeric molecular machines that remodel their substrates by converting the energy from ATP hydrolysis into mechanical force. This study focuses on the molecular chaperone ClpB, the bacterial homologue of Hsp104, which reactivates aggregated proteins under cellular stress conditions. Based on high-resolution crystal structures in different nucleotide states, mutational analysis and nucleotide-binding kinetics experiments, the ATPase cycle of the C-terminal nucleotide-binding domain (NBD2), one of the motor subunits of this AAA+ disaggregation machine, is dissected mechanistically. The results provide insights into nucleotide sensing, explaining how the conserved sensor 2 motif contributes to the discrimination between ADP and ATP binding. Furthermore, the role of a conserved active-site arginine (Arg621), which controls binding of the essential Mg 2+ ion, is described. Finally, a hypothesis is presented as to how the ATPase activity is regulated by a conformational switch that involves the essential Walker A lysine. In the proposed model, an unusual side-chain conformation of this highly conserved residue stabilizes a catalytically inactive state, thereby avoiding unnecessary ATP hydrolysis

Human developmental enhancers conserved between deuterostomes and protostomes.

Directory of Open Access Journals (Sweden)

Shoa L Clarke

Full Text Available The identification of homologies, whether morphological, molecular, or genetic, is fundamental to our understanding of common biological principles. Homologies bridging the great divide between deuterostomes and protostomes have served as the basis for current models of animal evolution and development. It is now appreciated that these two clades share a common developmental toolkit consisting of conserved transcription factors and signaling pathways. These patterning genes sometimes show common expression patterns and genetic interactions, suggesting the existence of similar or even conserved regulatory apparatus. However, previous studies have found no regulatory sequence conserved between deuterostomes and protostomes. Here we describe the first such enhancers, which we call bilaterian conserved regulatory elements (Bicores. Bicores show conservation of sequence and gene synteny. Sequence conservation of Bicores reflects conserved patterns of transcription factor binding sites. We predict that Bicores act as response elements to signaling pathways, and we show that Bicores are developmental enhancers that drive expression of transcriptional repressors in the vertebrate central nervous system. Although the small number of identified Bicores suggests extensive rewiring of cis-regulation between the protostome and deuterostome clades, additional Bicores may be revealed as our understanding of cis-regulatory logic and sample of bilaterian genomes continue to grow.

High efficiency diffusion molecular retention tumor targeting.

Directory of Open Access Journals (Sweden)

Yanyan Guo

Full Text Available Here we introduce diffusion molecular retention (DMR tumor targeting, a technique that employs PEG-fluorochrome shielded probes that, after a peritumoral (PT injection, undergo slow vascular uptake and extensive interstitial diffusion, with tumor retention only through integrin molecular recognition. To demonstrate DMR, RGD (integrin binding and RAD (control probes were synthesized bearing DOTA (for (111 In(3+, a NIR fluorochrome, and 5 kDa PEG that endows probes with a protein-like volume of 25 kDa and decreases non-specific interactions. With a GFP-BT-20 breast carcinoma model, tumor targeting by the DMR or i.v. methods was assessed by surface fluorescence, biodistribution of [(111In] RGD and [(111In] RAD probes, and whole animal SPECT. After a PT injection, both probes rapidly diffused through the normal and tumor interstitium, with retention of the RGD probe due to integrin interactions. With PT injection and the [(111In] RGD probe, SPECT indicated a highly tumor specific uptake at 24 h post injection, with 352%ID/g tumor obtained by DMR (vs 4.14%ID/g by i.v.. The high efficiency molecular targeting of DMR employed low probe doses (e.g. 25 ng as RGD peptide, which minimizes toxicity risks and facilitates clinical translation. DMR applications include the delivery of fluorochromes for intraoperative tumor margin delineation, the delivery of radioisotopes (e.g. toxic, short range alpha emitters for radiotherapy, or the delivery of photosensitizers to tumors accessible to light.

Geographies of Conservation I: De-extinction and Precision Conservation

OpenAIRE

Adams, William Mark

2016-01-01

Extinction has long been a central concern in biodiversity conservation. Today, de-extinction offers interesting possibilities of restoring charismatic species and ecosystem function, but also risks and costs. Most de-extinction depends on genetic engineering and synthetic biology. These technologies are also proposed for use in ‘gene tweaking’ in wild species to enhance their chance of survival. Within conservation, the resulting debates pit an optimistic world of high-tech ‘precision con...

Targeting N-Glycan Cryptic Sugar Moieties for Broad-Spectrum Virus Neutralization: Progress in Identifying Conserved Molecular Targets in Viruses of Distinct Phylogenetic Origins

Directory of Open Access Journals (Sweden)

Denong Wang

2015-03-01

Full Text Available Identifying molecular targets for eliciting broadly virus-neutralizing antibodies is one of the key steps toward development of vaccines against emerging viral pathogens. Owing to genomic and somatic diversities among viral species, identifying protein targets for broad-spectrum virus neutralization is highly challenging even for the same virus, such as HIV-1. However, viruses rely on host glycosylation machineries to synthesize and express glycans and, thereby, may display common carbohydrate moieties. Thus, exploring glycan-binding profiles of broad-spectrum virus-neutralizing agents may provide key information to uncover the carbohydrate-based virus-neutralizing epitopes. In this study, we characterized two broadly HIV-neutralizing agents, human monoclonal antibody 2G12 and Galanthus nivalis lectin (GNA, for their viral targeting activities. Although these agents were known to be specific for oligomannosyl antigens, they differ strikingly in virus-binding activities. The former is HIV-1 specific; the latter is broadly reactive and is able to neutralize viruses of distinct phylogenetic origins, such as HIV-1, severe acute respiratory syndrome coronavirus (SARS-CoV, and human cytomegalovirus (HCMV. In carbohydrate microarray analyses, we explored the molecular basis underlying the striking differences in the spectrum of anti-virus activities of the two probes. Unlike 2G12, which is strictly specific for the high-density Man9GlcNAc2Asn (Man9-clusters, GNA recognizes a number of N-glycan cryptic sugar moieties. These include not only the known oligomannosyl antigens but also previously unrecognized tri-antennary or multi-valent GlcNAc-terminating N-glycan epitopes (Tri/m-Gn. These findings highlight the potential of N-glycan cryptic sugar moieties as conserved targets for broad-spectrum virus neutralization and suggest the GNA-model of glycan-binding warrants focused investigation.

PMG: online generation of high-quality molecular pictures and storyboarded animations

Science.gov (United States)

Autin, Ludovic; Tufféry, Pierre

2007-01-01

The Protein Movie Generator (PMG) is an online service able to generate high-quality pictures and animations for which one can then define simple storyboards. The PMG can therefore efficiently illustrate concepts such as molecular motion or formation/dissociation of complexes. Emphasis is put on the simplicity of animation generation. Rendering is achieved using Dino coupled to POV-Ray. In order to produce highly informative images, the PMG includes capabilities of using different molecular representations at the same time to highlight particular molecular features. Moreover, sophisticated rendering concepts including scene definition, as well as modeling light and materials are available. The PMG accepts Protein Data Bank (PDB) files as input, which may include series of models or molecular dynamics trajectories and produces images or movies under various formats. PMG can be accessed at http://bioserv.rpbs.jussieu.fr/PMG.html. PMID:17478496

Traveling waves and conservation laws for highly nonlinear wave equations modeling Hertz chains

Science.gov (United States)

Przedborski, Michelle; Anco, Stephen C.

2017-09-01

A highly nonlinear, fourth-order wave equation that models the continuum theory of long wavelength pulses in weakly compressed, homogeneous, discrete chains with a general power-law contact interaction is studied. For this wave equation, all solitary wave solutions and all nonlinear periodic wave solutions, along with all conservation laws, are derived. The solutions are explicitly parameterized in terms of the asymptotic value of the wave amplitude in the case of solitary waves and the peak of the wave amplitude in the case of nonlinear periodic waves. All cases in which the solution expressions can be stated in an explicit analytic form using elementary functions are worked out. In these cases, explicit expressions for the total energy and total momentum for all solutions are obtained as well. The derivation of the solutions uses the conservation laws combined with an energy analysis argument to reduce the wave equation directly to a separable first-order differential equation that determines the wave amplitude in terms of the traveling wave variable. This method can be applied more generally to other highly nonlinear wave equations.

Counter-propagating dual-trap optical tweezers based on linear momentum conservation

International Nuclear Information System (INIS)

Ribezzi-Crivellari, M.; Huguet, J. M.; Ritort, F.

2013-01-01

We present a dual-trap optical tweezers setup which directly measures forces using linear momentum conservation. The setup uses a counter-propagating geometry, which allows momentum measurement on each beam separately. The experimental advantages of this setup include low drift due to all-optical manipulation, and a robust calibration (independent of the features of the trapped object or buffer medium) due to the force measurement method. Although this design does not attain the high-resolution of some co-propagating setups, we show that it can be used to perform different single molecule measurements: fluctuation-based molecular stiffness characterization at different forces and hopping experiments on molecular hairpins. Remarkably, in our setup it is possible to manipulate very short tethers (such as molecular hairpins with short handles) down to the limit where beads are almost in contact. The setup is used to illustrate a novel method for measuring the stiffness of optical traps and tethers on the basis of equilibrium force fluctuations, i.e., without the need of measuring the force vs molecular extension curve. This method is of general interest for dual trap optical tweezers setups and can be extended to setups which do not directly measure forces.

Counter-propagating dual-trap optical tweezers based on linear momentum conservation

Energy Technology Data Exchange (ETDEWEB)

Ribezzi-Crivellari, M.; Huguet, J. M. [Small Biosystems Lab, Dept. de Fisica Fonamental, Universitat de Barcelona, Avda. Diagonal 647, 08028 Barcelona (Spain); Ritort, F. [Small Biosystems Lab, Dept. de Fisica Fonamental, Universitat de Barcelona, Avda. Diagonal 647, 08028 Barcelona (Spain); Ciber-BBN de Bioingenieria, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid (Spain)

2013-04-15

We present a dual-trap optical tweezers setup which directly measures forces using linear momentum conservation. The setup uses a counter-propagating geometry, which allows momentum measurement on each beam separately. The experimental advantages of this setup include low drift due to all-optical manipulation, and a robust calibration (independent of the features of the trapped object or buffer medium) due to the force measurement method. Although this design does not attain the high-resolution of some co-propagating setups, we show that it can be used to perform different single molecule measurements: fluctuation-based molecular stiffness characterization at different forces and hopping experiments on molecular hairpins. Remarkably, in our setup it is possible to manipulate very short tethers (such as molecular hairpins with short handles) down to the limit where beads are almost in contact. The setup is used to illustrate a novel method for measuring the stiffness of optical traps and tethers on the basis of equilibrium force fluctuations, i.e., without the need of measuring the force vs molecular extension curve. This method is of general interest for dual trap optical tweezers setups and can be extended to setups which do not directly measure forces.

Polyketones and polysulfones for conservation in the ethylene polymer market

International Nuclear Information System (INIS)

Steinberg, M.

1977-01-01

The polyketones and polysulfones formed from the gas phase below 100 0 C have been found to be high molecular weight polymers which, depending on composition, either melt with difficulty, or decompose at temperatures of 250 0 C or higher. The higher temperature (> 100 0 C) catalyst induced reaction produces low molecular weight waxes. Design calculations indicate that for a G value of 10,000 and 50% energy deposition efficiency, it would take 331 megacuries of Co 60 to conserve 2 billion pounds of ethylene or 25% of the overall US consumption in the PE market by substituting CO and SO 2 . This saving amounts to as much as 280 million dollars at today's market price. Electron machine radiation with a 25% energy deposition efficiency requires a total beam power of 9800 KW. The use of machine radiation is preferred because of safety, availability, and lower initial investment. (author)

Gains of ubiquitylation sites in highly conserved proteins in the human lineage

Directory of Open Access Journals (Sweden)

Kim Dong Seon

2012-11-01

Full Text Available Abstract Background Post-translational modification of lysine residues of specific proteins by ubiquitin modulates the degradation, localization, and activity of these target proteins. Here, we identified gains of ubiquitylation sites in highly conserved regions of human proteins that occurred during human evolution. Results We analyzed human ubiquitylation site data and multiple alignments of orthologous mammalian proteins including those from humans, primates, other placental mammals, opossum, and platypus. In our analysis, we identified 281 ubiquitylation sites in 252 proteins that first appeared along the human lineage during primate evolution: one protein had four novel sites; four proteins had three sites each; 18 proteins had two sites each; and the remaining 229 proteins had one site each. PML, which is involved in neurodevelopment and neurodegeneration, acquired three sites, two of which have been reported to be involved in the degradation of PML. Thirteen human proteins, including ERCC2 (also known as XPD and NBR1, gained human-specific ubiquitylated lysines after the human-chimpanzee divergence. ERCC2 has a Lys/Gln polymorphism, the derived (major allele of which confers enhanced DNA repair capacity and reduced cancer risk compared with the ancestral (minor allele. NBR1 and eight other proteins that are involved in the human autophagy protein interaction network gained a novel ubiquitylation site. Conclusions The gain of novel ubiquitylation sites could be involved in the evolution of protein degradation and other regulatory networks. Although gains of ubiquitylation sites do not necessarily equate to adaptive evolution, they are useful candidates for molecular functional analyses to identify novel advantageous genetic modifications and innovative phenotypes acquired during human evolution.

Planning for land use and conservation: Assessing GIS-based conservation software for land use planning

Science.gov (United States)

Rob Baldwin; Ryan Scherzinger; Don Lipscomb; Miranda Mockrin; Susan Stein

2014-01-01

Recent advances in planning and ecological software make it possible to conduct highly technical analyses to prioritize conservation investments and inform local land use planning. We review these tools, termed conservation planning tools, and assess the knowledge of a key set of potential users: the land use planning community. We grouped several conservation software...

Molecular insight into human platelet antigens: structural and evolutionary conservation analyses offer new perspective to immunogenic disorders.

Science.gov (United States)

Landau, Meytal; Rosenberg, Nurit

2011-03-01

Human platelet antigens (HPAs) are polymorphisms in platelet membrane glycoproteins (GPs) that can stimulate production of alloantibodies once exposed to foreign platelets (PLTs) with different HPAs. These antibodies can cause neonatal alloimmune thrombocytopenia, posttransfusion purpura, and PLT transfusion refractoriness. Most HPAs are localized on the main PLT receptors: 1) integrin αIIbβ3, known as the fibrinogen receptor; 2) the GPIb-IX-V complex that functions as the receptor for von Willebrand factor; and 3) integrin α2β1, which functions as the collagen receptor. We analyzed the structural location and the evolutionary conservation of the residues associated with the HPAs to characterize the features that induce immunologic responses but do not cause inherited diseases. We found that all HPAs reside in positions located on the protein surface, apart from the ligand-binding site, and are evolutionary variable. Disease-causing mutations often reside in highly conserved and buried positions. In contrast, the HPAs affect residues on the protein surface that were not conserved throughout evolution; this explains their naive effect on the protein function. Nonetheless, the HPAs involve substitutions of solvent-exposed positions that lead to altered interfaces on the surface of the protein and might present epitopes foreign to the immune system. © 2010 American Association of Blood Banks.

78 FR 72533 - Energy Conservation Program: Energy Conservation Standards for Certain Consumer Products

Science.gov (United States)

2013-12-03

... published on October 23, 2013. That final rule adopted changes to definitions and energy conservation... revised definition and revised energy conservation standards for small duct high velocity central air... Congress has provided in the AEMTCA for the Secretary of Energy to revise definitions and energy...

High-Flux Carbon Molecular Sieve Membranes for Gas Separation.

Science.gov (United States)

Richter, Hannes; Voss, Hartwig; Kaltenborn, Nadine; Kämnitz, Susanne; Wollbrink, Alexander; Feldhoff, Armin; Caro, Jürgen; Roitsch, Stefan; Voigt, Ingolf

2017-06-26

Carbon membranes have great potential for highly selective and cost-efficient gas separation. Carbon is chemically stable and it is relative cheap. The controlled carbonization of a polymer coating on a porous ceramic support provides a 3D carbon material with molecular sieving permeation performance. The carbonization of the polymer blend gives turbostratic carbon domains of randomly stacked together sp 2 hybridized carbon sheets as well as sp 3 hybridized amorphous carbon. In the evaluation of the carbon molecular sieve membrane, hydrogen could be separated from propane with a selectivity of 10 000 with a hydrogen permeance of 5 m 3 (STP)/(m 2 hbar). Furthermore, by a post-synthesis oxidative treatment, the permeation fluxes are increased by widening the pores, and the molecular sieve carbon membrane is transformed from a molecular sieve carbon into a selective surface flow carbon membrane with adsorption controlled performance and becomes selective for carbon dioxide. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

RNA expression in a cartilaginous fish cell line reveals ancient 3′ noncoding regions highly conserved in vertebrates

Science.gov (United States)

Forest, David; Nishikawa, Ryuhei; Kobayashi, Hiroshi; Parton, Angela; Bayne, Christopher J.; Barnes, David W.

2007-01-01

We have established a cartilaginous fish cell line [Squalus acanthias embryo cell line (SAE)], a mesenchymal stem cell line derived from the embryo of an elasmobranch, the spiny dogfish shark S. acanthias. Elasmobranchs (sharks and rays) first appeared >400 million years ago, and existing species provide useful models for comparative vertebrate cell biology, physiology, and genomics. Comparative vertebrate genomics among evolutionarily distant organisms can provide sequence conservation information that facilitates identification of critical coding and noncoding regions. Although these genomic analyses are informative, experimental verification of functions of genomic sequences depends heavily on cell culture approaches. Using ESTs defining mRNAs derived from the SAE cell line, we identified lengthy and highly conserved gene-specific nucleotide sequences in the noncoding 3′ UTRs of eight genes involved in the regulation of cell growth and proliferation. Conserved noncoding 3′ mRNA regions detected by using the shark nucleotide sequences as a starting point were found in a range of other vertebrate orders, including bony fish, birds, amphibians, and mammals. Nucleotide identity of shark and human in these regions was remarkably well conserved. Our results indicate that highly conserved gene sequences dating from the appearance of jawed vertebrates and representing potential cis-regulatory elements can be identified through the use of cartilaginous fish as a baseline. Because the expression of genes in the SAE cell line was prerequisite for their identification, this cartilaginous fish culture system also provides a physiologically valid tool to test functional hypotheses on the role of these ancient conserved sequences in comparative cell biology. PMID:17227856

Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII) markers

Science.gov (United States)

2010-01-01

The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae (Asterid) species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested) and tree tomatoes (26 out of 41) for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with FST > 0.90), which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species. PMID:21637482

Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII) markers.

Science.gov (United States)

Enciso-Rodríguez, Felix; Martínez, Rodrigo; Lobo, Mario; Barrero, Luz Stella

2010-04-01

The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae (Asterid) species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested) and tree tomatoes (26 out of 41) for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with F(ST) > 0.90), which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species.

Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII markers

Directory of Open Access Journals (Sweden)

Felix Enciso-Rodríguez

2010-01-01

Full Text Available The Lulo or naranjilla (Solanum quitoense Lam. and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt. are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32 and tree tomatoes (n = 30 through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII in other Solanaceae (Asterid species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested and tree tomatoes (26 out of 41 for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with F ST > 0.90, which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species.

Conservation of boundary extension mechanisms between plants and animals

OpenAIRE

Mathur, Jaideep

2005-01-01

Locomotion clearly sets plants and animals apart. However, recent studies in higher plants reveal cell-biological and molecular features similar to those observed at the leading edge of animal cells and suggest conservation of boundary extension mechanisms between motile animal cells and nonmotile plant cells.

Eggshell membranes as a noninvasive sampling for molecular ...

African Journals Online (AJOL)

Noninvasive sampling is of prime essential on conservation genetics and molecular ecology. It is particularly preferred to use in the genetic identification of individuals and genetic analysis. A simple and efficient sampling is described for molecular studies from eggshell membranes in an endemic population of Chinese ...

Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

Science.gov (United States)

van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

2012-01-01

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at

Conservation genetics of the genus Martes: Assessing within-species movements, units to conserve, and connectivity across ecological and evolutionary time [Chapter 17

Science.gov (United States)

Michael K. Schwartz; Aritz Ruiz-Gonzalez; Ryuchi Masuda; Cino Pertoldi

2012-01-01

Understanding the physical and temporal factors that structure Martes populations is essential to the conservation and management of the 8 recognized Martes species. Recently, advances in 3 distinct subdisciplines in molecular ecology have provided insights into historical and contemporary environmental factors that have created population substructure and influenced...

Molecular events leading to HPV-induced high grade neoplasia

Directory of Open Access Journals (Sweden)

Saskia M. Wilting

2016-12-01

Full Text Available Cervical cancer is initiated by high-risk types of the human papillomavirus (hrHPV and develops via precursor stages, called cervical intraepithelial neoplasia (CIN. High-grade CIN lesions are considered true precancerous lesions when the viral oncogenes E6 and E7 are aberrantly expressed in the dividing cells. This results in abolishment of normal cell cycle control via p53 and pRb degradation. However, it has become clear that these viral oncogenes possess additional oncogenic properties, including interference with the DNA methylation machinery and mitotic checkpoints. Identification of the resulting molecular events leading to high-grade neoplasia will 1 increase our understanding of cervical carcinogenesis, 2 yield biomarkers for early diagnosis, and 3 identify therapeutic targets for HPV-induced (pre cancerous lesions.This review will briefly summarise current advances in our understanding of the molecular alterations in the host cell genome that occur during HPV-induced carcinogenesis.

Systematics of Spiny Predatory Katydids (Tettigoniidae: Listroscelidinae) from the Brazilian Atlantic Forest Based on Morphology and Molecular Data

Science.gov (United States)

Fialho, Verônica Saraiva; Chamorro-Rengifo, Juliana; Lopes-Andrade, Cristiano; Yotoko, Karla Suemy Clemente

2014-01-01

Listroscelidinae (Orthoptera: Tettigoniidae) are insectivorous Pantropical katydids whose taxonomy presents a long history of controversy, with several genera incertae sedis. This work focused on species occurring in the Brazilian Atlantic Forest, one of the world's most threatened biomes. We examined material deposited in scientific collections and visited 15 conservation units from Rio de Janeiro to southern Bahia between November 2011 and January 2012, catching 104 specimens from 10 conservation units. Based on morphological and molecular data we redefined Listroscelidini, adding a new tribe, new genus and eight new species to the subfamily. Using morphological analysis, we redescribed and added new geographic records for six species, synonymized two species and built a provisional identification key for the Atlantic Forest Listroscelidinae. Molecular results suggest two new species and a new genus to be described, possibly by the fission of the genus Hamayulus. We also proposed a 500 bp region in the final portion of the COI to be used as a molecular barcode. Our data suggest that the Atlantic Forest Listroscelidinae are seriously endangered, because they occur in highly preserved forest remnants, show high rates of endemism and have a narrow geographic distribution. Based on our results, we suggest future collection efforts must take into account the molecular barcode data to accelerate species recognition. PMID:25118712

Mistaken identity: activating conservative political identities induces "conservative" financial decisions.

Science.gov (United States)

Morris, Michael W; Carranza, Erica; Fox, Craig R

2008-11-01

Four studies investigated whether activating a social identity can lead group members to choose options that are labeled in words associated with that identity. When political identities were made salient, Republicans (but not Democrats) became more likely to choose the gamble or investment option labeled "conservative." This shift did not occur in a condition in which the same options were unlabeled. Thus, the mechanism underlying the effect appears to be not activated identity-related values prioritizing low risk, but rather activated identity-related language (the group label "conservative"). Indeed, when political identities were salient, Republicans favored options labeled "conservative" regardless of whether the options were low or high risk. Finally, requiring participants to explain the label "conservative" before making their choice did not diminish the effect, which suggests that it does not merely reflect inattention to content or construct accessibility. We discuss the implications of these results for the literatures on identity, priming, choice, politics, and marketing.

High Molecular Weight Polymers in the New Chemicals Program

Science.gov (United States)

There are three categories or types of High Molecular Weight (HMW, 10,000 daltons) polymers typically reviewed by the New Chemicals Program: Soluble, insoluble, and water absorbing. Each of the three types are treated differently.

High-risk Long QT Syndrome Mutations in the Kv7.1 (KCNQ1) Pore Disrupt the Molecular Basis for Rapid K+ Permeation

Science.gov (United States)

Burgess, Don E.; Bartos, Daniel C.; Reloj, Allison R.; Campbell, Kenneth S.; Johnson, Jonathan N.; Tester, David J.; Ackerman, Michael J.; Fressart, Véronique; Denjoy, Isabelle; Guicheney, Pascale; Moss, Arthur J.; Ohno, Seiko; Horie, Minoru; Delisle, Brian P.

2012-01-01

Type 1 long QT syndrome (LQT1) syndrome is caused by loss-of-function mutations in the KCNQ1, which encodes the K+ channel (Kv7.1) that underlies the slowly activating delayed rectifier K+ current in the heart. Intragenic risk stratification suggests LQT1 mutations that disrupt conserved amino acid residues in the pore are an independent risk factor for LQT1-related cardiac events. The purpose of this study is to determine possible molecular mechanisms that underlie the loss-of-function for these high-risk mutations. Extensive genotype-phenotype analyses of LQT1 patients showed that T322M-, T322A-, or G325R-Kv7.1 confer a high risk for LQT1-related cardiac events. Heterologous expression of these mutations with KCNE1 revealed they generated non-functional channels and caused dominant negative suppression of WT-Kv7.1 current. Molecular dynamic simulations (MDS) of analogous mutations in KcsA (T85M-, T85A-, and G88R-KcsA) demonstrated that they disrupted the symmetrical distribution of the carbonyl oxygen atoms in the selectivity filter, which upset the balance between the strong attractive and K+-K+ repulsive forces required for rapid K+ permeation. We conclude high-risk LQT1 mutations in the pore likely disrupt the architectural and physical properties of the K+ channel selectivity filter. PMID:23092362

High-risk long QT syndrome mutations in the Kv7.1 (KCNQ1) pore disrupt the molecular basis for rapid K(+) permeation.

Science.gov (United States)

Burgess, Don E; Bartos, Daniel C; Reloj, Allison R; Campbell, Kenneth S; Johnson, Jonathan N; Tester, David J; Ackerman, Michael J; Fressart, Véronique; Denjoy, Isabelle; Guicheney, Pascale; Moss, Arthur J; Ohno, Seiko; Horie, Minoru; Delisle, Brian P

2012-11-13

Type 1 long QT syndrome (LQT1) is caused by loss-of-function mutations in the KCNQ1 gene, which encodes the K(+) channel (Kv7.1) that underlies the slowly activating delayed rectifier K(+) current in the heart. Intragenic risk stratification suggests LQT1 mutations that disrupt conserved amino acid residues in the pore are an independent risk factor for LQT1-related cardiac events. The purpose of this study is to determine possible molecular mechanisms that underlie the loss of function for these high-risk mutations. Extensive genotype-phenotype analyses of LQT1 patients showed that T322M-, T322A-, or G325R-Kv7.1 confers a high risk for LQT1-related cardiac events. Heterologous expression of these mutations with KCNE1 revealed they generated nonfunctional channels and caused dominant negative suppression of WT-Kv7.1 current. Molecular dynamics simulations of analogous mutations in KcsA (T85M-, T85A-, and G88R-KcsA) demonstrated that they disrupted the symmetrical distribution of the carbonyl oxygen atoms in the selectivity filter, which upset the balance between the strong attractive and K(+)-K(+) repulsive forces required for rapid K(+) permeation. We conclude high-risk LQT1 mutations in the pore likely disrupt the architectural and physical properties of the K(+) channel selectivity filter.

Conservation of Charge and Conservation of Current

OpenAIRE

Eisenberg, Bob

2016-01-01

Conservation of current and conservation of charge are nearly the same thing: when enough is known about charge movement, conservation of current can be derived from conservation of charge, in ideal dielectrics, for example. Conservation of current is enforced implicitly in ideal dielectrics by theories that conserve charge. But charge movement in real materials like semiconductors or ionic solutions is never ideal. We present an apparently universal derivation of conservation of current and ...

STATUS REPORT ON DEVELOPMENT OF A HIGH-SPEED HIGH-INTENSITY MOLECULAR BEAM

Energy Technology Data Exchange (ETDEWEB)

Knuth, Eldon L.

1963-07-15

Status of a high-speed high-intensity molecular beam under development is described. Bases for designs of the several components are presented. Using an arc-heated source and a hypersonic jet, molecular energies exceeding 1 ev and beam intensities of the order of 10/sup 16/ molecules/ cm/sup 2/ sec are anticipated. A two-disk beam chopper and speed selector provides a means for analyzing the speed distribution in the generated beam, for chopping the beam into bursts of nearly monoenergetic molecules suitable for scattering studies using the time-of-flight technique, and for modulating the beam in order to facilitate detection. A through-flow ionization detector possesses the versatility required for scattering studies using the time-of-flight technique. A sorption pump and a turbo pump serve as central components of alternative pumping systems for the collimating chamber. Using the arc-heated source, the converging nozzle, the conduction-radiation-cooled skimmer, the turbo pump (turning at 3400 rpm), the chopperselector (acting only as a chopper), and the detector, an arc-heated beam is generated and detected. (auth)

What is a conservation actor?

Directory of Open Access Journals (Sweden)

Paul Jepson

2011-01-01

Full Text Available As a crisis-oriented discipline, conservation biology needs actions to understand the state of nature and thwart declines in biodiversity. Actors-traditionally individuals, institutions, and collectives-have been central to delivering such goals in practice. However, the definition of actors within the discipline has been narrow and their role in influencing conservation outcomes inadequately conceptualised. In this paper, we examine the question ′What is a conservation actor?′ Who or what creates the capacity to influence conservation values and actions? Drawing from theoretical developments in Actor-Network Theory and collective governance, we argue that the concept of an actor in conservation biology should be broadened to include non-humans, such as species and devices, because they have the agency and ability to influence project goals and outcomes. We illustrate this through four examples: the Asian elephant, International Union for Conservation of Nature red lists, the High Conservation Value approach, and an Integrated Conservation and Development Project. We argue that a broader conceptualisation of actors in conservation biology will produce new forms of understanding that could open up new areas of conservation research, enhance practice and draw attention to spheres of conservation activity that might require stronger oversight and governance.

High cumulants of conserved charges and their statistical uncertainties

Science.gov (United States)

Li-Zhu, Chen; Ye-Yin, Zhao; Xue, Pan; Zhi-Ming, Li; Yuan-Fang, Wu

2017-10-01

We study the influence of measured high cumulants of conserved charges on their associated statistical uncertainties in relativistic heavy-ion collisions. With a given number of events, the measured cumulants randomly fluctuate with an approximately normal distribution, while the estimated statistical uncertainties are found to be correlated with corresponding values of the obtained cumulants. Generally, with a given number of events, the larger the cumulants we measure, the larger the statistical uncertainties that are estimated. The error-weighted averaged cumulants are dependent on statistics. Despite this effect, however, it is found that the three sigma rule of thumb is still applicable when the statistics are above one million. Supported by NSFC (11405088, 11521064, 11647093), Major State Basic Research Development Program of China (2014CB845402) and Ministry of Science and Technology (MoST) (2016YFE0104800)

Species Richness and Community Structure on a High Latitude Reef: Implications for Conservation and Management

Directory of Open Access Journals (Sweden)

Wayne Houston

2011-07-01

Full Text Available In spite of the wealth of research on the Great Barrier Reef, few detailed biodiversity assessments of its inshore coral communities have been conducted. Effective conservation and management of marine ecosystems begins with fine-scale biophysical assessments focused on diversity and the architectural species that build the structural framework of the reef. In this study, we investigate key coral diversity and environmental attributes of an inshore reef system surrounding the Keppel Bay Islands near Rockhampton in Central Queensland, Australia, and assess their implications for conservation and management. The Keppels has much higher coral diversity than previously found. The average species richness for the 19 study sites was ~40 with representatives from 68% of the ~244 species previously described for the southern Great Barrier Reef. Using scleractinian coral species richness, taxonomic distinctiveness and coral cover as the main criteria, we found that five out of 19 sites had particularly high conservation value. A further site was also considered to be of relatively high value. Corals at this site were taxonomically distinct from the others (representatives of two families were found here but not at other sites and a wide range of functionally diverse taxa were present. This site was associated with more stressful conditions such as high temperatures and turbidity. Highly diverse coral communities or biodiversity ‘hotspots’ and taxonomically distinct reefs may act as insurance policies for climatic disturbance, much like Noah’s Arks for reefs. While improving water quality and limiting anthropogenic impacts are clearly important management initiatives to improve the long-term outlook for inshore reefs, identifying, mapping and protecting these coastal ‘refugia’ may be the key for ensuring their regeneration against catastrophic climatic disturbance in the meantime.

Conserved water molecules in bacterial serine hydroxymethyltransferases.

Science.gov (United States)

Milano, Teresa; Di Salvo, Martino Luigi; Angelaccio, Sebastiana; Pascarella, Stefano

2015-10-01

Water molecules occurring in the interior of protein structures often are endowed with key structural and functional roles. We report the results of a systematic analysis of conserved water molecules in bacterial serine hydroxymethyltransferases (SHMTs). SHMTs are an important group of pyridoxal-5'-phosphate-dependent enzymes that catalyze the reversible conversion of l-serine and tetrahydropteroylglutamate to glycine and 5,10-methylenetetrahydropteroylglutamate. The approach utilized in this study relies on two programs, ProACT2 and WatCH. The first software is able to categorize water molecules in a protein crystallographic structure as buried, positioned in clefts or at the surface. The other program finds, in a set of superposed homologous proteins, water molecules that occur approximately in equivalent position in each of the considered structures. These groups of molecules are referred to as 'clusters' and represent structurally conserved water molecules. Several conserved clusters of buried or cleft water molecules were found in the set of 11 bacterial SHMTs we took into account for this work. The majority of these clusters were not described previously. Possible structural and functional roles for the conserved water molecules are envisaged. This work provides a map of the conserved water molecules helpful for deciphering SHMT mechanism and for rational design of molecular engineering experiments. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

High-order conservative discretizations for some cases of the rigid body motion

International Nuclear Information System (INIS)

Kozlov, Roman

2008-01-01

Modified vector fields can be used to construct high-order structure-preserving numerical integrators for ordinary differential equations. In the present Letter we consider high-order integrators based on the implicit midpoint rule, which conserve quadratic first integrals. It is shown that these integrators are particularly suitable for the rigid body motion with an additional quadratic first integral. In this case high-order integrators preserve all four first integrals of motion. The approach is illustrated on the Lagrange top (a rotationally symmetric rigid body with a fixed point on the symmetry axis). The equations of motion are considered in the space fixed frame because in this frame Lagrange top admits a neat description. The Lagrange top motion includes the spherical pendulum and the planar pendulum, which swings in a vertical plane, as particular cases

Differential Regulation of Receptor Activation and Agonist Selectivity by Highly Conserved Tryptophans in the Nicotinic Acetylcholine Receptor Binding Site

OpenAIRE

Williams, Dustin K.; Stokes, Clare; Horenstein, Nicole A.; Papke, Roger L.

2009-01-01

We have shown previously that a highly conserved Tyr in the nicotinic acetylcholine receptor (nAChR) ligand-binding domain (LBD) (α7 Tyr188 or α4 Tyr195) differentially regulates the activity of acetylcholine (ACh) and the α7-selective agonist 3-(4-hydroxy,2-methoxybenzylidene)anabaseine (4OH-GTS-21) in α4β2 and α7 nAChR. In this study, we mutated two highly conserved LBD Trp residues in human α7 and α4β2 and expressed the receptors in Xenopus laevis oocytes. α7 Re...

Nasal Delivery of High Molecular Weight Drugs

Directory of Open Access Journals (Sweden)

Erdal Cevher

2009-09-01

Full Text Available Nasal drug delivery may be used for either local or systemic effects. Low molecular weight drugs with are rapidly absorbed through nasal mucosa. The main reasons for this are the high permeability, fairly wide absorption area, porous and thin endothelial basement membrane of the nasal epithelium. Despite the many advantages of the nasal route, limitations such as the high molecular weight (HMW of drugs may impede drug absorption through the nasal mucosa. Recent studies have focused particularly on the nasal application of HMW therapeutic agents such as peptide-protein drugs and vaccines intended for systemic effects. Due to their hydrophilic structure, the nasal bioavailability of peptide and protein drugs is normally less than 1%. Besides their weak mucosal membrane permeability and enzymatic degradation in nasal mucosa, these drugs are rapidly cleared from the nasal cavity after administration because of mucociliary clearance. There are many approaches for increasing the residence time of drug formulations in the nasal cavity resulting in enhanced drug absorption. In this review article, nasal route and transport mechanisms across the nasal mucosa will be briefly presented. In the second part, current studies regarding the nasal application of macromolecular drugs and vaccines with nanoand micro-particulate carrier systems will be summarised.

Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program?

Directory of Open Access Journals (Sweden)

Rocío Olmo

2017-05-01

Full Text Available Root-knot nematodes (RKNs; Meloidogyne spp. induce feeding cells (giant cells; GCs inside a pseudo-organ (gall from still unknown root cells. Understanding GCs ontogeny is essential to the basic knowledge of RKN–plant interaction and to discover novel and effective control strategies. Hence, we report for the first time in a model plant, Arabidopsis, molecular, and cellular features concerning ectopic de novo organogenesis of RKNs GCs in leaves. RKNs induce GCs in leaves with irregular shape, a reticulated cytosol, and fragmented vacuoles as GCs from roots. Leaf cells around the nematode enter G2-M shown by ProCycB1;1:CycB1;1(NT-GUS expression, consistent to multinucleated GCs. In addition, GCs nuclei present irregular and varied sizes. All these characteristics mentioned, being equivalent to GCs in root-galls. RKNs complete their life cycle forming a gall/callus-like structure in the leaf vascular tissues resembling auxin-induced callus with an auxin-response maxima, indicated by high expression of DR5::GUS that is dependent on leaf auxin-transport. Notably, induction of leaves calli/GCs requires molecular components from roots crucial for lateral roots (LRs, auxin-induced callus and root-gall formation, i.e., LBD16. Hence, LBD16 is a xylem pole pericycle specific and local marker in LR primordia unexpectedly induced locally in the vascular tissue of leaves after RKN infection. LBD16 is also fundamental for feeding site formation as RKNs could not stablish in 35S::LBD16-SRDX leaves, and likely it is also a conserved molecular hub between biotic and developmental signals in Arabidopsis either in roots or leaves. Moreover, RKNs induce the ectopic development of roots from leaf and root-galls, also formed in mutants compromised in LR formation, arf7/arf19, slr, and alf4. Therefore, nematodes must target molecular signatures to induce post-embryogenic de novo organogenesis through the LBD16 callus formation pathway partially different from those

Low-Intensity Agricultural Landscapes in Transylvania Support High Butterfly Diversity: Implications for Conservation

Science.gov (United States)

Loos, Jacqueline; Dorresteijn, Ine; Hanspach, Jan; Fust, Pascal; Rakosy, László; Fischer, Joern

2014-01-01

European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation to provide

Phylogeny and molecular signatures (conserved proteins and indels that are specific for the Bacteroidetes and Chlorobi species

Directory of Open Access Journals (Sweden)

Lorenzini Emily

2007-05-01

Full Text Available Abstract Background The Bacteroidetes and Chlorobi species constitute two main groups of the Bacteria that are closely related in phylogenetic trees. The Bacteroidetes species are widely distributed and include many important periodontal pathogens. In contrast, all Chlorobi are anoxygenic obligate photoautotrophs. Very few (or no biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them. Results Systematic blast searches were performed on each open reading frame in the genomes of Porphyromonas gingivalis W83, Bacteroides fragilis YCH46, B. thetaiotaomicron VPI-5482, Gramella forsetii KT0803, Chlorobium luteolum (formerly Pelodictyon luteolum DSM 273 and Chlorobaculum tepidum (formerly Chlorobium tepidum TLS to search for proteins that are uniquely present in either all or certain subgroups of Bacteroidetes and Chlorobi. These studies have identified > 600 proteins for which homologues are not found in other organisms. This includes 27 and 51 proteins that are specific for most of the sequenced Bacteroidetes and Chlorobi genomes, respectively; 52 and 38 proteins that are limited to species from the Bacteroidales and Flavobacteriales orders, respectively, and 5 proteins that are common to species from these two orders; 185 proteins that are specific for the Bacteroides genus. Additionally, 6 proteins that are uniquely shared by species from the Bacteroidetes and Chlorobi phyla (one of them also present in the Fibrobacteres have also been identified. This work also describes two large conserved inserts in DNA polymerase III (DnaE and alanyl-tRNA synthetase that are distinctive characteristics of the Chlorobi species and a 3 aa deletion in ClpB chaperone that is mainly found in various Bacteroidales, Flavobacteriales and Flexebacteraceae, but generally not found in the homologs from other organisms. Phylogenetic analyses of the Bacteroidetes and Chlorobi species is also

Essentials of Conservation Biotechnology: A mini review

Science.gov (United States)

Merlyn Keziah, S.; Subathra Devi, C.

2017-11-01

Equilibrium of biodiversity is essential for the maintenance of the ecosystem as they are interdependent on each other. The decline in biodiversity is a global problem and an inevitable threat to the mankind. Major threats include unsustainable exploitation, habitat destruction, fragmentation, transformation, genetic pollution, invasive exotic species and degradation. This review covers the management strategies of biotechnology which include sin situ, ex situ conservation, computerized taxonomic analysis through construction of phylogenetic trees, calculating genetic distance, prioritizing the group for conservation, digital preservation of biodiversities within the coding and decoding keys, molecular approaches to asses biodiversity like polymerase chain reaction, real time, randomly amplified polymorphic DNA, restriction fragment length polymorphism, amplified fragment length polymorphism, single sequence repeats, DNA finger printing, single nucleotide polymorphism, cryopreservation and vitrification.

High-pressure microscopy for tracking dynamic properties of molecular machines.

Science.gov (United States)

Nishiyama, Masayoshi

2017-12-01

High-pressure microscopy is one of the powerful techniques to visualize the effects of hydrostatic pressures on research targets. It could be used for monitoring the pressure-induced changes in the structure and function of molecular machines in vitro and in vivo. This review focuses on the dynamic properties of the assemblies and machines, analyzed by means of high-pressure microscopy measurement. We developed a high-pressure microscope that is optimized both for the best image formation and for the stability to hydrostatic pressure up to 150 MPa. Application of pressure could change polymerization and depolymerization processes of the microtubule cytoskeleton, suggesting a modulation of the intermolecular interaction between tubulin molecules. A novel motility assay demonstrated that high hydrostatic pressure induces counterclockwise (CCW) to clockwise (CW) reversals of the Escherichia coli flagellar motor. The present techniques could be extended to study how molecular machines in complicated systems respond to mechanical stimuli. Copyright © 2017 Elsevier B.V. All rights reserved.

High Molecular Weight Forms of Mammalian Respiratory Chain Complex II

Czech Academy of Sciences Publication Activity Database

Kovářová, Nikola; Mráček, Tomáš; Nůsková, Hana; Holzerová, Eliška; Vrbacký, Marek; Pecina, Petr; Hejzlarová, Kateřina; Klučková, Katarína; Rohlena, Jakub; Neužil, Jiří; Houštěk, Josef

2013-01-01

Roč. 8, č. 8 (2013), e71869 E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GPP303/10/P227; GA MŠk(CZ) LL1204; GA MZd(CZ) NT12370; GA ČR(CZ) GAP301/10/1937 Institutional research plan: CEZ:AV0Z50520701 Institutional support: RVO:67985823 Keywords : supercomplexes * high molecular weihgt forms of complex II * native electrophoretic systems Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.534, year: 2013

NFAT5 regulates HIV-1 in primary monocytes via a highly conserved long terminal repeat site.

Directory of Open Access Journals (Sweden)

Shahin Ranjbar

2006-12-01

Full Text Available To replicate, HIV-1 capitalizes on endogenous cellular activation pathways resulting in recruitment of key host transcription factors to its viral enhancer. RNA interference has been a powerful tool for blocking key checkpoints in HIV-1 entry into cells. Here we apply RNA interference to HIV-1 transcription in primary macrophages, a major reservoir of the virus, and specifically target the transcription factor NFAT5 (nuclear factor of activated T cells 5, which is the most evolutionarily divergent NFAT protein. By molecularly cloning and sequencing isolates from multiple viral subtypes, and performing DNase I footprinting, electrophoretic mobility shift, and promoter mutagenesis transfection assays, we demonstrate that NFAT5 functionally interacts with a specific enhancer binding site conserved in HIV-1, HIV-2, and multiple simian immunodeficiency viruses. Using small interfering RNA to ablate expression of endogenous NFAT5 protein, we show that the replication of three major HIV-1 viral subtypes (B, C, and E is dependent upon NFAT5 in human primary differentiated macrophages. Our results define a novel host factor-viral enhancer interaction that reveals a new regulatory role for NFAT5 and defines a functional DNA motif conserved across HIV-1 subtypes and representative simian immunodeficiency viruses. Inhibition of the NFAT5-LTR interaction may thus present a novel therapeutic target to suppress HIV-1 replication and progression of AIDS.

DNA barcoding and traditional taxonomy: an integrated approach for biodiversity conservation.

Science.gov (United States)

Sheth, Bhavisha P; Thaker, Vrinda S

2017-07-01

Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks. In this review, we discuss the basics of both these methods of biological identification (traditional taxonomy and DNA barcoding), the technical advances in integrative taxonomy, and future trends. We also present a comprehensive compilation of published examples of integrative taxonomy that refer to nine topics within biodiversity conservation. Morphological and molecular species limits were observed to be congruent in ∼41% of the 58 source studies. The majority of the studies highlighted the description of cryptic diversity through the use of molecular data, whereas research areas like endemism, biological invasion, and threatened species were less discussed in the literature.

Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity.

Science.gov (United States)

Boessenkool, Sanne; McGlynn, Gayle; Epp, Laura S; Taylor, David; Pimentel, Manuel; Gizaw, Abel; Nemomissa, Sileshi; Brochmann, Christian; Popp, Magnus

2014-04-01

Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited. © 2013 Society for Conservation Biology.

High pressure 129I Moessbauer studies of GeI4 molecular crystals

International Nuclear Information System (INIS)

Pasternak, M.P.; Taylor, R.D.

1989-01-01

The Moessbauer effect in 129 I in conjunction with Diamond-Anvil-Cell high pressure techniques was applied to investigate the high pressure phase(s) of the molecular crystal GeI 4 . The 129 I Quadrupole Interaction was the main probe for characterizing the intermolecular structural transformation with pressure. With increasing pressure, at about 15 GPAa, the onset of a partial molecular-association phase (HP1) is first observed. In HP1 two out of the four iodines strongly overlap to form linear chains of GeI 4 . The HP1 phase coexists with the low pressure (LP) molecular phase, but its population increases with increasing pressure. At P ∼20 GPa a second high pressure phase (HP2) is identified where all four iodines strongly overlap to form a three dimensional, fully molecular-associated structure. With increasing pressure and at P > 20 GPa, HP2 is the only phase up to P = 34 GPa, the highest pressure used. A significant hysteresis of the relative abundances with pressure is observed. The isomer shift of the HP2 and HP1 structures is considerably larger than that of the LP one. 11 refs., 3 figs

High pressure 129I Moessbauer studies of GeI4 molecular crystals

International Nuclear Information System (INIS)

Pasternak, M.P.; Los Alamos National Lab.; Taylor, R.D.

1990-01-01

The Moessbauer effect in 129 I in cunjunction with Diamond-Anvil-Cell high pressure techniques was applied to investigate the high pressure phase(s) of the molecular crystal GeI 4 . The 129 I Quadrupole Interaction was the main probe for characterizing the intermolecular structural transformation with pressure. With increasing pressure, at about 15 GPa, the onset of a partial molecular-association phase (HP1) is first observed. In HP1 two out of the four iodines strongly overlap to form linear chains of GeI 4 . The HP1 phase coexists with the low pressure (LP) molecular phase, but its population increases with increasing pressure. At P≅20 GPa a second high pressure phase (HP2) is identified where all four iodines strongly overlap to form a three dimensional, fully molecular-associated structure. With increasing pressure and at P>20 GPa, HP2 is the only phase up to P=34 GPa, the highest pressure used. A significant hysteresis of the relative abundances with pressure is observed. The isomer shift of the HP2 and HP1 structures is considerably larger than that of the LP one. (orig.)

Conservation strategies for Arapaima gigas (Schinz, 1822) and the Amazonian várzea ecosystem.

Science.gov (United States)

Hrbek, T; Crossa, M; Farias, I P

2007-12-01

In the present study we report a spatial autocorrelation analysis of molecular data obtained for Arapaima gigas, and the implication of this study for conservation and management. Arapaima is an important, but critically over-exploited giant food fish of the Amazonian várzea. Analysis of 14 variable microsatellite loci and 2,347 bp of mtDNA from 126 individuals sampled in seven localities within the Amazon basin suggests that Arapaima forms a continuous population with extensive genetic exchange among localities. Weak effect of isolation-by-distance is observed in microsatellite data, but not in mtDNA data. Spatial autocorrelation analysis of genetic and geographic data suggests that genetic exchange is significantly restricted at distances greater than 2,500 km. We recommend implementing a source-sink metapopulation management and conservation model by proposing replicate high quality várzea reserves in the upper, central, and lower Amazon basin. This conservation strategy would: 1) preserve all of the current genetic diversity of Arapaima; 2) create a set of reserves to supply immigrants for locally depleted populations; 3) preserve core várzea areas in the Amazon basin on which many other species depend. We stress that conservation strategies should not only preserve current genetic diversity, but also the evolutionary processes which have generated the observed patterns.

Biodiversity conservation in a telecoupled world

Directory of Open Access Journals (Sweden)

L. Roman Carrasco

2017-09-01

Conservation practitioners need to adopt a global perspective on telecoupling and focus on the new conservation opportunities represented by shaping the social norms of affluent consumers in emerging and high-income economies.

Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa

Directory of Open Access Journals (Sweden)

Scharfe Maren

2010-04-01

Full Text Available Abstract Background The constant increase in development and spread of bacterial resistance to antibiotics poses a serious threat to human health. New sequencing technologies are now on the horizon that will yield massive increases in our capacity for DNA sequencing and will revolutionize the drug discovery process. Since essential genes are promising novel antibiotic targets, the prediction of gene essentiality based on genomic information has become a major focus. Results In this study we demonstrate that pooled sequencing is applicable for the analysis of sequence variations of strain collections with more than 10 individual isolates. Pooled sequencing of 36 clinical Pseudomonas aeruginosa isolates revealed that essential and highly expressed proteins evolve at lower rates, whereas extracellular proteins evolve at higher rates. We furthermore refined the list of experimentally essential P. aeruginosa genes, and identified 980 genes that show no sequence variation at all. Among the conserved nonessential genes we found several that are involved in regulation, motility and virulence, indicating that they represent factors of evolutionary importance for the lifestyle of a successful environmental bacterium and opportunistic pathogen. Conclusion The detailed analysis of a comprehensive set of P. aeruginosa genomes in this study clearly disclosed detailed information of the genomic makeup and revealed a large set of highly conserved genes that play an important role for the lifestyle of this microorganism. Sequencing strain collections enables for a detailed and extensive identification of sequence variations as potential bacterial adaptation processes, e.g., during the development of antibiotic resistance in the clinical setting and thus may be the basis to uncover putative targets for novel treatment strategies.

Protocols for In Vitro Propagation, Conservation, Synthetic Seed Production, Microrhizome Production, and Molecular Profiling in Turmeric (Curcuma longa L.).

Science.gov (United States)

Nirmal Babu, K; Divakaran, Minoo; Pillai, Geetha S; Sumathi, V; Praveen, K; Raj, Rahul P; Akshita, H J; Ravindran, P N; Peter, K V

2016-01-01

Turmeric is a rhizomatous herbaceous perennial but cultivated as annual, belonging to the family Zingiberaceae. It is a native of India and South East Asia. The tuberous rhizomes or underground stems of turmeric are used from antiquity as condiments, a dye and as an aromatic stimulant in several medicines. Turmeric is an important crop in India and it is used as a spice, food preservative, coloring agent, cosmetic as well as for its medicinal properties. Propagation is done vegetatively with rhizome bits as seed materials. It is plagued by rhizome rot diseases most of which are mainly spread through infected seed rhizomes. Micropropagation will help in production of disease-free seed. Sexual reproduction is rare in turmeric, making recombinant breeding very difficult. In vitro technology can thus become the preferred choice and it can be utilized for multiplication, conservation of genetic resources, generating variability, gene transfer, molecular tagging, and their utility in crop improvement.

Bringing genetic diversity to the forefront of conservation policy and management

Czech Academy of Sciences Publication Activity Database

Hoban, S. M.; Hauffe, H. C.; Pérez-Espona, S.; Arntzen, J. W.; Bertorelle, G.; Bryja, Josef; Frith, K.; Gaggiotti, O. E.; Galbusera, P.; Godoy, J. A.; Hoelzel, A. R.; Nichols, R. A.; Primmer, C. R.; Russo, I.-R.; Segelbacher, G.; Siegismund, H. R.; Sihvonen, M.; Vernesi, C.; Vila, C.; Bruford, M. W.

2013-01-01

Roč. 5, č. 2 (2013), s. 593-598 ISSN 1877-7252 Institutional support: RVO:68081766 Keywords : Conservation genetics * Aichi target 13 * ConGRESS * Biodiversity management * Biodiversity policy Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.136, year: 2013

Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.

Science.gov (United States)

Elam, W Austin; Schrank, Travis P; Campagnolo, Andrew J; Hilser, Vincent J

2013-04-01

Intrinsically disordered (ID) proteins function in the absence of a unique stable structure and appear to challenge the classic structure-function paradigm. The extent to which ID proteins take advantage of subtle conformational biases to perform functions, and whether signals for such mechanism can be identified in proteome-wide studies is not well understood. Of particular interest is the polyproline II (PII) conformation, suggested to be highly populated in unfolded proteins. We experimentally determine a complete calorimetric propensity scale for the PII conformation. Projection of the scale into representative eukaryotic proteomes reveals significant PII bias in regions coding for ID proteins. Importantly, enrichment of PII in ID proteins, or protein segments, is also captured by other PII scales, indicating that this enrichment is robustly encoded and universally detectable regardless of the method of PII propensity determination. Gene ontology (GO) terms obtained using our PII scale and other scales demonstrate a consensus for molecular functions performed by high PII proteins across the proteome. Perhaps the most striking result of the GO analysis is conserved enrichment (P ontology reveals an enrichment of PII bias near disordered phosphorylation sites that is conserved throughout eukaryotes. Copyright © 2013 The Protein Society.

Preparation and Thermal Properties of Molecular-Bridged Expanded Graphite/Polyethylene Glycol Composite Phase Change Materials for Building Energy Conservation.

Science.gov (United States)

Zhang, Dong; Chen, Meizhu; Liu, Quantao; Wan, Jiuming; Hu, Jinxuan

2018-05-16

Using phase change materials (PCMs) in building envelopes became a reliable method to improve indoor comfort and reduce buildings' energy consumption. This research developed molecular-bridged expanded graphite (EG)/polyethylene glycol (PEG) composite PCMs (m-EPs) to conserve energy in buildings. The m-EPs were prepared through a vacuum absorption technique, and a titanate coupling agent was used to build a molecular bridge between EG and PEG. SEM, mercury intrusion porosimetry (MIP), the leakage test, microcalorimetry, X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared spectroscopy (FT-IR) were conducted to characterize the morphology, pore structure, absorbability, and modifying effects of the m-EPs. The phase change temperature, latent heat, thermal stability, and thermal conductivity of the m-EPs were determined by a differential scanning calorimeter (DSC), TGA, and a thermal constants analyzer. Results showed that the maximum mass ratio of PEG to EG without leakage was 1:7, and a stable connection was established in the m-EPs after modification. Compared with the unmodified EPs, the supercooling degree of the m-EPs reduced by about 3 °C, but the latent heats and initial decomposition temperatures increased by approximately 10% and 20 °C, respectively, which indicated an improvement in the thermal energy storage efficiency. The thermal conductivities of the m-EPs were 10 times higher than those of the pristine PEGs, which ensured a rapid responding to building temperature fluctuations.

Identification of Conserved and Novel MicroRNAs in Blueberry

Directory of Open Access Journals (Sweden)

Junyang Yue

2017-06-01

Full Text Available MicroRNAs (miRNAs are a class of small endogenous RNAs that play important regulatory roles in cells by negatively affecting gene expression at both transcriptional and post-transcriptional levels. There have been extensive studies aiming to identify miRNAs and to elucidate their functions in various plant species. In the present study, we employed the high-throughput sequencing technology to profile miRNAs in blueberry fruits. A total of 9,992,446 small RNA tags with sizes ranged from 18 to 30 nt were obtained, indicating that blueberry fruits have a large and diverse small RNA population. Bioinformatic analysis identified 412 conserved miRNAs belonging to 29 families, and 35 predicted novel miRNAs that are likely to be unique to blueberries. Among them, expression profiles of five conserved miRNAs were validated by stem loop qRT-PCR. Furthermore, the potential target genes of conserved and novel miRNAs were predicted and subjected to Gene Ontology (GO annotation. Enrichment analysis of the GO-represented biological processes and molecular functions revealed that these target genes were potentially involved in a wide range of metabolic pathways and developmental processes. Particularly, anthocyanin biosynthesis has been predicted to be directly or indirectly regulated by diverse miRNA families. This study is the first report on genome-wide miRNA profile analysis in blueberry and it provides a useful resource for further elucidation of the functional roles of miRNAs during fruit development and ripening.

Biodiversity conservation in a changing climate: a review of threats and implications for conservation planning in Myanmar.

Science.gov (United States)

Rao, Madhu; Saw Htun; Platt, Steven G; Tizard, Robert; Poole, Colin; Than Myint; Watson, James E M

2013-11-01

High levels of species richness and endemism make Myanmar a regional priority for conservation. However, decades of economic and political sanctions have resulted in low conservation investment to effectively tackle threats to biodiversity. Recent sweeping political reforms have placed Myanmar on the fast track to economic development-the expectation is increased economic investments focused on the exploitation of the country's rich, and relatively intact, natural resources. Within a context of weak regulatory capacity and inadequate environmental safeguards, rapid economic development is likely to have far-reaching negative implications for already threatened biodiversity and natural-resource-dependent human communities. Climate change will further exacerbate prevailing threats given Myanmar's high exposure and vulnerability. The aim of this review is to examine the implications of increased economic growth and a changing climate within the larger context of biodiversity conservation in Myanmar. We summarize conservation challenges, assess direct climatological impacts on biodiversity and conclude with recommendations for long-term adaptation approaches for biodiversity conservation.

A novel high resolution, high sensitivity SPECT detector for molecular imaging of cardiovascular diseases

Science.gov (United States)

Cusanno, F.; Argentieri, A.; Baiocchi, M.; Colilli, S.; Cisbani, E.; De Vincentis, G.; Fratoni, R.; Garibaldi, F.; Giuliani, F.; Gricia, M.; Lucentini, M.; Magliozzi, M. L.; Majewski, S.; Marano, G.; Musico, P.; Musumeci, M.; Santavenere, F.; Torrioli, S.; Tsui, B. M. W.; Vitelli, L.; Wang, Y.

2010-05-01

Cardiovascular diseases are the most common cause of death in western countries. Understanding the rupture of vulnerable atherosclerotic plaques and monitoring the effect of innovative therapies of heart failure is of fundamental importance. A flexible, high resolution, high sensitivity detector system for molecular imaging with radionuclides on small animal models has been designed for this aim. A prototype has been built using tungsten pinhole and LaBr3(Ce) scintillator coupled to Hamamatsu Flat Panel PMTs. Compact individual-channel readout has been designed, built and tested. Measurements with phantoms as well as pilot studies on mice have been performed, the results show that the myocardial perfusion in mice can be determined with sufficient precision. The detector will be improved replacing the Hamamatsu Flat Panel with Silicon Photomultipliers (SiPMs) to allow integration of the system with MRI scanners. Application of LaBr3(Ce) scintillator coupled to photosensor with high photon detection efficiency and excellent energy resolution will allow dual-label imaging to monitor simultaneously the cardiac perfusion and the molecular targets under investigation during the heart therapy.

Just Working with the Cellular Machine: A High School Game for Teaching Molecular Biology

Science.gov (United States)

Cardoso, Fernanda Serpa; Dumpel, Renata; Gomes da Silva, Luisa B.; Rodrigues, Carlos R.; Santos, Dilvani O.; Cabral, Lucio Mendes; Castro, Helena C.

2008-01-01

Molecular biology is a difficult comprehension subject due to its high complexity, thus requiring new teaching approaches. Herein, we developed an interdisciplinary board game involving the human immune system response against a bacterial infection for teaching molecular biology at high school. Initially, we created a database with several…

Crystal and molecular simulation of high-performance polymers.

Science.gov (United States)

Colquhoun, H M; Williams, D J

2000-03-01

Single-crystal X-ray analyses of oligomeric models for high-performance aromatic polymers, interfaced to computer-based molecular modeling and diffraction simulation, have enabled the determination of a range of previously unknown polymer crystal structures from X-ray powder data. Materials which have been successfully analyzed using this approach include aromatic polyesters, polyetherketones, polythioetherketones, polyphenylenes, and polycarboranes. Pure macrocyclic homologues of noncrystalline polyethersulfones afford high-quality single crystals-even at very large ring sizes-and have provided the first examples of a "protein crystallographic" approach to the structures of conventionally amorphous synthetic polymers.

Elevated levels of high-molecular-weight adiponectin in type 1 diabetes

DEFF Research Database (Denmark)

Leth, H.; Andersen, K.K.; Frystyk, J.

2008-01-01

BACKGROUND: Several studies have shown that type 1 diabetic patients have elevated total levels of the adipocyte-derived adipocytokine adiponectin. However, adiponectin circulates in three different subforms, and the high-molecular-weight (HMW) subform is believed to be the primary biologically...... active form. The effects of the medium-molecular-weight (MMW) subform and the low-molecular-weight (LMW) subform are still unresolved. PURPOSE: The objective of the study was to investigate the distribution of the three molecular subforms of adiponectin in well-characterized groups of type 1 diabetics...... with varying degrees of nephropathy as well as in healthy control subjects. STUDY POPULATION: Two hundred seven individuals were included: 58 type 1 diabetics with normoalbuminuria, 46 with microalbuminuria, 46 with macroalbuminuria, and 57 matched controls. METHODS: The HMW, MMW, and LMW subforms were...

Optimized spatial priorities for biodiversity conservation in China: a systematic conservation planning perspective.

Science.gov (United States)

Wu, Ruidong; Long, Yongcheng; Malanson, George P; Garber, Paul A; Zhang, Shuang; Li, Diqiang; Zhao, Peng; Wang, Longzhu; Duo, Hairui

2014-01-01

By addressing several key features overlooked in previous studies, i.e. human disturbance, integration of ecosystem- and species-level conservation features, and principles of complementarity and representativeness, we present the first national-scale systematic conservation planning for China to determine the optimized spatial priorities for biodiversity conservation. We compiled a spatial database on the distributions of ecosystem- and species-level conservation features, and modeled a human disturbance index (HDI) by aggregating information using several socioeconomic proxies. We ran Marxan with two scenarios (HDI-ignored and HDI-considered) to investigate the effects of human disturbance, and explored the geographic patterns of the optimized spatial conservation priorities. Compared to when HDI was ignored, the HDI-considered scenario resulted in (1) a marked reduction (∼9%) in the total HDI score and a slight increase (∼7%) in the total area of the portfolio of priority units, (2) a significant increase (∼43%) in the total irreplaceable area and (3) more irreplaceable units being identified in almost all environmental zones and highly-disturbed provinces. Thus the inclusion of human disturbance is essential for cost-effective priority-setting. Attention should be targeted to the areas that are characterized as moderately-disturbed, conservation. We delineated 23 primary large-scale priority areas that are significant for conserving China's biodiversity, but those isolated priority units in disturbed regions are in more urgent need of conservation actions so as to prevent immediate and severe biodiversity loss. This study presents a spatially optimized national-scale portfolio of conservation priorities--effectively representing the overall biodiversity of China while minimizing conflicts with economic development. Our results offer critical insights for current conservation and strategic land-use planning in China. The approach is transferable and easy

Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes

Directory of Open Access Journals (Sweden)

Kohane Isaac

2005-11-01

Full Text Available Abstract Background Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories. Results By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes. Conclusion We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged

Insights into the molecular evolution of the PDZ/LIM family and identification of a novel conserved protein motif.

Directory of Open Access Journals (Sweden)

Aartjan J W Te Velthuis

Full Text Available The PDZ and LIM domain-containing protein family is encoded by a diverse group of genes whose phylogeny has currently not been analyzed. In mammals, ten genes are found that encode both a PDZ- and one or several LIM-domains. These genes are: ALP, RIL, Elfin (CLP36, Mystique, Enigma (LMP-1, Enigma homologue (ENH, ZASP (Cypher, Oracle, LMO7 and the two LIM domain kinases (LIMK1 and LIMK2. As conventional alignment and phylogenetic procedures of full-length sequences fell short of elucidating the evolutionary history of these genes, we started to analyze the PDZ and LIM domain sequences themselves. Using information from most sequenced eukaryotic lineages, our phylogenetic analysis is based on full-length cDNA-, EST-derived- and genomic- PDZ and LIM domain sequences of over 25 species, ranging from yeast to humans. Plant and protozoan homologs were not found. Our phylogenetic analysis identifies a number of domain duplication and rearrangement events, and shows a single convergent event during evolution of the PDZ/LIM family. Further, we describe the separation of the ALP and Enigma subfamilies in lower vertebrates and identify a novel consensus motif, which we call 'ALP-like motif' (AM. This motif is highly-conserved between ALP subfamily proteins of diverse organisms. We used here a combinatorial approach to define the relation of the PDZ and LIM domain encoding genes and to reconstruct their phylogeny. This analysis allowed us to classify the PDZ/LIM family and to suggest a meaningful model for the molecular evolution of the diverse gene architectures found in this multi-domain family.

The existence of High Conservation Value Forest (HCVF in Perum Perhutani KPH Kendal to support Implementation of FSC Certification

Directory of Open Access Journals (Sweden)

Sulistyowati Sri

2018-01-01

Full Text Available High Conservation Value Forest (HCVF is the identification of High Conservation Values that are important and need to be protected. Under FSC certification mechanism, HCVF becomes one of Principles and Criteria to attain certification. In this study, we identify the existence of HCVF in Perum Perhutani KPH Kendal to support implementation process of FSC certification. Qualitative method was conducted through observation and secondary data from Perum Perhutani KPH Kendal. Data analysis showed through ecolabel certification, Perum Perhutani KPH Kendal has been identified HCVF area covering 2,715.5 hectares consists of HCV 1 until 6. Secondary Natural Forest (HAS Subah and Kaliwungu for Ulolanang and Pagerwunung Nature Reserve buffer zone include as HCV 1.1, conservation area of leopard (Panthera pardus melas and Pangolin (Manis javanica.for HCV 1.2, conservation area of lutung (Trachypiyhecus auratus as endemic species for CITES App I and Critically Endangered species include as HCV 1.3, Goa kiskendo for bats species habitat include as HCV 1.4, regions of interest species for Deer (Cervus timorensis and Kepodang (Oriolus chinensis as HCV 2.3, Germplasm Protection Region/ KPPN area with high biodiversity include as HCV 3, river border area and water springs for HCV 4. While, utilization of firewood, grass for cattle fodder include as HCV 5 and 14 cultural sites include as HCV 6. From monitoring and evaluation of HCVF data, showed that in 2011-2015 the level of diversity for flora and fauna were increased.

The existence of High Conservation Value Forest (HCVF) in Perum Perhutani KPH Kendal to support Implementation of FSC Certification

Science.gov (United States)

Sulistyowati, Sri; Hadi, Sudharto P.

2018-02-01

High Conservation Value Forest (HCVF) is the identification of High Conservation Values that are important and need to be protected. Under FSC certification mechanism, HCVF becomes one of Principles and Criteria to attain certification. In this study, we identify the existence of HCVF in Perum Perhutani KPH Kendal to support implementation process of FSC certification. Qualitative method was conducted through observation and secondary data from Perum Perhutani KPH Kendal. Data analysis showed through ecolabel certification, Perum Perhutani KPH Kendal has been identified HCVF area covering 2,715.5 hectares consists of HCV 1 until 6. Secondary Natural Forest (HAS) Subah and Kaliwungu for Ulolanang and Pagerwunung Nature Reserve buffer zone include as HCV 1.1, conservation area of leopard (Panthera pardus melas) and Pangolin (Manis javanica).for HCV 1.2, conservation area of lutung (Trachypiyhecus auratus) as endemic species for CITES App I and Critically Endangered species include as HCV 1.3, Goa kiskendo for bats species habitat include as HCV 1.4, regions of interest species for Deer (Cervus timorensis) and Kepodang (Oriolus chinensis) as HCV 2.3, Germplasm Protection Region/ KPPN area with high biodiversity include as HCV 3, river border area and water springs for HCV 4. While, utilization of firewood, grass for cattle fodder include as HCV 5 and 14 cultural sites include as HCV 6. From monitoring and evaluation of HCVF data, showed that in 2011-2015 the level of diversity for flora and fauna were increased.

Steroidogenic activity of high molecular weight forms of ACTH

International Nuclear Information System (INIS)

Gasson, J.C.

1979-01-01

The relative steroidogenic potencies of high molecular weight forms of adrenocorticotropic hormone (ACTH) were investigated using in vitro bioassays. In order to prepare pools of separated pro-ACTH/endorphin, ACTH biosynthetic intermediate and glycosylated ACTH (1-39), the protein present in serum-free tissue culture medium obtained from cultured AtT-20/D-16v mouse pituitary tumor cells was concentrated and fractionated by gel filtration. Based on sodium dodecyl sulfate polyacrylamide gel electrophoresis, over 97% of the immunoactive ACTH in each pool had the appropriate molecular weight. Suspensions of isolated rat and guinea pig adrenal cortical cells were prepared by enzymatic dissociation and mechanical dispersion. Cells were incubated in complete tissue culture medium overnight then used in a 2 hour steroid production assay. Synthetic hACTH(1-39) was used as a bioassay and immunoassay standard. The amounts of pro-ACTH/endorphin, ACTH biosynthetic intermediate and glycosylated ACTH(1-39) bioassayed were estimated by ACTH(17-24) radioimmunoassay. All three high molecular weight forms of ACTH were capable of stimulating the same maximal level of steroidogenesis, by both isolated rat and guinea pig adrenal cells, as hACTH(1-39). Glycosylated ACTH(1-39) was equipotent with hACTH(1-39); pro-ACTH/endorphin and ACTH biosynthetic intermediate were two orders of magnitude less potent than hACTH(1-39) in both bioassay systems

Loss of high-molecular-weight cytokeratin antigenicity in prostate tissue obtained by transurethral resections

DEFF Research Database (Denmark)

Multhaupt, H A; Fessler, J N; Warhol, M J

2000-01-01

could be restored in these specimens by antigen retrieval in a low pH citrate buffer using a microwave heat technique. Keratin staining in needle biopsies and total prostatectomies was unaffected. CONCLUSION: In summary, our results indicate the technique of transurethral resection results in a specific......OBJECTIVE: Staining of prostatic basal cells for the expression of high-molecular-weight cytokeratin has been suggested as a way of distinguishing benign from malignant prostate glands. We evaluated the utility of high-molecular-weight cytokeratin in the diagnosis of malignancy in prostate...... specimens obtained in various ways. DESIGN: Prostate tissues obtained from needle biopsies, transurethral resections, and total prostatectomies were immunostained with monoclonal antibody 34betaE12, an antibody directed against high-molecular-weight cytokeratins. RESULTS: Antiserum to high...

Evaluating local benefits from conservation in Nepal's Annapurna Conservation Area.

Science.gov (United States)

Spiteri, Arian; Nepal, Sanjay K

2008-09-01

Protected areas are integral to the global effort to conserve biodiversity, and, over the past two decades, protected area managers have begun to recognize that conservation objectives are next to impossible to achieve without considering the needs and concerns of local communities. Incentive-based programs (IBPs) have become a favored approach to protected area management, geared at fostering local stewardship by delivering benefits tied to conservation to local people. Effective IBPs require benefits to accrue to and be recognized by those experiencing the greatest consequences as a result of the protected area, and those likely to continue extractive activities if their livelihood needs are compromised. This research examines dispersal of IBP benefits, as perceived by local residents in Nepal's Annapurna Conservation Area. Results reported here are based on questionnaire interviews with 188 households conducted between September and December 2004. Results indicate that local residents primarily identify benefits from social development activities, provisions for resource extraction, and economic opportunities. Overall, benefits have been dispersed equally to households in villages on and off the main tourist route, and regardless of a household's participation in tourism. However, benefits are not effectively targeted to poorer residents, those highly dependent on natural resources, and those experiencing the most crop damage and livestock loss from protected wildlife. This article provides several suggestions for improving the delivery of conservation incentives.

Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts

Directory of Open Access Journals (Sweden)

Ouyang Shu

2005-09-01

Full Text Available Abstract Background The Solanaceae is a family of closely related species with diverse phenotypes that have been exploited for agronomic purposes. Previous studies involving a small number of genes suggested sequence conservation across the Solanaceae. The availability of large collections of Expressed Sequence Tags (ESTs for the Solanaceae now provides the opportunity to assess sequence conservation and divergence on a genomic scale. Results All available ESTs and Expressed Transcripts (ETs, 449,224 sequences for six Solanaceae species (potato, tomato, pepper, petunia, tobacco and Nicotiana benthamiana, were clustered and assembled into gene indices. Examination of gene ontologies revealed that the transcripts within the gene indices encode a similar suite of biological processes. Although the ESTs and ETs were derived from a variety of tissues, 55–81% of the sequences had significant similarity at the nucleotide level with sequences among the six species. Putative orthologs could be identified for 28–58% of the sequences. This high degree of sequence conservation was supported by expression profiling using heterologous hybridizations to potato cDNA arrays that showed similar expression patterns in mature leaves for all six solanaceous species. 16–19% of the transcripts within the six Solanaceae gene indices did not have matches among Solanaceae, Arabidopsis, rice or 21 other plant gene indices. Conclusion Results from this genome scale analysis confirmed a high level of sequence conservation at the nucleotide level of the coding sequence among Solanaceae. Additionally, the results indicated that part of the Solanaceae transcriptome is likely to be unique for each species.

Polyketones and polysulfones for conservation in the ethylene polymer market

International Nuclear Information System (INIS)

Steinberg, M.

1976-04-01

Because of the increase in cost of foreign oil, ethylene costs have increased markedly within the last several years. There is a sizable incentive to reduce raw material cost for basic polymer manufacture. Polyketones, synthesized from ethylene and CO, and polysulfones, synthesized from ethylene and SO 2 , utilizing high energy radiation, offers one such possibility. CO and SO 2 , usually considered as wastes and pollutants from fossil fuel burning power plants, are converted to useful materials. The polyketones and polysulfones formed from the gas phase below 100 0 C have found to be high molecular weight polymers which, depending on composition, either melt with difficulty, or decompose at temperatures of 250 0 C or higher. The higher temperature (greater than 100 0 C) catalyzed reaction produces low molecular weight waxes. Design calculations indicate that for a G value of 10,000 and 50 percent energy deposition efficiency, it would take 331 MCi of 60 Co to conserve 2 billion pounds of ethylene or 25 percent of the overall U. S. consumption in the PE market by substituting CO and SO 2 . This savings amounts to as much as $280 million at today's market price. Electron machine radiation with a 25 percent energy deposition efficiency requires a total beam power of 9800 kW

Genetic diversity and population structure of Prunus mira (Koehne from the Tibet plateau in China and recommended conservation strategies.

Directory of Open Access Journals (Sweden)

Wenquan Bao

Full Text Available Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17 within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%, whereas morphological analyses revealed low variation (1.30%-36.17% within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units

Evolutionary conserved neural signature of early life stress affects animal social competence.

Science.gov (United States)

Nyman, Cecilia; Fischer, Stefan; Aubin-Horth, Nadia; Taborsky, Barbara

2018-01-31

In vertebrates, the early social environment can persistently influence behaviour and social competence later in life. However, the molecular mechanisms underlying variation in animal social competence are largely unknown. In rats, high-quality maternal care causes an upregulation of hippocampal glucocorticoid receptors ( gr ) and reduces offspring stress responsiveness. This identifies gr regulation as a candidate mechanism for maintaining variation in animal social competence. We tested this hypothesis in a highly social cichlid fish, Neolamprologus pulcher , reared with or without caring parents. We find that the molecular pathway translating early social experience into later-life alterations of the stress axis is homologous across vertebrates: fish reared with parents expressed the glucocorticoid receptor gr1 more in the telencephalon. Furthermore, expression levels of the transcription factor egr-1 (early growth response 1) were associated with gr1 expression in the telencephalon and hypothalamus. When blocking glucocorticoid receptors (GR) with an antagonist, mifepristone (RU486), parent-reared individuals showed more socially appropriate, submissive behaviour when intruding on a larger conspecific's territory. Remarkably, mifepristone-treated fish were less attacked by territory owners and had a higher likelihood of territory takeover. Our results indicate that early social-environment effects on stress axis programming are mediated by an evolutionary conserved molecular pathway, which is causally involved in environmentally induced variation of animal social competence. © 2018 The Author(s).

Energy conservation in nationalised transportation sector

Energy Technology Data Exchange (ETDEWEB)

Sinha, R C

1980-01-01

About 60% of high speed diesel is consumed by the road transport industry. The hike in fuel prices calls for urgent measures to conserve diesel. The paper discusses the various measures undertaken to conserve diesel in the nationalized transport sector.

Synthesis and reforming of high molecular-weigth compounds by the utilization of radiation

International Nuclear Information System (INIS)

Machi, Sueo

1976-01-01

Radiation effects on the synthesis are reforming of high molecular-weight compounds are reviewed. The report is divided into four main parts. The first part deals with the characteristics of the radiation processing. The reaction can be started in a wide range of temperature including very low temperature. Catalysts are unnecessary. The reaction velocity is fast, and the reaction in solid phase can be started uniformly. And the quality of products is well controllable. The second part deals with the synthesis of high molecular-weight compounds by radiation polymerization. Radical polymerization and ionizing polymerization, gas phase and liquid phase polymerization, the polymerization and copolymerization of fluorine-containing monomers, and solid phase polymerization and low temperature polymerization are included in this part. Attention is directed to the continuous production system for the radiation polymerization of ethylene developed by Japan Atomic Energy Research Institute. The third part deals with the reforming of high molecular-weight compounds by radiation graft polymerization. The combination of backbone polymers and monomers for reforming plastics and fibers, the membranes for reverse osmosis, porous membranes, and ion exchange membranes are included. The fourth part deals with the reforming of high molecular-weight compounds by the cross-linking. Polyethylene, PVC, ethyl acrylate copolymer and the like are included. (Iwakiri, K.)

A conservative region of the mercuric reductase gene (merA) as a molecular marker of bacterial mercury resistance Região conservada do gene da mercúrio redutase (merA) como marcador molecular da resistência bacteriana ao mercúrio

OpenAIRE

Adriana Sotero-Martins; Michele Silva de Jesus; Michele Lacerda; Josino Costa Moreira; Ana Luzia Lauria Filgueiras; Paulo Rubens Guimarães Barrocas

2008-01-01

The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II) to Hg0, which is dependent of the mercuric reductase enzyme (MerA) activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA) gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains.O mecanismo de resistência bacteriana ao mercúrio mais comum é baseada na redução do Hg(II) a Hg0, através da ativida...

The Effect of Interactive, Three Dimensional, High Speed Simulations on High School Science Students' Conceptions of the Molecular Structure of Water.

Science.gov (United States)

Hakerem, Gita; And Others

The Water and Molecular Networks (WAMNet) Project uses graduate student written Reduced Instruction Set Computing (RISC) computer simulations of the molecular structure of water to assist high school students learn about the nature of water. This study examined: (1) preconceptions concerning the molecular structure of water common among high…

Evaluation of presenting conserved foods

Directory of Open Access Journals (Sweden)

Asl Soleimani H

1998-08-01

Full Text Available Food, it's production and preserving has been one of the most important problems in human life. Limitation of production due to climatic, geographic and papulational situations and conservation due to providance and prosecting for solution of one of the most fundamental human needs, has been discussed much. Difference between the lands, temperature, humidity and rainfall on one hand and texture and accumulation of papulation on the other hand, not only has limited the amount and kind of food production but also has improved the preserving methods as much as possible. Extra production in fertile lands and confirmed need for receiving food in deserts and dry areas, makes the need of exchanging and transfer of food inevitable because of economic and ethical matters and sanitation of food. Avoidance of being contaminated and resistance against decay seems very important and vital. So process of preserving and conserving of eaw or cooked food became a fundamental problem. In previous 200 years, many advanced methods have been designed for preserving food in which the role of conserving and packing in vital often. Because of industrial production, conserved food have a great influence on sanitation of people nutrition, and herefor the rate of diseases from consumption of contaminated food has been reduced in industrial countries and the tensancy of people to use conventional food has been decreased gradually. Because of high cost of industrial conserved food production some people produce conserved foods in the way which is not hygienic. That may have a high risk when ingested. In this article we discuss about unwarranted conserved foods productions.

Comparison of theoretical proteomes: identification of COGs with conserved and variable pI within the multimodal pI distribution.

Science.gov (United States)

Nandi, Soumyadeep; Mehra, Nipun; Lynn, Andrew M; Bhattacharya, Alok

2005-09-09

Theoretical proteome analysis, generated by plotting theoretical isoelectric points (pI) against molecular masses of all proteins encoded by the genome show a multimodal distribution for pI. This multimodal distribution is an effect of allowed combinations of the charged amino acids, and not due to evolutionary causes. The variation in this distribution can be correlated to the organisms ecological niche. Contributions to this variation maybe mapped to individual proteins by studying the variation in pI of orthologs across microorganism genomes. The distribution of ortholog pI values showed trimodal distributions for all prokaryotic genomes analyzed, similar to whole proteome plots. Pairwise analysis of pI variation show that a few COGs are conserved within, but most vary between, the acidic and basic regions of the distribution, while molecular mass is more highly conserved. At the level of functional grouping of orthologs, five groups vary significantly from the population of orthologs, which is attributed to either conservation at the level of sequences or a bias for either positively or negatively charged residues contributing to the function. Individual COGs conserved in both the acidic and basic regions of the trimodal distribution are identified, and orthologs that best represent the variation in levels of the acidic and basic regions are listed. The analysis of pI distribution by using orthologs provides a basis for resolution of theoretical proteome comparison at the level of individual proteins. Orthologs identified that significantly vary between the major acidic and basic regions maybe used as representative of the variation of the entire proteome.

Diesel conservation: GSRTC'S experience

Energy Technology Data Exchange (ETDEWEB)

Ramesh Kumar, I V

1980-01-01

The Gujarat State Road Transport Corporation (GSRTC) in India has a fleet of about 6000 buses. The increasing cost of fuel and lubricants added to uncertainty in supplies, has necessitated the need for conserving High Speed Diesel Oil (HSD). GSRTC had achieved an overall average Kilometre Per Litre (kmpl) of 4.44 in the year 1976-1977 due to a variety of measures. In the year 1978-1979 the average kmpl was 4.52 and it is expected to be 4.60 for 1979-1980. The case study outlined describes the measures taken by GSRTC in conserving high speed diesel oil by various methods.

Optimising molecular diagnostic capacity for effective control of tuberculosis in high-burden settings.

Science.gov (United States)

Sabiiti, W; Mtafya, B; Kuchaka, D; Azam, K; Viegas, S; Mdolo, A; Farmer, E C W; Khonga, M; Evangelopoulos, D; Honeyborne, I; Rachow, A; Heinrich, N; Ntinginya, N E; Bhatt, N; Davies, G R; Jani, I V; McHugh, T D; Kibiki, G; Hoelscher, M; Gillespie, S H

2016-08-01

The World Health Organization's 2035 vision is to reduce tuberculosis (TB) associated mortality by 95%. While low-burden, well-equipped industrialised economies can expect to see this goal achieved, it is challenging in the low- and middle-income countries that bear the highest burden of TB. Inadequate diagnosis leads to inappropriate treatment and poor clinical outcomes. The roll-out of the Xpert(®) MTB/RIF assay has demonstrated that molecular diagnostics can produce rapid diagnosis and treatment initiation. Strong molecular services are still limited to regional or national centres. The delay in implementation is due partly to resources, and partly to the suggestion that such techniques are too challenging for widespread implementation. We have successfully implemented a molecular tool for rapid monitoring of patient treatment response to anti-tuberculosis treatment in three high TB burden countries in Africa. We discuss here the challenges facing TB diagnosis and treatment monitoring, and draw from our experience in establishing molecular treatment monitoring platforms to provide practical insights into successful optimisation of molecular diagnostic capacity in resource-constrained, high TB burden settings. We recommend a holistic health system-wide approach for molecular diagnostic capacity development, addressing human resource training, institutional capacity development, streamlined procurement systems, and engagement with the public, policy makers and implementers of TB control programmes.

An assessment of high carbon stock and high conservation value approaches to sustainable oil palm cultivation in Gabon

Science.gov (United States)

Austin, Kemen G.; Lee, Michelle E.; Clark, Connie; Forester, Brenna R.; Urban, Dean L.; White, Lee; Kasibhatla, Prasad S.; Poulsen, John R.

2017-01-01

Industrial-scale oil palm cultivation is rapidly expanding in Gabon, where it has the potential to drive economic growth, but also threatens forest, biodiversity and carbon resources. The Gabonese government is promoting an ambitious agricultural expansion strategy, while simultaneously committing to minimize negative environmental impacts of oil palm agriculture. This study estimates the extent and location of suitable land for oil palm cultivation in Gabon, based on an analysis of recent trends in plantation permitting. We use the resulting suitability map to evaluate two proposed approaches to minimizing negative environmental impacts: a High Carbon Stock (HCS) approach, which emphasizes forest protection and climate change mitigation, and a High Conservation Value (HCV) approach, which focuses on safeguarding biodiversity and ecosystems. We quantify the forest area, carbon stock, and biodiversity resources protected under each approach, using newly developed maps of priority species distributions and forest biomass for Gabon. We find 2.7-3.9 Mha of suitable or moderately suitable land that avoid HCS areas, 4.4 million hectares (Mha) that avoid HCV areas, and 1.2-1.7 Mha that avoid both. This suggests that Gabon’s oil palm production target could likely be met without compromising important ecosystem services, if appropriate safeguards are put in place. Our analysis improves understanding of suitability for oil palm in Gabon, determines how conservation strategies align with national targets for oil palm production, and informs national land use planning.

A high-order relaxation method with projective integration for solving nonlinear systems of hyperbolic conservation laws

Science.gov (United States)

Lafitte, Pauline; Melis, Ward; Samaey, Giovanni

2017-07-01

We present a general, high-order, fully explicit relaxation scheme which can be applied to any system of nonlinear hyperbolic conservation laws in multiple dimensions. The scheme consists of two steps. In a first (relaxation) step, the nonlinear hyperbolic conservation law is approximated by a kinetic equation with stiff BGK source term. Then, this kinetic equation is integrated in time using a projective integration method. After taking a few small (inner) steps with a simple, explicit method (such as direct forward Euler) to damp out the stiff components of the solution, the time derivative is estimated and used in an (outer) Runge-Kutta method of arbitrary order. We show that, with an appropriate choice of inner step size, the time step restriction on the outer time step is similar to the CFL condition for the hyperbolic conservation law. Moreover, the number of inner time steps is also independent of the stiffness of the BGK source term. We discuss stability and consistency, and illustrate with numerical results (linear advection, Burgers' equation and the shallow water and Euler equations) in one and two spatial dimensions.

Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel.

Science.gov (United States)

Brito, José C; Godinho, Raquel; Martínez-Freiría, Fernando; Pleguezuelos, Juan M; Rebelo, Hugo; Santos, Xavier; Vale, Cândida G; Velo-Antón, Guillermo; Boratyński, Zbyszek; Carvalho, Sílvia B; Ferreira, Sónia; Gonçalves, Duarte V; Silva, Teresa L; Tarroso, Pedro; Campos, João C; Leite, João V; Nogueira, Joana; Alvares, Francisco; Sillero, Neftalí; Sow, Andack S; Fahd, Soumia; Crochet, Pierre-André; Carranza, Salvador

2014-02-01

Deserts and arid regions are generally perceived as bare and rather homogeneous areas of low diversity. The Sahara is the largest warm desert in the world and together with the arid Sahel displays high topographical and climatic heterogeneity, and has experienced recent and strong climatic oscillations that have greatly shifted biodiversity distribution and community composition. The large size, remoteness and long-term political instability of the Sahara-Sahel, have limited knowledge on its biodiversity. However, over the last decade, there have been an increasing number of published scientific studies based on modern geomatic and molecular tools, and broad sampling of taxa of these regions. This review tracks trends in knowledge about biodiversity patterns, processes and threats across the Sahara-Sahel, and anticipates needs for biodiversity research and conservation. Recent studies are changing completely the perception of regional biodiversity patterns. Instead of relatively low species diversity with distribution covering most of the region, studies now suggest a high rate of endemism and larger number of species, with much narrower and fragmented ranges, frequently limited to micro-hotspots of biodiversity. Molecular-based studies are also unravelling cryptic diversity associated with mountains, which together with recent distribution atlases, allows identifying integrative biogeographic patterns in biodiversity distribution. Mapping of multivariate environmental variation (at 1 km × 1 km resolution) of the region illustrates main biogeographical features of the Sahara-Sahel and supports recently hypothesised dispersal corridors and refugia. Micro-scale water-features present mostly in mountains have been associated with local biodiversity hotspots. However, the distribution of available data on vertebrates highlights current knowledge gaps that still apply to a large proportion of the Sahara-Sahel. Current research is providing insights into key

A conservative region of the mercuric reductase gene (merA as a molecular marker of bacterial mercury resistance Região conservada do gene da mercúrio redutase (merA como marcador molecular da resistência bacteriana ao mercúrio

Directory of Open Access Journals (Sweden)

Adriana Sotero-Martins

2008-06-01

Full Text Available The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II to Hg0, which is dependent of the mercuric reductase enzyme (MerA activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains.O mecanismo de resistência bacteriana ao mercúrio mais comum é baseada na redução do Hg(II a Hg0, através da atividade da enzima mercúrio redutase (MerA. O uso do fragmento de 431 pb amplificado de uma região conservada do gene merA, que codifica a enzima MerA,foi utilizado como marcador molecular deste mecanismo, permitindo a identificação de bactérias resistentes ao mercúrio.

Conservation strategies for Arapaima gigas (Schinz, 1822 and the Amazonian várzea ecosystem

Directory of Open Access Journals (Sweden)

T. Hrbek

Full Text Available In the present study we report a spatial autocorrelation analysis of molecular data obtained for Arapaima gigas, and the implication of this study for conservation and management. Arapaima is an important, but critically over-exploited giant food fish of the Amazonian várzea. Analysis of 14 variable microsatellite loci and 2,347 bp of mtDNA from 126 individuals sampled in seven localities within the Amazon basin suggests that Arapaima forms a continuous population with extensive genetic exchange among localities. Weak effect of isolation-by-distance is observed in microsatellite data, but not in mtDNA data. Spatial autocorrelation analysis of genetic and geographic data suggests that genetic exchange is significantly restricted at distances greater than 2,500 km. We recommend implementing a source-sink metapopulation management and conservation model by proposing replicate high quality várzea reserves in the upper, central, and lower Amazon basin. This conservation strategy would: 1 preserve all of the current genetic diversity of Arapaima; 2 create a set of reserves to supply immigrants for locally depleted populations; 3 preserve core várzea areas in the Amazon basin on which many other species depend. We stress that conservation strategies should not only preserve current genetic diversity, but also the evolutionary processes which have generated the observed patterns.

Adaptive sampling strategies with high-throughput molecular dynamics

Science.gov (United States)

Clementi, Cecilia

Despite recent significant hardware and software developments, the complete thermodynamic and kinetic characterization of large macromolecular complexes by molecular simulations still presents significant challenges. The high dimensionality of these systems and the complexity of the associated potential energy surfaces (creating multiple metastable regions connected by high free energy barriers) does not usually allow to adequately sample the relevant regions of their configurational space by means of a single, long Molecular Dynamics (MD) trajectory. Several different approaches have been proposed to tackle this sampling problem. We focus on the development of ensemble simulation strategies, where data from a large number of weakly coupled simulations are integrated to explore the configurational landscape of a complex system more efficiently. Ensemble methods are of increasing interest as the hardware roadmap is now mostly based on increasing core counts, rather than clock speeds. The main challenge in the development of an ensemble approach for efficient sampling is in the design of strategies to adaptively distribute the trajectories over the relevant regions of the systems' configurational space, without using any a priori information on the system global properties. We will discuss the definition of smart adaptive sampling approaches that can redirect computational resources towards unexplored yet relevant regions. Our approaches are based on new developments in dimensionality reduction for high dimensional dynamical systems, and optimal redistribution of resources. NSF CHE-1152344, NSF CHE-1265929, Welch Foundation C-1570.

Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene

Energy Technology Data Exchange (ETDEWEB)

Cawkwell, M. J., E-mail: cawkwell@lanl.gov; Niklasson, Anders M. N. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Dattelbaum, Dana M. [Weapons Experiments Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2015-02-14

The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene.

Science.gov (United States)

Cawkwell, M J; Niklasson, Anders M N; Dattelbaum, Dana M

2015-02-14

The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

Conservation when landowners have bargaining power

DEFF Research Database (Denmark)

Lennox, Gareth D.; Gaston, Kevin J.; Acs, Szvetlana

2013-01-01

agreement. Implicitly assumed in such studies is therefore that those who ``produce'' biodiversity (landowners) receive none of the surplus available from trade. Instead, landowners could use their bargaining power to gain profits from conservation investments. We employ game theory to determine the surplus...... landowners could obtain in negotiations over conservation agreements, and the consequent effects on conservation outcomes, when enrolment decisions are governed by continuous variables (e.g. the proportion of a property to enrol). In addition, we consider how landowner uncertainty regarding the opportunity...... costs of other landowners affects these outcomes. Landowners' ability to gain surplus is highly variable and reflects variation in the substitutability of different properties for achieving a specified conservation objective. The ability of landowners to obtain profits from conservation agreements...

High-temperature annealing of graphite: A molecular dynamics study

Science.gov (United States)

Petersen, Andrew; Gillette, Victor

2018-05-01

A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.

Conservation mycology in Australia and the potential role of citizen science.

Science.gov (United States)

Irga, Peter J; Barker, Katherine; Torpy, Fraser R

2018-04-23

Fungi are undoubtedly important for ecosystem functioning, however they are relatively poorly considered in biodiversity conservation planning. Fungi have been omitted or given scant attention in most biodiversity policy documents, management plans and formal conservation schedules throughout the world. This oversight may be due to a general lack of awareness in the scientific community, compounded by a scarcity of mycology-associated curricula at the tertiary level, along with a lack of mycologists in research institutions. While molecular advancements the systematic cataloging of fungi and facilitate insights into fungal communities, the scarcity of professional mycologists in the environmental sciences hampers conservation efforts. Conversely, citizen science initiatives are making significant contributions to the mycology discipline, by both increasing awareness as well as extending the scope of fungal surveys. Future research by professional and amateur mycologists into the distribution and functionality in ecosystems will help us identify wider, and more effective conservation goals. This article is protected by copyright. All rights reserved.

Equity trade-offs in conservation decision making.

Science.gov (United States)

Law, Elizabeth A; Bennett, Nathan J; Ives, Christopher D; Friedman, Rachel; Davis, Katrina J; Archibald, Carla; Wilson, Kerrie A

2018-04-01

Conservation decisions increasingly involve multiple environmental and social objectives, which result in complex decision contexts with high potential for trade-offs. Improving social equity is one such objective that is often considered an enabler of successful outcomes and a virtuous ideal in itself. Despite its idealized importance in conservation policy, social equity is often highly simplified or ill-defined and is applied uncritically. What constitutes equitable outcomes and processes is highly normative and subject to ethical deliberation. Different ethical frameworks may lead to different conceptions of equity through alternative perspectives of what is good or right. This can lead to different and potentially conflicting equity objectives in practice. We promote a more transparent, nuanced, and pluralistic conceptualization of equity in conservation decision making that particularly recognizes where multidimensional equity objectives may conflict. To help identify and mitigate ethical conflicts and avoid cases of good intentions producing bad outcomes, we encourage a more analytical incorporation of equity into conservation decision making particularly during mechanistic integration of equity objectives. We recommend that in conservation planning motivations and objectives for equity be made explicit within the problem context, methods used to incorporate equity objectives be applied with respect to stated objectives, and, should objectives dictate, evaluation of equity outcomes and adaptation of strategies be employed during policy implementation. © 2017 Society for Conservation Biology.

Evolutionary conservation and network structure characterize genes of phenotypic relevance for mitosis in human.

Directory of Open Access Journals (Sweden)

Marek Ostaszewski

Full Text Available The impact of gene silencing on cellular phenotypes is difficult to establish due to the complexity of interactions in the associated biological processes and pathways. A recent genome-wide RNA knock-down study both identified and phenotypically characterized a set of important genes for the cell cycle in HeLa cells. Here, we combine a molecular interaction network analysis, based on physical and functional protein interactions, in conjunction with evolutionary information, to elucidate the common biological and topological properties of these key genes. Our results show that these genes tend to be conserved with their corresponding protein interactions across several species and are key constituents of the evolutionary conserved molecular interaction network. Moreover, a group of bistable network motifs is found to be conserved within this network, which are likely to influence the network stability and therefore the robustness of cellular functioning. They form a cluster, which displays functional homogeneity and is significantly enriched in genes phenotypically relevant for mitosis. Additional results reveal a relationship between specific cellular processes and the phenotypic outcomes induced by gene silencing. This study introduces new ideas regarding the relationship between genotype and phenotype in the context of the cell cycle. We show that the analysis of molecular interaction networks can result in the identification of genes relevant to cellular processes, which is a promising avenue for future research.

Conserved regulators of nucleolar size revealed by global phenotypic analyses.

Science.gov (United States)

Neumüller, Ralph A; Gross, Thomas; Samsonova, Anastasia A; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

2013-08-20

Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I-mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I-mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry-based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules.

Conserved Regulators of Nucleolar Size Revealed by Global Phenotypic Analyses

Science.gov (United States)

Neumüller, Ralph A.; Gross, Thomas; Samsonova, Anastasia A.; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P.; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

2014-01-01

Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I–mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I–mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry–based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules. PMID:23962978

Molecular cogs of the insect circadian clock.

Science.gov (United States)

Shirasu, Naoto; Shimohigashi, Yasuyuki; Tominaga, Yoshiya; Shimohigashi, Miki

2003-08-01

During the last five years, enormous progress has been made in understanding the molecular basis of circadian systems, mainly by molecular genetic studies using the mouse and fly. Extensive evidence has revealed that the core clock machinery involves "clock genes" and "clock proteins" functioning as molecular cogs. These participate in transcriptional/translational feedback loops and many homologous clock-components in the fruit fly Drosophila are also expressed in mammalian clock tissues with circadian rhythms. Thus, the mechanisms of the central clock seem to be conserved across animal kingdom. However, some recent studies imply that the present widely accepted molecular models of circadian clocks may not always be supported by the experimental evidence.

Free radicals. High-resolution spectroscopy and molecular structure

International Nuclear Information System (INIS)

Hirota, E.

1983-01-01

High-resolution, high-sensitivity spectroscopy using CW laser and microwave sources has been applied to free radicals and transient molecules to establish their existence and to explore their properties in detail. The radicals studied were mainly generated by discharge-induced reactions. A few molecules are used as typical examples to illustrate the results so far obtained. The molecular and electronic structures of free radicals, intramolecular motions of large amplitudes in some labile molecules, and metastable electronic states of carbenes are given special emphasis. The significance of the present spectroscopic results in other related fields such as astronomy and atmospheric chemistry is stressed. 4 figures, 3 tables

High impact polystyrene (HIPS). Predicting its molecular, morphological and mechanical properties

International Nuclear Information System (INIS)

Luciani, C; Estenoz, D; Morales, G; Meira, G

2004-01-01

A mathematical model that is able to predict the molecular and morphological structure of high impact polystyrene (HIPS) and the Fluidity Index (MFI) is presented. The model is divided into two parts: a) the estimation of the material's molecular and morphological properties, simulating the polymerization process in discontinuous mass based on the recipe and the conditions of synthesis; and b) the prediction of rheological variables (viscosity at low deformation speeds and relaxation time), and of the MFI, based on average molecular and morphological variables. The model also combines with empirical correlations proposed in the literature [1] in order to estimate impact strength (IS). The predictions for a), b) and impact strength were co-validated by independent data and resulted in a good fit (CW)

Making conservation work for everyone

Energy Technology Data Exchange (ETDEWEB)

Wiersma, J. [Veridian Corp., Ajax, ON (Canada)

2004-07-01

This presentation discussed the economic value of conservation, the optimal deployment of energy conservation. A sample load profile was presented to demonstrate how much electricity the average residential customer uses on a summer day. The average customer does not have the tools to understand the financial consequences of conservation for different types of equipment at different times of the day. Smart metering technology could help in this regard. Accurate unsubsidized prices are also considered to be the best incentive to conserve because customers will reduce electricity use when the prices are high. It was also suggested that standards for new appliances should be increased effectively to their economic value. The enablers to energy conservation include solid consumer education programs, real time metering in places where it is cost effective, real time pricing in places where it is practical, and power rates that reflect real costs. Barriers to energy conservation include the residual economic advantage that may be insufficient to justify investment; support from local distribution companies and transmission companies if the lost revenue adjustment mechanism (LRAM) is not sufficient to recover lost revenue and if LDCs are not sufficiently involved in the design of the electricity conservation program. 7 figs.

Use of electroporation for high-molecular-weight DNA-mediated gene transfer.

Science.gov (United States)

Jastreboff, M M; Ito, E; Bertino, J R; Narayanan, R

1987-08-01

Electroporation was used to introduce high-molecular-weight DNA into murine hematopoietic cells and NIH3T3 cells. CCRF-CEM cells were stably transfected with SV2NEO plasmid and the genomic DNA from G-418-resistant clones (greater than 65 kb) was introduced into mouse bone marrow and NIH3T3 cells by electroporation. NEO sequences and expression were detected in the hematopoietic tissues of lethally irradiated mice, with 24% of individual spleen colonies expressing NEO. The frequency of genomic DNA transfer into NIH3T3 cells was 0.25 X 10(-3). Electroporation thus offers a powerful mode of gene transfer not only of cloned genes but also of high-molecular-weight DNA into cells.

Disassembled DJ-1 high molecular weight complex in cortex mitochondria from Parkinson's disease patients

Directory of Open Access Journals (Sweden)

Adler Charles

2009-07-01

Full Text Available Abstract Correction to Nural H, He P, Beach T, Sue L, Xia W, Shen Y. Disassembled DJ-1 high molecular weight complex in cortex mitochondria from Parkinson's disease patients Molecular Neurodegeneration 2009, 4:23.

Inhibitory control and visuo-spatial reversibility in Piaget’s seminal number conservation task: A high-density ERP study.

Directory of Open Access Journals (Sweden)

Gregoire eBorst

2013-12-01

Full Text Available The present high-density ERP study on 13 adults aimed to determine whether number conservation relies on the ability to inhibit the overlearned length-equals-number strategy and then imagine the shortening of the row that was lengthened. Participants performed the number-conservation task and, after the EEG session, the mental imagery task. In the number-conservation task, first two rows with the same number of tokens and the same length were presented on a computer screen (COV condition and then, the tokens in one of the two rows were spread apart (INT condition. Participants were instructed to determine whether the two rows had an identical number of tokens. In the mental imagery task, two rows with different lengths but the same number of tokens were presented and participants were instructed to imagine the tokens in the longer row aligning with the tokens in the shorter row. In the number-conservation task, we found that the amplitudes of the centro-parietal N2 and fronto-central P3 were higher in the INT than in the COV conditions. In addition, the differences in response times between the two conditions were correlated with the differences in the amplitudes of the fronto-central P3. In light of previous results reported on the number-conservation task in adults, the present results suggest that inhibition might be necessary to succeed the number-conservation task in adults even when the transformation of the length of one of the row is displayed. Finally, we also reported correlations between the speed at which participants could imagine the shortening of one of the row in the mental imagery task, the speed at which participants could determine that the two rows had the same number of tokens after the tokens in one of the row were spread apart and the latency of the late positive parietal component in the number-conservation task. Therefore, performing the number-conservation task might involve mental transformation processes in adults.

Elucidating the composition and conservation of the autophagy pathway in photosynthetic eukaryotes

Science.gov (United States)

Shemi, Adva; Ben-Dor, Shifra; Vardi, Assaf

2015-01-01

Aquatic photosynthetic eukaryotes represent highly diverse groups (green, red, and chromalveolate algae) derived from multiple endosymbiosis events, covering a wide spectrum of the tree of life. They are responsible for about 50% of the global photosynthesis and serve as the foundation for oceanic and fresh water food webs. Although the ecophysiology and molecular ecology of some algal species are extensively studied, some basic aspects of algal cell biology are still underexplored. The recent wealth of genomic resources from algae has opened new frontiers to decipher the role of cell signaling pathways and their function in an ecological and biotechnological context. Here, we took a bioinformatic approach to explore the distribution and conservation of TOR and autophagy-related (ATG) proteins (Atg in yeast) in diverse algal groups. Our genomic analysis demonstrates conservation of TOR and ATG proteins in green algae. In contrast, in all 5 available red algal genomes, we could not detect the sequences that encode for any of the 17 core ATG proteins examined, albeit TOR and its interacting proteins are conserved. This intriguing data suggests that the autophagy pathway is not conserved in red algae as it is in the entire eukaryote domain. In contrast, chromalveolates, despite being derived from the red-plastid lineage, retain and express ATG genes, which raises a fundamental question regarding the acquisition of ATG genes during algal evolution. Among chromalveolates, Emiliania huxleyi (Haptophyta), a bloom-forming coccolithophore, possesses the most complete set of ATG genes, and may serve as a model organism to study autophagy in marine protists with great ecological significance. PMID:25915714

smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni

Science.gov (United States)

2012-01-01

Background MicroRNAs (miRNAs) constitute a family of small RNA (sRNA) population that regulates the gene expression and plays an important role in plant development, metabolism, signal transduction and stress response. Extensive studies on miRNAs have been performed in different plants such as Arabidopsis thaliana, Oryza sativa etc. and volume of the miRNA database, mirBASE, has been increasing on day to day basis. Stevia rebaudiana Bertoni is an important perennial herb which accumulates high concentrations of diterpene steviol glycosides which contributes to its high indexed sweetening property with no calorific value. Several studies have been carried out for understanding molecular mechanism involved in biosynthesis of these glycosides, however, information about miRNAs has been lacking in S. rebaudiana. Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs irrespective of availability of genome sequence data. Results To identify miRNAs in S. rebaudiana, sRNA library was constructed and sequenced using Illumina genome analyzer II. A total of 30,472,534 reads representing 2,509,190 distinct sequences were obtained from sRNA library. Based on sequence similarity, we identified 100 miRNAs belonging to 34 highly conserved families. Also, we identified 12 novel miRNAs whose precursors were potentially generated from stevia EST and nucleotide sequences. All novel sequences have not been earlier described in other plant species. Putative target genes were predicted for most conserved and novel miRNAs. The predicted targets are mainly mRNA encoding enzymes regulating essential plant metabolic and signaling pathways. Conclusions This study led to the identification of 34 highly conserved miRNA families and 12 novel potential miRNAs indicating that specific miRNAs exist in stevia species. Our results provided information on stevia miRNAs and their targets building a foundation for future studies to

Human Intellectual Disability Genes Form Conserved Functional Modules in Drosophila

Science.gov (United States)

Oortveld, Merel A. W.; Keerthikumar, Shivakumar; Oti, Martin; Nijhof, Bonnie; Fernandes, Ana Clara; Kochinke, Korinna; Castells-Nobau, Anna; van Engelen, Eva; Ellenkamp, Thijs; Eshuis, Lilian; Galy, Anne; van Bokhoven, Hans; Habermann, Bianca; Brunner, Han G.; Zweier, Christiane; Verstreken, Patrik; Huynen, Martijn A.; Schenck, Annette

2013-01-01

Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules. PMID:24204314

Survey of high-velocity molecular gas in the vicinity of Herbig-Haro objects. I

International Nuclear Information System (INIS)

Edwards, S.; Snell, R.L.

1983-01-01

A survey of high-velocity molecular gas toward 49 Herbig-Haro objects is presented. Observations of the 12 CO J = 1-0 transition obtained with the 14 m telescope of the Five College Radio Astronomy Observatory reveal three new spatially extended high-velocity molecular outflows. One is in the NGC 1333 region near HH 12, and two are in the NGC 7129 region, the first near LkHα 234 and the second near a far-infrared source. The relationship between optical Herbin-Haro emission knots and large-scale motions of the ambient molecular material is investigated, and the properties of high-velocity molecular outflows in the vicinity of Herbig-Haro objects are discussed. Of 11 energetic outflows in the vicinity of Herbig-Haro objects, eight are found in four pairs separated by 0.2-1.0 pc. We estimate that energetic outflows characterized by mass loss rates > or =10 -7 M/sub sun/ yr -1 occur for at least 10 4 yr once in the lifetime of all stars with masses greater than 1M/sub sun/

Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria

Directory of Open Access Journals (Sweden)

Ochman Howard

2009-09-01

Full Text Available Abstract Background Because bacteria do not have a robust fossil record, attempts to infer the timing of events in their evolutionary history requires comparisons of molecular sequences. This use of molecular clocks is based on the assumptions that substitution rates for homologous genes or sites are fairly constant through time and across taxa. Violation of these conditions can lead to erroneous inferences and result in estimates that are off by orders of magnitude. In this study, we examine the consistency of substitution rates among a set of conserved genes in diverse bacterial lineages, and address the questions regarding the validity of molecular dating. Results By examining the evolution of 16S rRNA gene in obligate endosymbionts, which can be calibrated by the fossil record of their hosts, we found that the rates are consistent within a clade but varied widely across different bacterial lineages. Genome-wide estimates of nonsynonymous and synonymous substitutions suggest that these two measures are highly variable in their rates across bacterial taxa. Genetic drift plays a fundamental role in determining the accumulation of substitutions in 16S rRNA genes and at nonsynonymous sites. Moreover, divergence estimates based on a set of universally conserved protein-coding genes also exhibit low correspondence to those based on 16S rRNA genes. Conclusion Our results document a wide range of substitution rates across genes and bacterial taxa. This high level of variation cautions against the assumption of a universal molecular clock for inferring divergence times in bacteria. However, by applying relative-rate tests to homologous genes, it is possible to derive reliable local clocks that can be used to calibrate bacterial evolution. Reviewers This article was reviewed by Adam Eyre-Walker, Simonetta Gribaldo and Tal Pupko (nominated by Dan Graur.

Conservation Below The Species Level: Suitable Evolutionarily Significant Units Among Mountain Vipers (The Montivipera Raddei Complex) in Iran.

Science.gov (United States)

Behrooz, Roozbeh; Kaboli, Mohammad; Arnal, Véronique; Nazarizadeh, Masoud; Asadi, Atefeh; Salmanian, Amin; Ahmadi, Mohsen; Montgelard, Claudine

2018-02-01

Northern and western mountains of Iran are among the most important biodiversity and endemism hot spots for reptiles in the Middle East. Among herpetofauna, the montivipers represent an emblematic and fragmented endemic group for which estimating their level of genetic differentiation and defining conservation priorities is urgently needed. Here, we present the most comprehensive phylogenetic study on the Montivipera raddei species group comprising all five known taxa, among which three are endemic to Iran. Based on two mitochondrial genes, phylogenetic and phylogeographic analyses revealed three major lineages each presenting very contrasting distribution area. The Iranian montivipers are highly structured in clades showing low genetic diversity and corresponding to high altitude summits. Molecular dating revealed the role of Quaternary paleo-climatic oscillations and altitudinal movements of montivipers in shaping genetic diversity and differentiation of these sky-island taxa. In addition, the best scenario of historical biogeography allowed identifying three possible refugial areas in Iran most likely arising by vicariance. Based on our mitochondrial results and pending additional data, we recognize three candidate species among the Montivipera raddei complex: M. raddei, M.latifii and M. kuhrangica that are coherent with their geographical distribution. We propose that the most appropriate Evolutionary Significant Units for conservation of the montivipers are represented by thirteen units among which six are recognized as high priority. Finally, we suggest some recommendations to the IUCN as well as to the Iranian conservation policies with respect to conservation prioritization. © The American Genetic Association 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A Brief Review of Molecular Techniques to Assess Plant Diversity

Directory of Open Access Journals (Sweden)

Ibrahim A. Arif

2010-05-01

Full Text Available Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD, amplified fragment length polymorphism (AFLP, microsatellites and single nucleotide polymorphisms (SNP have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species.

A Brief Review of Molecular Techniques to Assess Plant Diversity

Science.gov (United States)

Arif, Ibrahim A.; Bakir, Mohammad A.; Khan, Haseeb A.; Al Farhan, Ahmad H.; Al Homaidan, Ali A.; Bahkali, Ali H.; Sadoon, Mohammad Al; Shobrak, Mohammad

2010-01-01

Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species. PMID:20559503

New approaches in mathematical biology: Information theory and molecular machines

International Nuclear Information System (INIS)

Schneider, T.

1995-01-01

My research uses classical information theory to study genetic systems. Information theory was founded by Claude Shannon in the 1940's and has had an enormous impact on communications engineering and computer sciences. Shannon found a way to measure information. This measure can be used to precisely characterize the sequence conservation at nucleic-acid binding sites. The resulting methods, by completely replacing the use of ''consensus sequences'', provide better models for molecular biologists. An excess of conservation led us to do experimental work on bacteriophage T7 promoters and the F plasmid IncD repeats. The wonderful fidelity of telephone communications and compact disk (CD) music can be traced directly to Shannon's channel capacity theorem. When rederived for molecular biology, this theorem explains the surprising precision of many molecular events. Through connections with the Second Law of Thermodyanmics and Maxwell's Demon, this approach also has implications for the development of technology at the molecular level. Discussions of these topics are held on the internet news group bionet.info-theo. (author). (Abstract only)

Energy conservation in India: a profile

International Nuclear Information System (INIS)

Anon.

1992-01-01

The decade and half since the oil crisis of 1973 has been a period that has witnessed a steady growth of the energy conservation ethos in India. Housekeeping and low risk conservation options have been largely preferred so far. The IMWG (Inter-Ministerial Working Group on Utilization and Conservation of Energy) study did not evaluate potential saving through the introduction of high risk and high pay-off technologies. The potential for energy conservation in India is substantial. However, some of the barriers to achieving the potential in the past have been energy prices which deviate from rational tariffs and prices, a lack of information on specific measures and of options for achieving energy conservation, paucity of capital for schemes requiring technology upgradation and efficiency improvements, and the inadequacy if institutional arrangement for promoting energy conservation in different sectors of the economy. Recent efforts pursued by several organizations however provide some basis for optimism. Given the growing capital intensity of the energy sector in India, more vigorous efforts are likely to be made in the future. In particular, success stories in some industrial units indicate that decentralized efforts by the units themselves can achieve a great deal in improving the efficiency of energy use, particularly in the Indian industry. Policies to promote such programmes would help accelerate energy conservation efforts in industrial units and in other sectors. It is therefore hoped that the intensity of energy use in several sectors of the indian economy will be reduced significantly in the coming years. (author). 3 refs., 3 tabs

Existence of CD8α-like dendritic cells with a conserved functional specialization and a common molecular signature in distant mammalian species.

Science.gov (United States)

Contreras, Vanessa; Urien, Céline; Guiton, Rachel; Alexandre, Yannick; Vu Manh, Thien-Phong; Andrieu, Thibault; Crozat, Karine; Jouneau, Luc; Bertho, Nicolas; Epardaud, Mathieu; Hope, Jayne; Savina, Ariel; Amigorena, Sebastian; Bonneau, Michel; Dalod, Marc; Schwartz-Cornil, Isabelle

2010-09-15

The mouse lymphoid organ-resident CD8alpha(+) dendritic cell (DC) subset is specialized in Ag presentation to CD8(+) T cells. Recent evidence shows that mouse nonlymphoid tissue CD103(+) DCs and human blood DC Ag 3(+) DCs share similarities with CD8alpha(+) DCs. We address here whether the organization of DC subsets is conserved across mammals in terms of gene expression signatures, phenotypic characteristics, and functional specialization, independently of the tissue of origin. We study the DC subsets that migrate from the skin in the ovine species that, like all domestic animals, belongs to the Laurasiatheria, a distinct phylogenetic clade from the supraprimates (human/mouse). We demonstrate that the minor sheep CD26(+) skin lymph DC subset shares significant transcriptomic similarities with mouse CD8alpha(+) and human blood DC Ag 3(+) DCs. This allowed the identification of a common set of phenotypic characteristics for CD8alpha-like DCs in the three mammalian species (i.e., SIRP(lo), CADM1(hi), CLEC9A(hi), CD205(hi), XCR1(hi)). Compared to CD26(-) DCs, the sheep CD26(+) DCs show 1) potent stimulation of allogeneic naive CD8(+) T cells with high selective induction of the Ifngamma and Il22 genes; 2) dominant efficacy in activating specific CD8(+) T cells against exogenous soluble Ag; and 3) selective expression of functional pathways associated with high capacity for Ag cross-presentation. Our results unravel a unifying definition of the CD8alpha(+)-like DCs across mammalian species and identify molecular candidates that could be used for the design of vaccines applying to mammals in general.

The Highly Conserved Proline at Position 438 in Pseudorabies Virus gH Is Important for Regulation of Membrane Fusion

OpenAIRE

Schröter, Christina; Klupp, Barbara G.; Fuchs, Walter; Gerhard, Marika; Backovic, Marija; Rey, Felix A.; Mettenleiter, Thomas C.

2014-01-01

Membrane fusion in herpesviruses requires viral glycoproteins (g) gB and gH/gL. While gB is considered the actual fusion protein but is nonfusogenic per se, the function of gH/gL remains enigmatic. Crystal structures for different gH homologs are strikingly similar despite only moderate amino acid sequence conservation. A highly conserved sequence motif comprises the residues serine-proline-cysteine corresponding to positions 437 to 439 in pseudorabies virus (PrV) gH. The PrV-gH structure sho...

Theory of Excitation Transfer between Two-Dimensional Semiconductor and Molecular Layers

Science.gov (United States)

Specht, Judith F.; Verdenhalven, Eike; Bieniek, Björn; Rinke, Patrick; Knorr, Andreas; Richter, Marten

2018-04-01

The geometry-dependent energy transfer rate from an electrically pumped inorganic semiconductor quantum well into an organic molecular layer is studied theoretically. We focus on Förster-type nonradiative excitation transfer between the organic and inorganic layers and include quasimomentum conservation and intermolecular coupling between the molecules in the organic film. (Transition) partial charges calculated from density-functional theory are used to calculate the coupling elements. The partial charges describe the spatial charge distribution and go beyond the common dipole-dipole interaction. We find that the transfer rates are highly sensitive to variations in the geometry of the hybrid inorganic-organic system. For instance, the transfer efficiency is improved by up to 2 orders of magnitude by tuning the spatial arrangement of the molecules on the surface: Parameters of importance are the molecular packing density along the effective molecular dipole axis and the distance between the molecules and the surface. We also observe that the device performance strongly depends on the orientation of the molecular dipole moments relative to the substrate dipole moments determined by the inorganic crystal structure. Moreover, the operating regime is identified where inscattering dominates over unwanted backscattering from the molecular layer into the substrate.

Violations of conservation laws in viscous liquid dynamics

DEFF Research Database (Denmark)

Dyre, Jeppe

2007-01-01

The laws expressing conservation of momentum and energy apply to any isolated system, but these laws are violated for highly viscous liquids under laboratory conditions because of the unavoidable interactions with the measuring equipment over the long times needed to study the dynamics. Moreover,......, although particle number conservation applies strictly for any liquid, the solidity of viscous liquids implies that even this conservation law is apparently violated in coarse-grained descriptions of density fluctuations.......The laws expressing conservation of momentum and energy apply to any isolated system, but these laws are violated for highly viscous liquids under laboratory conditions because of the unavoidable interactions with the measuring equipment over the long times needed to study the dynamics. Moreover...

MOLECULAR DIAGNOSTICS OF YERSINIA RUCKERI

Directory of Open Access Journals (Sweden)

Yu. Rud

2014-06-01

Full Text Available Purpose. The analysis of nucleotide sequences of the 16S rDNA gene of virulent strains of Yersinia ruckeri and to develop the method of molecular diagnostic of enteric redmouth disease. Methodology. By the method of CLUSTALW algorithm in MEGA software version 6.0 the nucleotide sequences of the 16S rDNA gene of virulent strains of Yersinia ruckeri were analysed. For development of molecular diagnostic of Y. ruckeri the method of polymerase chain reaction (PCR was used. Primer selection was carried out in software VectorNTI11 and on-line-service BLAST. The PCR products were investigated by the methods of sequencing and nucleotide analysis. Findings. Based on PCR assay the method of molecular diagnostic of enteric redmouth disease agent, bacterium Y. ruckeri was developed. It was shown that specific oligonucleotide primers generated PCR products in size of 600 base pairs. PCR products were investigated by the sequencing that showed right targeting of primers in reaction. Originality. Among high-conservative gene of 16S rDNA of Y. ruckeri the fragment of DNA was determined to which the specific primers for rapid diagnostic of virulent strains were selected. Practical Value. Rapid diagnostic of yersiniosis will allow to identify an agent of this infectious disease, bacterium Y. ruckeri, and to provide the prophylactic or medical measures in the fish farming of Ukraine.

Genetic species identification in weatherfish and first molecular confirmation of Oriental Weatherfish Misgurnus anguillicaudatus (Cantor, 1842 in Central Europe

Directory of Open Access Journals (Sweden)

Belle Christina C.

2017-01-01

Full Text Available The Oriental Weatherfish is considered a globally invasive fish species. In Europe, several reported feral populations of Oriental Weatherfish display an overlapping distribution range with native weatherfish Misgurnus fossilis, a declining species of international conservation and aquatic management concern. Morphologically distinguishing the different weatherfish species can be difficult, as their coloration is highly variable, many species reveal high phenotypic plasticity, and morphological traits like coloration might be not obvious or might be degraded during field sampling and after preservation. Herein, we analysed suspicious weatherfish specimens from southern Germany, demonstrating the usefulness of molecular genetic species identifications in this genus. We present the first molecular genetic species record of Misgurnus anguillicaudatus in Central Europe, and confirm the range expansion of Oriental Weatherfish into the river Inn catchment in southern Germany. As accurate species identification is crucial both in the context of monitoring and conserving native endangered species, and in early detection and prevention of biological invasion, we suggest the standard use of genetic species identification if morphological traits are not obvious.

Designing an educative curriculum unit for teaching molecular geometry in high school chemistry

Science.gov (United States)

Makarious, Nader N.

Chemistry is a highly abstract discipline that is taught and learned with the aid of various models. Among the most challenging, yet a fundamental topic in general chemistry at the high school level, is molecular geometry. This study focused on developing exemplary educative curriculum materials pertaining to the topic of molecular geometry. The methodology used in this study consisted of several steps. First, a diverse set of models were analyzed to determine to what extent each model serves its purpose in teaching molecular geometry. Second, a number of high school teachers and college chemistry professors were asked to share their experiences on using models in teaching molecular geometry through an online questionnaire. Third, findings from the comparative analysis of models, teachers’ experiences, literature review on models and students’ misconceptions, the curriculum expectations of the Next Generation Science Standards and their emphasis on three-dimensional learning and nature of science (NOS) contributed to the development of the molecular geometry unit. Fourth, the developed unit was reviewed by fellow teachers and doctoral-level science education experts and was revised to further improve its coherence and clarity in support of teaching and learning of the molecular geometry concepts. The produced educative curriculum materials focus on the scientific practice of developing and using models as promoted in the Next Generations Science Standards (NGSS) while also addressing nature of science (NOS) goals. The educative features of the newly developed unit support teachers’ pedagogical knowledge (PK) and pedagogical content knowledge (PCK). The unit includes an overview, teacher’s guide, and eight detailed lesson plans with inquiry oriented modeling activities replete with models and suggestions for teachers, as well as formative and summative assessment tasks. The unit design process serves as a model for redesigning other instructional units in

Comparison of theoretical proteomes: Identification of COGs with conserved and variable pI within the multimodal pI distribution

Directory of Open Access Journals (Sweden)

Lynn Andrew M

2005-09-01

Full Text Available Abstract Background Theoretical proteome analysis, generated by plotting theoretical isoelectric points (pI against molecular masses of all proteins encoded by the genome show a multimodal distribution for pI. This multimodal distribution is an effect of allowed combinations of the charged amino acids, and not due to evolutionary causes. The variation in this distribution can be correlated to the organisms ecological niche. Contributions to this variation maybe mapped to individual proteins by studying the variation in pI of orthologs across microorganism genomes. Results The distribution of ortholog pI values showed trimodal distributions for all prokaryotic genomes analyzed, similar to whole proteome plots. Pairwise analysis of pI variation show that a few COGs are conserved within, but most vary between, the acidic and basic regions of the distribution, while molecular mass is more highly conserved. At the level of functional grouping of orthologs, five groups vary significantly from the population of orthologs, which is attributed to either conservation at the level of sequences or a bias for either positively or negatively charged residues contributing to the function. Individual COGs conserved in both the acidic and basic regions of the trimodal distribution are identified, and orthologs that best represent the variation in levels of the acidic and basic regions are listed. Conclusion The analysis of pI distribution by using orthologs provides a basis for resolution of theoretical proteome comparison at the level of individual proteins. Orthologs identified that significantly vary between the major acidic and basic regions maybe used as representative of the variation of the entire proteome.

Highly conserved small subunit residues influence rubisco large subunit catalysis.

Science.gov (United States)

Genkov, Todor; Spreitzer, Robert J

2009-10-30

The chloroplast enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the rate-limiting step of photosynthetic CO(2) fixation. With a deeper understanding of its structure-function relationships and competitive inhibition by O(2), it may be possible to engineer an increase in agricultural productivity and renewable energy. The chloroplast-encoded large subunits form the active site, but the nuclear-encoded small subunits can also influence catalytic efficiency and CO(2)/O(2) specificity. To further define the role of the small subunit in Rubisco function, the 10 most conserved residues in all small subunits were substituted with alanine by transformation of a Chlamydomonas reinhardtii mutant that lacks the small subunit gene family. All the mutant strains were able to grow photosynthetically, indicating that none of the residues is essential for function. Three of the substitutions have little or no effect (S16A, P19A, and E92A), one primarily affects holoenzyme stability (L18A), and the remainder affect catalysis with or without some level of associated structural instability (Y32A, E43A, W73A, L78A, P79A, and F81A). Y32A and E43A cause decreases in CO(2)/O(2) specificity. Based on the x-ray crystal structure of Chlamydomonas Rubisco, all but one (Glu-92) of the conserved residues are in contact with large subunits and cluster near the amino- or carboxyl-terminal ends of large subunit alpha-helix 8, which is a structural element of the alpha/beta-barrel active site. Small subunit residues Glu-43 and Trp-73 identify a possible structural connection between active site alpha-helix 8 and the highly variable small subunit loop between beta-strands A and B, which can also influence Rubisco CO(2)/O(2) specificity.

Cortical cytasters: a highly conserved developmental trait of Bilateria with similarities to Ctenophora

Directory of Open Access Journals (Sweden)

Salinas-Saavedra Miguel

2011-12-01

Full Text Available Abstract Background Cytasters (cytoplasmic asters are centriole-based nucleation centers of microtubule polymerization that are observable in large numbers in the cortical cytoplasm of the egg and zygote of bilaterian organisms. In both protostome and deuterostome taxa, cytasters have been described to develop during oogenesis from vesicles of nuclear membrane that move to the cortical cytoplasm. They become associated with several cytoplasmic components, and participate in the reorganization of cortical cytoplasm after fertilization, patterning the antero-posterior and dorso-ventral body axes. Presentation of the hypothesis The specific resemblances in the development of cytasters in both protostome and deuterostome taxa suggest that an independent evolutionary origin is unlikely. An assessment of published data confirms that cytasters are present in several protostome and deuterostome phyla, but are absent in the non-bilaterian phyla Cnidaria and Ctenophora. We hypothesize that cytasters evolved in the lineage leading to Bilateria and were already present in the most recent common ancestor shared by protostomes and deuterostomes. Thus, cytasters would be an ancient and highly conserved trait that is homologous across the different bilaterian phyla. The alternative possibility is homoplasy, that is cytasters have evolved independently in different lineages of Bilateria. Testing the hypothesis So far, available published information shows that appropriate observations have been made in eight different bilaterian phyla. All of them present cytasters. This is consistent with the hypothesis of homology and conservation. However, there are several important groups for which there are no currently available data. The hypothesis of homology predicts that cytasters should be present in these groups. Increasing the taxonomic sample using modern techniques uniformly will test for evolutionary patterns supporting homology, homoplasy, or secondary loss of

A highly conserved basidiomycete peptide synthetase produces a trimeric hydroxamate siderophore.

Science.gov (United States)

Brandenburger, Eileen; Gressler, Markus; Leonhardt, Robin; Lackner, Gerald; Habel, Andreas; Hertweck, Christian; Brock, Matthias; Hoffmeister, Dirk

2017-08-25

The model white-rot basidiomycete Ceriporiopsis ( Gelatoporia ) subvermispora B encodes putative natural product biosynthesis genes. Among them is the gene for the seven-domain nonribosomal peptide synthetase CsNPS2. It is a member of the as-yet uncharacterized fungal type VI siderophore synthetase family which is highly conserved and widely distributed among the basidiomycetes. These enzymes include only one adenylation (A) domain, i.e., one complete peptide synthetase module and two thiolation/condensation (T-C) di-domain partial modules which, together, constitute an AT 1 C 1 T 2 C 2 T 3 C 3 domain setup. The full-length CsNPS2 enzyme (274.5 kDa) was heterologously produced as polyhistidine fusion in Aspergillus niger as soluble and active protein. N 5 -acetyl- N 5 -hydroxy-l-ornithine (l-AHO) and N 5 - cis -anhydromevalonyl- N 5 -hydroxy-l-ornithine (l-AMHO) were accepted as substrates, as assessed in vitro using the substrate-dependent [ 32 P]ATP-pyrophosphate radioisotope exchange assay. Full-length holo -CsNPS2 catalyzed amide bond formation between three l-AHO molecules to release the linear l-AHO trimer, called basidioferrin, as product in vitro , which was verified by LC-HRESIMS. Phylogenetic analyses suggest that type VI family siderophore synthetases are widespread in mushrooms and have evolved in a common ancestor of basidiomycetes. Importance : The basidiomycete nonribosomal peptide synthetase CsNPS2 represents a member of a widely distributed but previously uninvestigated class (type VI) of fungal siderophore synthetases. Genes orthologous to CsNPS2 are highly conserved across various phylogenetic clades of the basidiomycetes. Hence, our work serves as a broadly applicable model for siderophore biosynthesis and iron metabolism in higher fungi. Also, our results on the amino acid substrate preference of CsNPS2 supports further understanding of the substrate selectivity of fungal adenylation domains. Methodologically, this report highlights the

High molecular weight DNA assembly in vivo for synthetic biology applications.

Science.gov (United States)

Juhas, Mario; Ajioka, James W

2017-05-01

DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.

High molecular weight poly(L-lactide) and poly(ethylene oxide) blends : Thermal characterization and physical properties

NARCIS (Netherlands)

Nijenhuis, AJ; Colstee, E; Grijpma, DW; Pennings, AJ

1996-01-01

The miscibility of high molecular weight poly(L-lactide) (PLLA) with high molecular weight poly(ethylene oxide) (PEG) was studied by differential scanning calorimetry. Ail blends containing up to 50 weight% PEO showed single glass transition temperatures. The PLLA and PEO melting temperatures were

Toward an integrative molecular approach to wildlife disease.

Science.gov (United States)

DeCandia, Alexandra L; Dobson, Andrew P; vonHoldt, Bridgett M

2018-01-29

Pathogens pose serious threats to human health, agricultural investment, and biodiversity conservation through the emergence of zoonoses, spillover to domestic livestock, and epizootic outbreaks. As such, wildlife managers are often tasked with mitigating the negative effects of disease. Yet, parasites form a major component of biodiversity that often persist. This is due to logistical challenges of implementing management strategies and to insufficient understanding of host-parasite dynamics. We advocate for an inclusive understanding of molecular diversity in driving parasite infection and variable host disease states in wildlife systems. More specifically, we examine the roles of genetic, epigenetic, and commensal microbial variation in disease pathogenesis. These include mechanisms underlying parasite virulence and host resistance and tolerance, and the development, regulation, and parasite subversion of immune pathways, among other processes. Case studies of devil facial tumor disease in Tasmanian devils (Sarcophilus harrisii) and chytridiomycosis in globally distributed amphibians exemplify the broad range of questions that can be addressed by examining different facets of molecular diversity. For particularly complex systems, integrative molecular analyses present a promising frontier that can provide critical insights necessary to elucidate disease dynamics operating across scales. These insights enable more accurate risk assessment, reconstruction of transmission pathways, discernment of optimal intervention strategies, and development of more effective and ecologically sound treatments that minimize damage to the host population and environment. Such measures are crucial when mitigating threats posed by wildlife disease to humans, domestic animals, and species of conservation concern. © 2018 Society for Conservation Biology.

Equal channel angular extrusion of ultra-high molecular weight polyethylene

Energy Technology Data Exchange (ETDEWEB)

Reinitz, Steven D., E-mail: Steven.D.Reinitz.TH@Dartmouth.edu; Engler, Alexander J.; Carlson, Evan M.; Van Citters, Douglas W.

2016-10-01

Ultra-high molecular weight polyethylene (UHMWPE), a common bearing surface in total joint arthroplasty, is subject to material property tradeoffs associated with conventional processing techniques. For orthopaedic applications, radiation-induced cross-linking is used to enhance the wear resistance of the material, but cross-linking also restricts relative chain movement in the amorphous regions and hence decreases toughness. Equal Channel Angular Extrusion (ECAE) is proposed as a novel mechanism by which entanglements can be introduced to the polymer bulk during consolidation, with the aim of imparting the same tribological benefits of conventional processing without complete inhibition of chain motion. ECAE processing at temperatures near the crystalline melt for UHMWPE produces (1) increased entanglements compared to control materials; (2) increasing entanglements with increasing temperature; and (3) mechanical properties between values for untreated polyethylene and for cross-linked polyethylene. These results support additional research in ECAE-processed UHMWPE for joint arthroplasty applications. - Highlights: • A new processing method for ultra-high molecular weight polyethylene is introduced. • The process produces a highly entangled polyethylene material. • Entanglements are hypothesized to enhance the wear resistance of polyethylene. • This process eliminates the trade-off between mechanical and wear properties.

The adhesive properties of chlorinated ultra-high molecular weight polyethylene

NARCIS (Netherlands)

Menting, H.N.A.M.; Voets, P.E.L.; Lemstra, P.J.

1995-01-01

Ultra-high molecular weight polyethylene (UHMW-PE) is well known for its abrasion and chemical resistance. Recently we developed a new application for UHMW-PE as a liner in elastomeric hoses. It was found that the adhesion between UHMW-PE and elastomers such as ethylene-propylene-diene monomer

Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.

Directory of Open Access Journals (Sweden)

Ranyee A Chiang

2008-08-01

Full Text Available The evolution of enzymes affects how well a species can adapt to new environmental conditions. During enzyme evolution, certain aspects of molecular function are conserved while other aspects can vary. Aspects of function that are more difficult to change or that need to be reused in multiple contexts are often conserved, while those that vary may indicate functions that are more easily changed or that are no longer required. In analogy to the study of conservation patterns in enzyme sequences and structures, we have examined the patterns of conservation and variation in enzyme function by analyzing graph isomorphisms among enzyme substrates of a large number of enzyme superfamilies. This systematic analysis of substrate substructures establishes the conservation patterns that typify individual superfamilies. Specifically, we determined the chemical substructures that are conserved among all known substrates of a superfamily and the substructures that are reacting in these substrates and then examined the relationship between the two. Across the 42 superfamilies that were analyzed, substantial variation was found in how much of the conserved substructure is reacting, suggesting that superfamilies may not be easily grouped into discrete and separable categories. Instead, our results suggest that many superfamilies may need to be treated individually for analyses of evolution, function prediction, and guiding enzyme engineering strategies. Annotating superfamilies with these conserved and reacting substructure patterns provides information that is orthogonal to information provided by studies of conservation in superfamily sequences and structures, thereby improving the precision with which we can predict the functions of enzymes of unknown function and direct studies in enzyme engineering. Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized

Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.

Science.gov (United States)

Chiang, Ranyee A; Sali, Andrej; Babbitt, Patricia C

2008-08-01

The evolution of enzymes affects how well a species can adapt to new environmental conditions. During enzyme evolution, certain aspects of molecular function are conserved while other aspects can vary. Aspects of function that are more difficult to change or that need to be reused in multiple contexts are often conserved, while those that vary may indicate functions that are more easily changed or that are no longer required. In analogy to the study of conservation patterns in enzyme sequences and structures, we have examined the patterns of conservation and variation in enzyme function by analyzing graph isomorphisms among enzyme substrates of a large number of enzyme superfamilies. This systematic analysis of substrate substructures establishes the conservation patterns that typify individual superfamilies. Specifically, we determined the chemical substructures that are conserved among all known substrates of a superfamily and the substructures that are reacting in these substrates and then examined the relationship between the two. Across the 42 superfamilies that were analyzed, substantial variation was found in how much of the conserved substructure is reacting, suggesting that superfamilies may not be easily grouped into discrete and separable categories. Instead, our results suggest that many superfamilies may need to be treated individually for analyses of evolution, function prediction, and guiding enzyme engineering strategies. Annotating superfamilies with these conserved and reacting substructure patterns provides information that is orthogonal to information provided by studies of conservation in superfamily sequences and structures, thereby improving the precision with which we can predict the functions of enzymes of unknown function and direct studies in enzyme engineering. Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized and uncharacterized

Evaluating private land conservation in the Cape Lowlands, South Africa.

Science.gov (United States)

Von Hase, Amrei; Rouget, Mathieu; Cowling, Richard M

2010-10-01

Evaluation is important for judiciously allocating limited conservation resources and for improving conservation success through learning and strategy adjustment. We evaluated the application of systematic conservation planning goals and conservation gains from incentive-based stewardship interventions on private land in the Cape Lowlands and Cape Floristic Region, South Africa. We collected spatial and nonspatial data (2003-2007) to determine the number of hectares of vegetation protected through voluntary contractual and legally nonbinding (informal) agreements with landowners; resources spent on these interventions; contribution of the agreements to 5- and 20-year conservation goals for representation and persistence in the Cape Lowlands of species and ecosystems; and time and staff required to meet these goals. Conservation gains on private lands across the Cape Floristic Region were relatively high. In 5 years, 22,078 ha (27,800 ha of land) and 46,526 ha (90,000 ha of land) of native vegetation were protected through contracts and informal agreements, respectively. Informal agreements often were opportunity driven and cheaper and faster to execute than contracts. All contractual agreements in the Cape Lowlands were within areas of high conservation priority (identified through systematic conservation planning), which demonstrated the conservation plan's practical application and a high level of overlap between resource investment (approximately R1.14 million/year in the lowlands) and priority conservation areas. Nevertheless, conservation agreements met only 11% of 5-year and 9% of 20-year conservation goals for Cape Lowlands and have made only a moderate contribution to regional persistence of flora to date. Meeting the plan's conservation goals will take three to five times longer and many more staff members to maintain agreements than initially envisaged. © 2010 Society for Conservation Biology.

Butterflies of the high altitude Atacama Desert: habitat use and conservation

Directory of Open Access Journals (Sweden)

Emma eDespland

2014-09-01

Full Text Available The butterfly fauna of the high-altitude desert of Northern Chile, though depauperate, shows high endemism, is poorly known and is of considerable conservation concern. This study surveys butterflies along the Andean slope between 2400 and 500 m asl (prepuna, puna and Andean steppe habitats as well as in high and low altitude wetlands and in the neoriparian vegetation of agricultural sites. We also include historical sightings from museum records. We compare abundances between altitudes, between natural and impacted sites, as well as between two sampling years with different precipitation regimes. The results confirm high altitudinal turnover and show greatest similarity between wetland and slope faunas at similar altitudes. Results also underscore vulnerability to weather fluctuations, particularly in the more arid low-altitude sites, where abundances were much lower in the low precipitation sampling season and several species were not observed at all. Finally, we show that some species have shifted to the neoriparian vegetation of the agricultural landscape, whereas others were only observed in less impacted habitats dominated by native plants. These results suggest that acclimation to novel habitats depends on larval host plant use. The traditional agricultural environment can provide habitat for many, but not all, native butterfly species, but an estimation of the value of these habitats requires better understanding of butterfly life-history strategies and relationships with host plants.

Conservative Protestantism and attitudes toward corporal punishment, 1986-2014.

Science.gov (United States)

Hoffmann, John P; Ellison, Christopher G; Bartkowski, John P

2017-03-01

Research indicates that conservative Protestants are highly supportive of corporal punishment. Yet, Americans' support for this practice has waned during the past several decades. This study aggregates repeated cross-sectional data from the General Social Surveys (GSS) to consider three models that address whether attitudes toward spanking among conservative Protestants shifted relative to those of other Americans from 1986 to 2014. Although initial results reveal a growing gap between conservative Protestants and the broader American public, we find that average levels of support have remained most robust among less educated conservative Protestants, with some erosion among more highly educated conservative Protestants. Moreover, trends in variability suggest that conservative Protestants exhibit more cohesive support for this practice than do others. These results provide a window into the cultural contours of religious change and the social factors that facilitate such change. Copyright © 2016 Elsevier Inc. All rights reserved.

Setting priorities for private land conservation in fire-prone landscapes: Are fire risk reduction and biodiversity conservation competing or compatible objectives?

Science.gov (United States)

Syphard, Alexandra D.; Butsic, Van; Bar-Massada, Avi; Keeley, Jon E.; Tracey, Jeff A.; Fisher, Robert N.

2016-01-01

Although wildfire plays an important role in maintaining biodiversity in many ecosystems, fire management to protect human assets is often carried out by different agencies than those tasked for conserving biodiversity. In fact, fire risk reduction and biodiversity conservation are often viewed as competing objectives. Here we explored the role of management through private land conservation and asked whether we could identify private land acquisition strategies that fulfill the mutual objectives of biodiversity conservation and fire risk reduction, or whether the maximization of one objective comes at a detriment to the other. Using a fixed budget and number of homes slated for development, we simulated 20 years of housing growth under alternative conservation selection strategies, and then projected the mean risk of fires destroying structures and the area and configuration of important habitat types in San Diego County, California, USA. We found clear differences in both fire risk projections and biodiversity impacts based on the way conservation lands are prioritized for selection, but these differences were split between two distinct groupings. If no conservation lands were purchased, or if purchases were prioritized based on cost or likelihood of development, both the projected fire risk and biodiversity impacts were much higher than if conservation lands were purchased in areas with high fire hazard or high species richness. Thus, conserving land focused on either of the two objectives resulted in nearly equivalent mutual benefits for both. These benefits not only resulted from preventing development in sensitive areas, but they were also due to the different housing patterns and arrangements that occurred as development was displaced from those areas. Although biodiversity conflicts may still arise using other fire management strategies, this study shows that mutual objectives can be attained through land-use planning in this region. These results likely

Quantifying solute transport processes: are chemically "conservative" tracers electrically conservative?

Science.gov (United States)

Singha, Kamini; Li, Li; Day-Lewis, Frederick D.; Regberg, Aaron B.

2012-01-01

The concept of a nonreactive or conservative tracer, commonly invoked in investigations of solute transport, requires additional study in the context of electrical geophysical monitoring. Tracers that are commonly considered conservative may undergo reactive processes, such as ion exchange, thus changing the aqueous composition of the system. As a result, the measured electrical conductivity may reflect not only solute transport but also reactive processes. We have evaluated the impacts of ion exchange reactions, rate-limited mass transfer, and surface conduction on quantifying tracer mass, mean arrival time, and temporal variance in laboratory-scale column experiments. Numerical examples showed that (1) ion exchange can lead to resistivity-estimated tracer mass, velocity, and dispersivity that may be inaccurate; (2) mass transfer leads to an overestimate in the mobile tracer mass and an underestimate in velocity when using electrical methods; and (3) surface conductance does not notably affect estimated moments when high-concentration tracers are used, although this phenomenon may be important at low concentrations or in sediments with high and/or spatially variable cation-exchange capacity. In all cases, colocated groundwater concentration measurements are of high importance for interpreting geophysical data with respect to the controlling transport processes of interest.

Rovibrational coupling in molecular nitrogen at high temperature: An atomic-level study

Energy Technology Data Exchange (ETDEWEB)

Valentini, Paolo, E-mail: vale0142@umn.edu; Norman, Paul, E-mail: norma198@umn.edu; Zhang, Chonglin, E-mail: zhang993@umn.edu; Schwartzentruber, Thomas E., E-mail: schwart@aem.umn.edu [Department of Aerospace Engineering and Mechanics, College of Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

2014-05-15

This article contains an atomic-level numerical investigation of rovibrational relaxation in molecular nitrogen at high temperature (>4000 K), neglecting dissociation. We conduct our study with the use of pure Molecular Dynamics (MD) and Classical Trajectory Calculations (CTC) Direct Simulation Monte Carlo (DSMC), verified to produce statistically identical results at the conditions of interest here. MD and CTC DSMC solely rely on the specification of a potential energy surface: in this work, the site-site Ling-Rigby potential. Additionally, dissociation is prevented by modeling the N–N bond either as a harmonic or an anharmonic spring. The selected molecular model was shown to (i) recover the shear viscosity (obtained from equilibrium pure MD Green-Kubo calculations) of molecular nitrogen over a wide range of temperatures, up to dissociation; (ii) predict well the near-equilibrium rotational relaxation behavior of N{sub 2}; (iii) reproduce vibrational relaxation times in excellent accordance with the Millikan-White correlation and previous semi-classical trajectory calculations in the low temperature range, i.e., between 4000 K and 10 000 K. By simulating isothermal relaxations in a periodic box, we found that the traditional two-temperature model assumptions become invalid at high temperatures (>10 000 K), due to a significant coupling between rotational and vibrational modes for bound states. This led us to add a modification to both the Jeans and the Landau-Teller equations to include a coupling term, essentially described by an additional relaxation time for internal energy equilibration. The degree of anharmonicity of the N{sub 2} bond determines the strength of the rovibrational coupling. Although neglecting N{sub 2} dissociation only provides a partial description of a nitrogen system at very high temperatures, high-energy trends for bound-bound transitions are essential to understand nonequilibrium gas flows, with possible implications on rovibration

Rovibrational coupling in molecular nitrogen at high temperature: An atomic-level study

International Nuclear Information System (INIS)

Valentini, Paolo; Norman, Paul; Zhang, Chonglin; Schwartzentruber, Thomas E.

2014-01-01

This article contains an atomic-level numerical investigation of rovibrational relaxation in molecular nitrogen at high temperature (>4000 K), neglecting dissociation. We conduct our study with the use of pure Molecular Dynamics (MD) and Classical Trajectory Calculations (CTC) Direct Simulation Monte Carlo (DSMC), verified to produce statistically identical results at the conditions of interest here. MD and CTC DSMC solely rely on the specification of a potential energy surface: in this work, the site-site Ling-Rigby potential. Additionally, dissociation is prevented by modeling the N–N bond either as a harmonic or an anharmonic spring. The selected molecular model was shown to (i) recover the shear viscosity (obtained from equilibrium pure MD Green-Kubo calculations) of molecular nitrogen over a wide range of temperatures, up to dissociation; (ii) predict well the near-equilibrium rotational relaxation behavior of N 2 ; (iii) reproduce vibrational relaxation times in excellent accordance with the Millikan-White correlation and previous semi-classical trajectory calculations in the low temperature range, i.e., between 4000 K and 10 000 K. By simulating isothermal relaxations in a periodic box, we found that the traditional two-temperature model assumptions become invalid at high temperatures (>10 000 K), due to a significant coupling between rotational and vibrational modes for bound states. This led us to add a modification to both the Jeans and the Landau-Teller equations to include a coupling term, essentially described by an additional relaxation time for internal energy equilibration. The degree of anharmonicity of the N 2 bond determines the strength of the rovibrational coupling. Although neglecting N 2 dissociation only provides a partial description of a nitrogen system at very high temperatures, high-energy trends for bound-bound transitions are essential to understand nonequilibrium gas flows, with possible implications on rovibration

Promoting Effective Monitoring and Conservation through Online ...

African Journals Online (AJOL)

... communicates major findings of submitted records to relevant authorities concerned with conservation and advocacy thus contributing to a much wider sharing and dissemination of important aspects while contributing to avifaunal conservation. Through networking the system provides a highly attractive and authoritative, ...

A Resource Conservation Unit.

Science.gov (United States)

Porter, Philip D.

1979-01-01

Describes a variety of learning activities for teaching elementary and junior high students about air, water, and energy conservation techniques. Suggests community resources, social studies objectives, language skills, and 20 activities. (CK)

High molecular weight polysaccharide that binds and inhibits virus

Science.gov (United States)

Konowalchuk, Thomas W

2014-01-14

This invention provides a high molecular weight polysaccharide capable of binding to and inhibiting virus and related pharmaceutical formulations and methods on inhibiting viral infectivity and/or pathogenicity, as well as immunogenic compositions. The invention further methods of inhibiting the growth of cancer cells and of ameliorating a symptom of aging. Additionally, the invention provides methods of detecting and/or quantifying and/or isolating viruses.

High molecular weight polysaccharide that binds and inhibits virus

Energy Technology Data Exchange (ETDEWEB)

Konowalchuk, Thomas W.; Konowalchuk, Jack

2017-07-18

This invention provides a high molecular weight polysaccharide capable of binding to and inhibiting virus and related pharmaceutical formulations and methods of inhibiting viral infectivity and/or pathogenicity, as well as immunogenic compositions. The invention further includes methods of inhibiting the growth of cancer cells and of ameliorating a symptom of aging. Additionally, the invention provides methods of detecting and/or quantifying and/or isolating viruses.

In Vivo Characterization of a Vertebrate Ultra-conserved Enhancer

Energy Technology Data Exchange (ETDEWEB)

Poulin, Francis; Nobrega, Marcelo A.; Plajzer-Frick, Ingrid; Holt, Amy; Afzal, Veena; Rubin, Edward M.; Pennacchio, Len

2004-10-01

Genomic sequence comparisons between human, mouse and pufferfish (Takifugu rubripes (Fugu))have revealed a set of extremely conserved noncoding sequences. While this high degree of sequence conservation suggests severe evolutionary constraint and predicts a lack of tolerance to change in order to retain in vivo functionality, such elements have been minimally explored experimentally. In this study, we describe the in-depth characterization of an ancient conserved enhancer, Dc2 located near the dachshund gene, which displays a human-Fugu identity of 84 percent over 424 basepairs (bp). In addition to this large overall conservation, we find that Dc2 is characterized by the presence of a large block of sequence (144 bp) that is completely identical between human, mouse, chicken, zebrafish and Fugu. Through the testing of reporter vector constructs in transgenic mice, we observed that the 424 bp Dc2 conserved element is necessary and sufficient for brain tissue enhancer activity. In vivo analyses also revealed that the 144 bp 100 percent conserved sequence is necessary, but not sufficient, to replicate Dc2 enhancer function. However, the introduction of two separate 16 bp insertions into the highly conserved enhancer core did not cause any detectable modification of its in vivo activity. Our observations indicate that the 144 bp 100 percent conserved element is tolerant of change at least at the resolution of this transgenic mouse assay and suggest that purifying selection on Dc2 sequence might not be as strong as we predicted or that some unknown property also constrains this highly conserved enhancer sequence.

Development of solvent-free offset ink using vegetable oil esters and high molecular-weight resin.

Science.gov (United States)

Park, Jung Min; Kim, Young Han; Kim, Sung Bin

2013-01-01

In the development of solvent-free offset ink, the roles of resin molecular weight and used solvent on the ink performance were evaluated by examining the relationship between the various properties of resin and solvent and print quality. To find the best performing resin, the soy-oil fatty acid methyl ester (FAME) was applied to the five modified-phenolic resins having different molecular weights. It is found from the experimental results that the ink made of higher molecular weight and better solubility resin gives better printability and print quality. It is because larger molecular weight resin with better solubility gives higher rate of ink transfer. From the ink application of different esters to high molecular weight resin, the best printing performance was yielded from the soy-oil fatty acid butyl ester (FABE). It is due to its high kinematic viscosity resulting in the smallest change of ink transfer weight upon multiple number of printing, which improves the stability of ink quality.

Conservation laws and nuclear transport models

International Nuclear Information System (INIS)

Gale, C.; Das Gupta, S.

1990-01-01

We discuss the consequences of energy and angular momentum conservation for nucleon-nucleon scattering in a nuclear environment during high-energy heavy-ion collisions. We describe algorithms that ensure stricter enforcement of such conservation laws within popular microscopic models of intermediate-energy heavy-ion collisions. We find that the net effects on global observables are small

DNA-based identification reveals illegal trade of threatened shark species in a global elasmobranch conservation hotspot.

Science.gov (United States)

Feitosa, Leonardo Manir; Martins, Ana Paula Barbosa; Giarrizzo, Tommaso; Macedo, Wagner; Monteiro, Iann Leonardo; Gemaque, Romário; Nunes, Jorge Luiz Silva; Gomes, Fernanda; Schneider, Horácio; Sampaio, Iracilda; Souza, Rosália; Sales, João Bráullio; Rodrigues-Filho, Luís Fernando; Tchaicka, Lígia; Carvalho-Costa, Luís Fernando

2018-02-20

Here, we report trading of endangered shark species in a world hotspot for elasmobranch conservation in Brazil. Data on shark fisheries are scarce in Brazil, although the northern and northeastern regions have the highest indices of shark bycatch. Harvest is made primarily with processed carcasses lacking head and fins, which hampers reliable species identification and law enforcement on illegal catches. We used partial sequences of two mitochondrial genes (COI and/or NADH2) to identify 17 shark species from 427 samples being harvested and marketed on the northern coast of Brazil. Nine species (53%) are listed under some extinction threat category according to Brazilian law and international authorities (IUCN - International Union for Conservation of Nature; CITES - Convention on International Trade of Endangered Species of Wild Fauna and Flora). The number increases to 13 (76%) if we also consider the Near Threatened category. Hammerhead sharks are under threat worldwide, and composed 18.7% of samples, with Sphyrna mokarran being the fourth most common species among samples. As illegal trade of threatened shark species is a worldwide conservation problem, molecular identification of processed meat or specimens lacking diagnostic body parts is a highly effective tool for species identification and law enforcement.

Conservation potential of agricultural water conservation subsidies

Science.gov (United States)

Huffaker, Ray

2008-07-01

A current policy subsidizes farmers to invest in improved on-farm irrigation efficiency, expecting water to be conserved off farm. Contrary to expectation, water has been increasingly depleted in some regions after such improvements. This paper investigates the policy's failure to conserve water consistently by (1) formulating an economic model of irrigated crop production to determine a profit-maximizing irrigator's range of responses to a subsidy and (2) embedding these responses into hypothetical streamflow diagrams to ascertain their potential to conserve water under various hydrologic regimes. Testable hypotheses are developed to predict the conservation potential of a subsidy in real-world application.

Conservation businesses and conservation planning in a biological diversity hotspot.

Science.gov (United States)

Di Minin, Enrico; Macmillan, Douglas Craig; Goodman, Peter Styan; Escott, Boyd; Slotow, Rob; Moilanen, Atte

2013-08-01

The allocation of land to biological diversity conservation competes with other land uses and the needs of society for development, food, and extraction of natural resources. Trade-offs between biological diversity conservation and alternative land uses are unavoidable, given the realities of limited conservation resources and the competing demands of society. We developed a conservation-planning assessment for the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biological diversity hotspot. Our objective was to enhance biological diversity protection while promoting sustainable development and providing spatial guidance in the resolution of potential policy conflicts over priority areas for conservation at risk of transformation. The conservation-planning assessment combined spatial-distribution models for 646 conservation features, spatial economic-return models for 28 alternative land uses, and spatial maps for 4 threats. Nature-based tourism businesses were competitive with other land uses and could provide revenues of >US$60 million/year to local stakeholders and simultaneously help meeting conservation goals for almost half the conservation features in the planning region. Accounting for opportunity costs substantially decreased conflicts between biological diversity, agricultural use, commercial forestry, and mining. Accounting for economic benefits arising from conservation and reducing potential policy conflicts with alternative plans for development can provide opportunities for successful strategies that combine conservation and sustainable development and facilitate conservation action. © 2013 Society for Conservation Biology.

A Kinematic Conservation Law in Free Surface Flow

OpenAIRE

Gavrilyuk , Sergey; Kalisch , Henrik; Khorsand , Zahra

2015-01-01

The Green-Naghdi system is used to model highly nonlinear weakly dispersive waves propagating at the surface of a shallow layer of a perfect fluid. The system has three associated conservation laws which describe the conservation of mass, momentum, and energy due to the surface wave motion. In addition, the system features a fourth conservation law which is the main focus of this note. It will be shown how this fourth conservation law can be interpreted in terms of a concrete kinematic quanti...

Conservation of Mangifera sylvatica

DEFF Research Database (Denmark)

Akhter, Sayma

and conservation of these valuable species. The present study considers an underutilised and threatened species of Bangladesh, namely wild mango (Mangifera sylvatica Roxb.). Although this wild mango is one of the genetically closest species to the common mango (Mangifera indica L.) research is very limited...... and mostly focused on wood quality and phylogenetic relationships. Therefore, this study investigated the conservation potential of wild mango considering its contribution for food, nutrition and livelihoods. To do so, an assessment was made of the current and future distribution of the species, which...... explored. The study conveyed five key messages: 1. Wild mango may become extinct under future climate change scenarios so it is high time to start thinking about conservation initiatives. 2. Wild mango is a small sized mango with a large kernel in relation to other Mangifera species which provides...

Conservation and Role of Electrostatics in Thymidylate Synthase.

Science.gov (United States)

Garg, Divita; Skouloubris, Stephane; Briffotaux, Julien; Myllykallio, Hannu; Wade, Rebecca C

2015-11-27

Conservation of function across families of orthologous enzymes is generally accompanied by conservation of their active site electrostatic potentials. To study the electrostatic conservation in the highly conserved essential enzyme, thymidylate synthase (TS), we conducted a systematic species-based comparison of the electrostatic potential in the vicinity of its active site. Whereas the electrostatics of the active site of TS are generally well conserved, the TSs from minimal organisms do not conform to the overall trend. Since the genomes of minimal organisms have a high thymidine content compared to other organisms, the observation of non-conserved electrostatics was surprising. Analysis of the symbiotic relationship between minimal organisms and their hosts, and the genetic completeness of the thymidine synthesis pathway suggested that TS from the minimal organism Wigglesworthia glossinidia (W.g.b.) must be active. Four residues in the vicinity of the active site of Escherichia coli TS were mutated individually and simultaneously to mimic the electrostatics of W.g.b TS. The measured activities of the E. coli TS mutants imply that conservation of electrostatics in the region of the active site is important for the activity of TS, and suggest that the W.g.b. TS has the minimal activity necessary to support replication of its reduced genome.

Isotopic and molecular fractionation in combustion; three routes to molecular marker validation, including direct molecular 'dating' (GC/AMS)

Science.gov (United States)

Currie, L. A.; Klouda, G. A.; Benner, B. A.; Garrity, K.; Eglinton, T. I.

The identification of unique isotopic, elemental, and molecular markers for sources of combustion aerosol has growing practical importance because of the potential effects of fine particle aerosol on health, visibility and global climate. It is urgent, therefore, that substantial efforts be directed toward the validation of assumptions involving the use of such tracers for source apportionment. We describe here three independent routes toward carbonaceous aerosol molecular marker identification and validation: (1) tracer regression and multivariate statistical techniques applied to field measurements of mixed source, carbonaceous aerosols; (2) a new development in aerosol 14C metrology: direct, pure compound accelerator mass spectrometry (AMS) by off-line GC/AMS ('molecular dating'); and (3) direct observation of isotopic and molecular source emissions during controlled laboratory combustion of specific fuels. Findings from the combined studies include: independent support for benzo( ghi)perylene as a motor vehicle tracer from the first (statistical) and second (direct 'dating') studies; a new indication, from the third (controlled combustion) study, of a relation between 13C isotopic fractionation and PAH molecular fractionation, also linked with fuel and stage of combustion; and quantitative data showing the influence of both fuel type and combustion conditions on the yields of such species as elemental carbon and PAH, reinforcing the importance of exercising caution when applying presumed conservative elemental or organic tracers to fossil or biomass burning field data as in the first study.

Adapting the bioblitz to meet conservation needs.

Science.gov (United States)

Parker, Sophie S; Pauly, Gregory B; Moore, James; Fraga, Naomi S; Knapp, John J; Principe, Zachary; Brown, Brian V; Randall, John M; Cohen, Brian S; Wake, Thomas A

2018-03-01

When conservation strategies require new, field-based information, practitioners must find the best ways to rapidly deliver high-quality survey data. To address this challenge, several rapid-assessment approaches have been developed since the early 1990s. These typically involve large areas, take many months to complete, and are not appropriate when conservation-relevant survey data are urgently needed for a specific locale. In contrast, bioblitzes are designed for quick collection of site-specific survey data. Although bioblitzes are commonly used to achieve educational or public-engagement goals, conservation practitioners are increasingly using a modified bioblitz approach to generate conservation-relevant data while simultaneously enhancing research capacity and building working partnerships focused on conservation concerns. We term these modified events expert bioblitzes. Several expert bioblitzes have taken place on lands of conservation concern in Southern California and have involved collaborative efforts of government agencies, nonprofit organizations, botanic gardens, museums, and universities. The results of expert bioblitzes directly informed on-the-ground conservation and decision-making; increased capacity for rapid deployment of expert bioblitzes in the future; and fostered collaboration and communication among taxonomically and institutionally diverse experts. As research and conservation funding becomes increasingly scarce, expert bioblitzes can play an increasingly important role in biodiversity conservation. © 2018 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Molecular exploration of the highly radiation resistant cyanobacterium Arthrospira sp. PCC 8005

Science.gov (United States)

Badri, Hanène; Leys, Natalie; Wattiez, Ruddy

Arthrospira (Spirulina) is a photosynthetic cyanobacterium able to use sunlight to release oxygen from water and remove carbon dioxide and nitrate from water. In addition, it is suited for human consumption (edible). For these traits, the cyanobacterium Arthrospira sp. PCC 8005 was selected by the European Space Agency (ESA) as part of the life support system MELiSSA for recycling oxygen, water, and food during future long-haul space missions. However, during such extended missions, Arthrospira sp. PCC 8005 will be exposed to continuous artificial illumination and harmful cosmic radiation. The aim of this study was to investigate how Arthrospira will react and behave when exposed to such stress environment. The cyanobacterium Arthrospira sp. PCC 8005 was exposed to high gamma rays doses in order to unravel in details the response of this bacterium following such stress. Test results showed that after acute exposure to high doses of 60Co gamma radiation upto 3200 Gy, Arthrospira filaments were still able to restart photosynthesis and proliferate normally. Doses above 3200 Gy, did have a detrimental effect on the cells, and delayed post-irradiation proliferation. The photosystem activity, measured as the PSII quantum yield immediately after irradiation, decreased significantly at radiation doses above 3200 Gy. Likewise through pigment content analysis a significant decrease in phycocyanin was observed following exposure to 3200 Gy. The high tolerance of this bacterium to 60Co gamma rays (i.e. ca. 1000x more resistant than human cells for example) raised our interest to investigate in details the cellular and molecular mechanisms behind this amazing resistance. Optimised DNA, RNA and protein extraction methods and a new microarray chip specific for Arthrospira sp. PCC 8005 were developed to identify the global cellular and molecular response following exposure to 3200 Gy and 5000 Gy A total of 15,29 % and 30,18 % genes were found differentially expressed in RNA

Questioning current practice in brown bear, Ursus arctos, conservation in Europe that undervalues taxonomy

Energy Technology Data Exchange (ETDEWEB)

Gippoliti, S.

2016-07-01

The present paper highlights problems associated with the currently–accepted taxonomy of brown bear, Ursus arctos, and their consequences for conservation at the European level. The enormous morphological variability within Ursus arctos is not acknowledged in current taxonomy and conservation practice. Seven major clades are recognized in Ursus arctos by molecular researchers, and although Western Europe maintains most of the populations belonging to the relict Clade 1 brown bear lineage, no reference to this is made in current conservation policy. Furthermore, the tiny population of Apennine brown bears, characterized by unique skull morphology, is not even recognized as a distinct ESU (evolutionari significant unit) by current European legislation, nor is it included in the IUCN Red List. This may have serious consequences as brown bear conservation in Western Europe has been mainly based on restocking and reintroduction programs. (Author)

Melting curves of molecular hydrogen and molecular deuterium under high pressures between 20 and 373 K

International Nuclear Information System (INIS)

Diatschenko, V.; Chu, C.W.; Liebenberg, D.H.; Young, D.A.; Ross, M.; Mills, R.L.

1985-01-01

We determined the melting curve of molecular hydrogen and molecular deuterium at closely spaced intervals from 20 to 373 K by two different techniques using high-pressure diamond cells. The cells were loaded with liquid at low temperature or with compressed gas at room temperature. Empirical functions for the melting curves were evaluated from least-squares fits of the data. Values of the compressibility and Debye temperature were computed at melting, and the results are compared with those calculated from various theoretical models. The good agreement shows that the models are generally valid, although small systematic deviations may point the way toward refinements in modeling. Our study also demonstrates the need to determine a one-piece intermolecular potential valid over a wide pressure range by refitting all experimental data, including the shock data recently made available

Mitochondrial tRNA gene translocations in highly eusocial bees

Directory of Open Access Journals (Sweden)

Daniela Silvestre

2006-01-01

Full Text Available Mitochondrial gene rearrangement events, especially involving tRNA genes, have been described more frequently as more complete mitochondrial genome sequences are becoming available. In the present work, we analyzed mitochondrial tRNA gene rearrangements between two bee species belonging to the tribes Apini and Meliponini within the "corbiculate Apidae". Eleven tRNA genes are in different genome positions or strands. The molecular events responsible for each translocation are explained. Considering the high number of rearrangements observed, the data presented here contradict the general rule of high gene order conservation among closely related organisms, and also represent a powerful molecular tool to help solve questions about phylogeny and evolution in bees.

Novel urban ecosystems, biodiversity, and conservation

International Nuclear Information System (INIS)

Kowarik, Ingo

2011-01-01

With increasing urbanization the importance of cities for biodiversity conservation grows. This paper reviews the ways in which biodiversity is affected by urbanization and discusses the consequences of different conservation approaches. Cities can be richer in plant species, including in native species, than rural areas. Alien species can lead to both homogenization and differentiation among urban regions. Urban habitats can harbor self-sustaining populations of rare and endangered native species, but cannot replace the complete functionality of (semi-)natural remnants. While many conservation approaches tend to focus on such relict habitats and native species in urban settings, this paper argues for a paradigm shift towards considering the whole range of urban ecosystems. Although conservation attitudes may be challenged by the novelty of some urban ecosystems, which are often linked to high numbers of nonnative species, it is promising to consider their associated ecosystem services, social benefits, and possible contribution to biodiversity conservation. - Highlights: → This paper reviews biotic responses to urbanization and urban conservation approaches. → Cities may be rich in both native and nonnative species. → Urban habitats cannot replace the functionality of natural remnants. → However, even novel urban habitats may harbour rare and endangered species. → Conservation approaches should consider the perspective of novel urban ecosystems. - This paper reviews the ways in which biodiversity is affected by urbanization and argues for expanding urban conservation approaches.

Novel urban ecosystems, biodiversity, and conservation

Energy Technology Data Exchange (ETDEWEB)

Kowarik, Ingo, E-mail: kowarik@tu-berlin.de [Department of Ecology, Technische Universitaet Berlin, Rothenburgstr. 12, D 12165 Berlin (Germany)

2011-08-15

With increasing urbanization the importance of cities for biodiversity conservation grows. This paper reviews the ways in which biodiversity is affected by urbanization and discusses the consequences of different conservation approaches. Cities can be richer in plant species, including in native species, than rural areas. Alien species can lead to both homogenization and differentiation among urban regions. Urban habitats can harbor self-sustaining populations of rare and endangered native species, but cannot replace the complete functionality of (semi-)natural remnants. While many conservation approaches tend to focus on such relict habitats and native species in urban settings, this paper argues for a paradigm shift towards considering the whole range of urban ecosystems. Although conservation attitudes may be challenged by the novelty of some urban ecosystems, which are often linked to high numbers of nonnative species, it is promising to consider their associated ecosystem services, social benefits, and possible contribution to biodiversity conservation. - Highlights: > This paper reviews biotic responses to urbanization and urban conservation approaches. > Cities may be rich in both native and nonnative species. > Urban habitats cannot replace the functionality of natural remnants. > However, even novel urban habitats may harbour rare and endangered species. > Conservation approaches should consider the perspective of novel urban ecosystems. - This paper reviews the ways in which biodiversity is affected by urbanization and argues for expanding urban conservation approaches.

High Performance Shape Memory Polyurethane Synthesized with High Molecular Weight Polyol as the Soft Segment

Directory of Open Access Journals (Sweden)

Manzoor Ahmad

2012-05-01

Full Text Available Shape memory polyurethanes (SMPUs are typically synthesized using polyols of low molecular weight (MW~2,000 g/mol as it is believed that the high density of cross-links in these low molecular weight polyols are essential for high mechanical strength and good shape memory effect. In this study, polyethylene glycol (PEG-6000 with MW ~6000 g/mol as the soft segment and diisocyanate as the hard segment were used to synthesize SMPUs, and the results were compared with the SMPUs with polycaprolactone PCL-2000. The study revealed that although the PEG-6000-based SMPUs have lower maximum elongations at break (425% and recovery stresses than those of PCL-based SMPUs, they have much better recovery ratios (up to 98% and shape fixity (up to 95%, hence better shape memory effect. Furthermore, PEG-based SMPUs showed a much shorter actuation time of < 10 s for up to 90% shape recovery compared to typical actuation times of tens of seconds to a few minutes for common SMPUs, demonstrated their great potential for applications in microsystems and other engineering components.

Molecular species identification and population genetics of ...

African Journals Online (AJOL)

Molecular genetic techniques, such as DNA barcoding and genotyping, are increasingly being used to assist with the conservation and management of chondrichthyans worldwide. Southern Africa is a shark biodiversity hotspot, with a large number of endemic species. According to the IUCN Red List, a quarter of South ...

Lasers in the Conservation of Artworks

CERN Document Server

Nimmrichter, Johann; Schreiner, Manfred; LACONA VI Proceedings

2007-01-01

Within the last decades, the use of lasers in artworks conservation became an important tool for many conservators, scientists, architects and other experts, who are involved in the care of monuments and artefacts or laser technology. For the first time in 1995 Professor Costas Fotakis brought together restorers and scientists to discuss the potential of lasers in art conservation. Since then the field of "Lasers in the Conservation of Artworks" has gained enormously in importance. Nowadays restorers and laser scientists work close together in order to develop new fields of applications during the last years. Furthermore a large number of national and international research projects have been carried out by conservator-restorers, architects and scientists. In the last 10 years a number of historical and artistic high quality monuments (e.g. St. Stephens Cathedral in Vienna) have been cleaned or measured by laser and brought the laser in the spectra of tools which are useful in the sensible field of artworks. ...

Molecular phylogeny of the genus Saguinus (Platyrrhini, Primates based on the ND1 mitochondrial gene and implications for conservation

Directory of Open Access Journals (Sweden)

Claudia Helena Tagliaro

2005-03-01

Full Text Available The systematics of the subfamily Callitrichinae (Platyrrhini, Primates, a group of small monkeys from South America and Panama, remains an area of considerable discussion despite many investigations, there being continuing controversy over subgeneric taxonomic classifications based on morphological characters. The purpose of our research was to help elucidate the phylogenetic relationships within the monkey genus Saguinus (Callitrichinae using a molecular approach to discover whether or not the two different sections containing hairy-faced and bare-faced species are monophyletic, whether Saguinus midas midas and Saguinus bicolor are more closely related than are S. midas midas and Saguinus midas niger, and if Saguinus fuscicollis melanoleucus and Saguinus fuscicollis weddelli really are different species. We sequenced the 957 bp ND1 mitochondrial gene of 21 Saguinus monkeys (belonging to six species and nine morphotypes and one Cebus monkey (the outgroup and constructed phylogenetic trees using maximum parsimony, neighbor joining, and maximum likelihood methods. The phylogenetic trees obtained divided the genus Saguinus into two groups, one containing the small-bodied species S. fuscicollis and the other, the large-bodied species S. mystax, S. leucopus, S. oedipus, S. midas, S. bicolor. The most derived taxa, S. midas and S. bicolor, grouped together, while S. fuscicollis melanoleucus and S. f. weddelli showed divergence values that did not support the division of these morphotypes into subspecies. On the other hand, S. midas individuals showed divergence compatible with the existence of three subspecies, two of them with the same morphotype as the subspecies S. midas niger. The results of our study suggest that there is at least one Saguinus subspecies that has not yet been described and that the conservation status of Saguinus species and subspecies should be carefully revised using modern molecular approaches.

Detection of Waterborne Viruses Using High Affinity Molecularly Imprinted Polymers.

Science.gov (United States)

Altintas, Zeynep; Gittens, Micah; Guerreiro, Antonio; Thompson, Katy-Anne; Walker, Jimmy; Piletsky, Sergey; Tothill, Ibtisam E

2015-07-07

Molecularly imprinted polymers (MIPs) are artificial receptor ligands which can recognize and specifically bind to a target molecule. They are more resistant to chemical and biological damage and inactivation than antibodies. Therefore, target specific-MIP nanoparticles are aimed to develop and implemented to biosensors for the detection of biological toxic agents such as viruses, bacteria, and fungi toxins that cause many diseases and death due to the environmental contamination. For the first time, a molecularly imprinted polymer (MIP) targeting the bacteriophage MS2 as the template was investigated using a novel solid-phase synthesis method to obtain the artificial affinity ligand for the detection and removal of waterborne viruses through optical-based sensors. A high affinity between the artificial ligand and the target was found, and a regenerative MIP-based virus detection assay was successfully developed using a new surface plasmon resonance (SPR)-biosensor which provides an alternative technology for the specific detection and removal of waterborne viruses that lead to high disease and death rates all over the world.

Raman spectroscopy on simple molecular systems at very high density

International Nuclear Information System (INIS)

Schiferl, D.; LeSar, R.S.; Moore, D.S.

1988-01-01

We present an overview of how Raman spectroscopy is done on simple molecular substances at high pressures. Raman spectroscopy is one of the most powerful tools for studying these substances. It is often the quickest means to explore changes in crystal and molecular structures, changes in bond strength, and the formation of new chemical species. Raman measurements have been made at pressures up to 200 GPa (2 Mbar). Even more astonishing is the range of temperatures (4-5200/degree/K) achieved in various static and dynamic (shock-wave) pressure experiments. One point we particularly wish to emphasize is the need for a good theoretical understanding to properly interpret and use experimental results. This is particularly true at ultra-high pressures, where strong crystal field effects can be misinterpreted as incipient insulator-metal transitions. We have tried to point out apparatus, techniques, and results that we feel are particularly noteworthy. We have also included some of the /open quotes/oral tradition/close quotes/ of high pressure Raman spectroscopy -- useful little things that rarely or never appear in print. Because this field is rapidly expanding, we discuss a number of exciting new techniques that have been informally communicated to us, especially those that seem to open new possibilities. 58 refs., 18 figs

Carbon payments and low-cost conservation.

Science.gov (United States)

Crossman, Neville D; Bryan, Brett A; Summers, David M

2011-08-01

A price on carbon is expected to generate demand for carbon offset schemes. This demand could drive investment in tree-based monocultures that provide higher carbon yields than diverse plantings of native tree and shrub species, which sequester less carbon but provide greater variation in vegetation structure and composition. Economic instruments such as species conservation banking, the creation and trading of credits that represent biological-diversity values on private land, could close the financial gap between monocultures and more diverse plantings by providing payments to individuals who plant diverse species in locations that contribute to conservation and restoration goals. We studied a highly modified agricultural system in southern Australia that is typical of many temperate agriculture zones globally (i.e., has a high proportion of endangered species, high levels of habitat fragmentation, and presence of non-native species). We quantified the economic returns from agriculture and from carbon plantings (monoculture and mixed tree and shrubs) under six carbon-price scenarios. We also identified high-priority locations for restoration of cleared landscapes with mixed tree and shrub carbon plantings. Depending on the price of carbon, direct annual payments to landowners of AU$7/ha/year to $125/ha/year (US$6-120/ha/year) may be sufficient to augment economic returns from a carbon market and encourage tree plantings that contribute more to the restoration of natural systems and endangered species habitats than monocultures. Thus, areas of high priority for conservation and restoration may be restored relatively cheaply in the presence of a carbon market. Overall, however, less carbon is sequestered by mixed native tree and shrub plantings. © 2011 Society for Conservation Biology.

Impacts of Tropical Forest Disturbance Upon Avifauna on a Small Island with High Endemism: Implications for Conservation

Directory of Open Access Journals (Sweden)

Martin Thomas

2010-01-01

Full Text Available Tropical forests are rapidly being lost across Southeast Asia and this is predicted to have severe implications for many of the region′s bird species. However, relationships between forest disturbance and avifaunal assemblages remain poorly understood, particularly on small island ecosystems such as those found in the biodiversity ′hotspot′ of Wallacea. This study examines how avifaunal richness varies across a disturbance gradient in a forest reserve on Buton Island, southeast Sulawesi. Particular emphasis is placed upon examining responses in endemic and red-listed species with high conservation importance. Results indicate that overall avian richness increases between primary and 30-year-old regenerating secondary forest and then decreases through disturbed secondary forest, but is highest in cleared farmland. However, high species richness in farmland does not signify high species distinctiveness; bird community composition here differs significantly from that found in forest sites, and is poor in supporting forest specialists and endemic species. Certain large-bodied endemics such as the Knobbed Hornbill (Rhyticeros cassidix appear to be sensitive to moderate disturbance, with populations occurring at greatest density within primary forest. However, overall endemic species richness, as well as that of endemic frugivores and insectivores, is similar in primary and secondary forest types. Results indicate that well-established secondary forest in particular has an important role in supporting species with high conservational importance, possessing community composition similar to that found in primary forest and supporting an equally high richness of endemic species.

Cretaceous park of sex determination: sex chromosomes are conserved across iguanas.

Science.gov (United States)

Rovatsos, Michail; Pokorná, Martina; Altmanová, Marie; Kratochvíl, Lukáš

2014-03-01

Many poikilothermic vertebrate lineages, especially among amphibians and fishes, possess a rapid turnover of sex chromosomes, while in endotherms there is a notable stability of sex chromosomes. Reptiles in general exhibit variability in sex-determining systems; as typical poikilotherms, they might be expected to have a rapid turnover of sex chromosomes. However, molecular data which would enable the testing of the stability of sex chromosomes are lacking in most lineages. Here, we provide molecular evidence that sex chromosomes are highly conserved across iguanas, one of the most species-rich clade of reptiles. We demonstrate that members of the New World families Iguanidae, Tropiduridae, Leiocephalidae, Phrynosomatidae, Dactyloidae and Crotaphytidae, as well as of the family Opluridae which is restricted to Madagascar, all share homologous sex chromosomes. As our sampling represents the majority of the phylogenetic diversity of iguanas, the origin of iguana sex chromosomes can be traced back in history to the basal splitting of this group which occurred during the Cretaceous period. Iguanas thus show a stability of sex chromosomes comparable to mammals and birds and represent the group with the oldest sex chromosomes currently known among amniotic poikilothermic vertebrates.

Setting priorities for private land conservation in fire-prone landscapes: Are fire risk reduction and biodiversity conservation competing or compatible objectives?

Directory of Open Access Journals (Sweden)

Alexandra D. Syphard

2016-09-01

Full Text Available Although wildfire plays an important role in maintaining biodiversity in many ecosystems, fire management to protect human assets is often carried out by different agencies than those tasked for conserving biodiversity. In fact, fire risk reduction and biodiversity conservation are often viewed as competing objectives. Here we explored the role of management through private land conservation and asked whether we could identify private land acquisition strategies that fulfill the mutual objectives of biodiversity conservation and fire risk reduction, or whether the maximization of one objective comes at a detriment to the other. Using a fixed budget and number of homes slated for development, we simulated 20 years of housing growth under alternative conservation selection strategies, and then projected the mean risk of fires destroying structures and the area and configuration of important habitat types in San Diego County, California, USA. We found clear differences in both fire risk projections and biodiversity impacts based on the way conservation lands are prioritized for selection, but these differences were split between two distinct groupings. If no conservation lands were purchased, or if purchases were prioritized based on cost or likelihood of development, both the projected fire risk and biodiversity impacts were much higher than if conservation lands were purchased in areas with high fire hazard or high species richness. Thus, conserving land focused on either of the two objectives resulted in nearly equivalent mutual benefits for both. These benefits not only resulted from preventing development in sensitive areas, but they were also due to the different housing patterns and arrangements that occurred as development was displaced from those areas. Although biodiversity conflicts may still arise using other fire management strategies, this study shows that mutual objectives can be attained through land-use planning in this region

Thermal characterization of Ag and Ag + N ion implanted ultra-high molecular weight polyethylene (UHMWPE)

Science.gov (United States)

Sokullu Urkac, E.; Oztarhan, A.; Tihminlioglu, F.; Kaya, N.; Ila, D.; Muntele, C.; Budak, S.; Oks, E.; Nikolaev, A.; Ezdesir, A.; Tek, Z.

2007-08-01

Most of total hip joints are composed of ultra-high molecular weight polyethylene (UHMWPE). However, as ultra-high molecular weight polyethylene is too stable in a body, wear debris may accumulate and cause biological response such as bone absorption and loosening of prosthesis. In this study, ultra-high molecular weight polyethylene samples were Ag and Ag + N hybrid ion implanted by using MEVVA ion implantation technique to improve its surface properties. Samples were implanted with a fluence of 1017 ion/cm2 and extraction voltage of 30 kV. Implanted and unimplanted samples were investigated by thermo-gravimetry analysis (TGA), differential scanning calorimetry (DSC), X-ray diffraction (XRD) analysis, scanning electron microscopy (SEM), optical microscopy (OM) and contact Angle measurement. Thermal characterization results showed that the ion bombardment induced an increase in the % crystallinity, onset and termination degradation temperatures of UHMWPE.

ACYLTRANSFERASE ACTIVITIES OF THE HIGH-MOLECULAR-MASS ESSENTIAL PENICILLIN-BINDING PROTEINS

NARCIS (Netherlands)

ADAM, M; DAMBLON, C; JAMIN, M; ZORZI, W; DUSART, [No Value; GALLENI, M; ELKHARROUBI, A; PIRAS, G; SPRATT, BG; KECK, W; COYETTE, J; GHUYSEN, JM; NGUYENDISTECHE, M; FRERE, JM

1991-01-01

The high-molecular-mass penicillin-binding proteins (HMM-PBPs), present in the cytoplasmic membranes of all eubacteria, are involved in important physiological events such as cell elongation, septation or shape determination. Up to now it has, however, been very difficult or impossible to study the

Energy conservation and pomeron loops in high energy evolution

International Nuclear Information System (INIS)

Gustafson, Goesta

2007-01-01

We present a formalism which modifies the Mueller Dipole Model such that it incorporates energy-momentum conservation as well as important colour suppressed effects in the cascade evolution. The formalism is implemented in a Monte Carlo simulation program, and the results are compared to inclusive data from HERA and the Tevatron. We here find a generally very good agreement between our model and the experimental data. (author)

On simulation of local fluxes in molecular junctions

Science.gov (United States)

Cabra, Gabriel; Jensen, Anders; Galperin, Michael

2018-05-01

We present a pedagogical review of the current density simulation in molecular junction models indicating its advantages and deficiencies in analysis of local junction transport characteristics. In particular, we argue that current density is a universal tool which provides more information than traditionally simulated bond currents, especially when discussing inelastic processes. However, current density simulations are sensitive to the choice of basis and electronic structure method. We note that while discussing the local current conservation in junctions, one has to account for the source term caused by the open character of the system and intra-molecular interactions. Our considerations are illustrated with numerical simulations of a benzenedithiol molecular junction.

Noise exposure and hearing conservation practices in an industry with high incidence of workers' compensation claims for hearing loss.

Science.gov (United States)

Daniell, William E; Swan, Susan S; McDaniel, Mary M; Stebbins, John G; Seixas, Noah S; Morgan, Michael S

2002-10-01

Washington State has experienced a striking increase in workers' compensation claims for hearing loss. This cross-sectional study examined noise exposures and hearing conservation practices in one industry with a high rate of hearing loss claims. We evaluated 10 representative foundries with personal noise dosimetry, management interviews, employee interviews, and existing audiometry. Noise levels routinely exceeded 85 dBA. All companies were out of compliance with hearing conservation regulations. Most employees with important findings on audiograms were not aware of their findings. There was a significant positive correlation between management-interview scores and worksite-average employee-interview scores (r = 0.70, P = 0.02). Companies where more effort is put into hearing conservation program activities can achieve a greater positive impact on employee awareness. However, there were broad deficiencies even in the better programs in this sample, suggesting that workers in this industry probably face a continuing substantial risk of occupational hearing loss. Copyright 2002 Wiley-Liss, Inc.

Species status and conservation issues of New Zealand's endemic Latrodectus spider species (Araneae: Theridiidae)

DEFF Research Database (Denmark)

Vink, Cor J; Sirvid, Phillip J; Malumbres-Olarte, Jagoba

2008-01-01

New Zealand has two endemic widow spiders, Latrodectus katipo Powell, 1871 and L. atritus Urquhart, 1890. Both species face many conservation threats and are actively managed. The species status of the Latrodectus spiders of New Zealand was assessed using molecular (COI, ITS1, ITS2...

Chemical modification of high molecular weight polyethylene through gamma radiation for biomaterials applications

International Nuclear Information System (INIS)

Raposo, Matheus P.; Rocha, Marisa C.G.

2015-01-01

Ultra high molecular weight polyethylene has been used in the medical field due to its high mechanical properties compared to the other polymers. Its main application is in the development of orthopedic implants, which requires high resistance to abrasion. One of the most used methods is the introduction of crosslinks in the polymer through gamma irradiation. In order to prevent oxidation reactions, studies have been developed using tacoferol (vitamin E) as an antioxidant for the material. The ascorbic acid (vitamin C), however, has been appointed as a viable alternative for vitamin E. In this work, a high molecular weight polyethylene grade (HMWPE) and polyethylene samples formulated with vitamin C were submitted to gamma radiation. Thermodynamic-mechanical methods and gel content determinations were used to characterize the samples obtained. The sample containing 1% of vitamin C and irradiated with 50 KGy of gamma radiation presented the highest content of crosslinks. (author)

Protocols for In Vitro Propagation, Conservation, Synthetic Seed Production, Embryo Rescue, Microrhizome Production, Molecular Profiling, and Genetic Transformation in Ginger (Zingiber officinale Roscoe.).

Science.gov (United States)

Nirmal Babu, K; Samsudeen, K; Divakaran, Minoo; Pillai, Geetha S; Sumathi, V; Praveen, K; Ravindran, P N; Peter, K V

2016-01-01

Ginger is a rhizomatous plant that belongs to the family Zingiberaceae. It is a herbaceous perennial but cultivated as annual, with crop duration of 7-10 months. Ginger is native to India and Tropical South Asia. The tuberous rhizomes or underground stems of ginger are used as condiment, an aromatic stimulant, and food preservative as well as in traditional medicine. Ginger is propagated vegetatively with rhizome bits as seed material. Cultivation of ginger is plagued by rhizome rot diseases, most of which are mainly spread through infected seed rhizomes. Micropropagation will help in production of disease-free planting material. Sexual reproduction is absent in ginger, making recombinant breeding very impossible. In vitro technology can thus become the preferred choice as it can be utilized for multiplication, conservation of genetic resources, generating variability, gene transfer, molecular tagging, and their utility in crop improvement of these crops.

Ranking multiple docking solutions based on the conservation of inter-residue contacts

KAUST Repository

Oliva, Romina M.

2013-06-17

Molecular docking is the method of choice for investigating the molecular basis of recognition in a large number of functional protein complexes. However, correctly scoring the obtained docking solutions (decoys) to rank native-like (NL) conformations in the top positions is still an open problem. Herein we present CONSRANK, a simple and effective tool to rank multiple docking solutions, which relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. First it calculates a conservation rate for each inter-residue contact, then it ranks decoys according to their ability to match the more frequently observed contacts. We applied CONSRANK to 102 targets from three different benchmarks, RosettaDock, DOCKGROUND, and Critical Assessment of PRedicted Interactions (CAPRI). The method performs consistently well, both in terms of NL solutions ranked in the top positions and of values of the area under the receiver operating characteristic curve. Its ideal application is to solutions coming from different docking programs and procedures, as in the case of CAPRI targets. For all the analyzed CAPRI targets where a comparison is feasible, CONSRANK outperforms the CAPRI scorers. The fraction of NL solutions in the top ten positions in the RosettaDock, DOCKGROUND, and CAPRI benchmarks is enriched on average by a factor of 3.0, 1.9, and 9.9, respectively. Interestingly, CONSRANK is also able to specifically single out the high/medium quality (HMQ) solutions from the docking decoys ensemble: it ranks 46.2 and 70.8% of the total HMQ solutions available for the RosettaDock and CAPRI targets, respectively, within the top 20 positions. © 2013 Wiley Periodicals, Inc.

High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL

Science.gov (United States)

Stone, John E.; Messmer, Peter; Sisneros, Robert; Schulten, Klaus

2016-01-01

Large scale molecular dynamics simulations produce terabytes of data that is impractical to transfer to remote facilities. It is therefore necessary to perform visualization tasks in-situ as the data are generated, or by running interactive remote visualization sessions and batch analyses co-located with direct access to high performance storage systems. A significant challenge for deploying visualization software within clouds, clusters, and supercomputers involves the operating system software required to initialize and manage graphics acceleration hardware. Recently, it has become possible for applications to use the Embedded-system Graphics Library (EGL) to eliminate the requirement for windowing system software on compute nodes, thereby eliminating a significant obstacle to broader use of high performance visualization applications. We outline the potential benefits of this approach in the context of visualization applications used in the cloud, on commodity clusters, and supercomputers. We discuss the implementation of EGL support in VMD, a widely used molecular visualization application, and we outline benefits of the approach for molecular visualization tasks on petascale computers, clouds, and remote visualization servers. We then provide a brief evaluation of the use of EGL in VMD, with tests using developmental graphics drivers on conventional workstations and on Amazon EC2 G2 GPU-accelerated cloud instance types. We expect that the techniques described here will be of broad benefit to many other visualization applications. PMID:27747137

Multidisciplinary approach for the esophageal carcinoma with intent to conserve the esophagus centering on high-dose radiotherapy and concurrent chemotherapy

International Nuclear Information System (INIS)

Murakami, Masao; Kuroda, Yasumasa; Okamoto, Yoshiaki

1997-01-01

Forty-seven patients with operable squamous cell carcinoma of the thoracic esophagus were treated by initial concurrent chemoradiotherapy (CDDP-5 FU-44 Gy) followed by definitive high-dose of radiotherapy (CRT group: 35 patients) or surgery (CRT-S group: 12 patients). Clinical CR rate showed 86% in CRT group; and pathological CR rate 18% in CRT-S group. The overall median survival was 45 months, survival at 1, 3, 5 years being 96%, 52%, 48%, respectively. No treatment-related mortality was observed. The rate of the 'esophagus conservation' was 66%. Our results demonstrated that the multidisciplinary approach with intent to conserve the esophagus centering on high-dose radiotherapy and concurrent chemotherapy provides a significant improvement of both survival and quality of life in patients with operable esophageal carcinoma. (author)

The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis in the grasslands of Queensland, Australia.

Directory of Open Access Journals (Sweden)

Jane Melville

Full Text Available Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora, which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1 revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis) in the grasslands of Queensland, Australia.

Science.gov (United States)

Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

2014-01-01

Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

Phylogeography and genetic structure of a Tertiary relict tree species, Tapiscia sinensis (Tapisciaceae): implications for conservation.

Science.gov (United States)

Zhang, Jinju; Li, Zuozhou; Fritsch, Peter W; Tian, Hua; Yang, Aihong; Yao, Xiaohong

2015-10-01

The phylogeography of plant species in sub-tropical China remains largely unclear. This study used Tapiscia sinensis, an endemic and endangered tree species widely but disjunctly distributed in sub-tropical China, as a model to reveal the patterns of genetic diversity and phylogeographical history of Tertiary relict plant species in this region. The implications of the results are discussed in relation to its conservation management. Samples were taken from 24 populations covering the natural geographical distribution of T. sinensis. Genetic structure was investigated by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA). Phylogenetic relationships among haplotypes were constructed with maximum parsimony and haplotype network methods. Historical population expansion events were tested with pairwise mismatch distribution analysis and neutrality tests. Species potential range was deduced by ecological niche modelling (ENM). A low level of genetic diversity was detected at the population level. A high level of genetic differentiation and a significant phylogeographical structure were revealed. The mean divergence time of the haplotypes was approx. 1·33 million years ago. Recent range expansion in this species is suggested by a star-like haplotype network and by the results from the mismatch distribution analysis and neutrality tests. Climatic oscillations during the Pleistocene have had pronounced effects on the extant distribution of Tapiscia relative to the Last Glacial Maximum (LGM). Spatial patterns of molecular variation and ENM suggest that T. sinensis may have retreated in south-western and central China and colonized eastern China prior to the LGM. Multiple montane refugia for T. sinense existing during the LGM are inferred in central and western China. The populations adjacent to or within these refugia of T. sinense should be given high priority in the development of conservation policies and management strategies for

Cool C-shocks and high-velocity flows in molecular clouds

International Nuclear Information System (INIS)

Smith, M.D.; Brand, P.W.J.L.

1990-01-01

C-shocks can be driven through dense clouds when the neutrals and magnetic field interact weakly due to a paucity of ions. We develop a method for calculating C-shock properties with the aim of interpreting the observed high-velocity molecular hydrogen. A high Mach number approximation, corresponding to low temperatures, is employed. Under strong cooling conditions the flow is continuous even though a subsonic region may be present downstream. Analytic expressions for the maximum temperature, dissociation fraction, self-ionization level and J-shock transition are derived. (author)

Governance factors in the identification of global conservation priorities for mammals.

Science.gov (United States)

Eklund, Johanna; Arponen, Anni; Visconti, Piero; Cabeza, Mar

2011-09-27

Global conservation priorities have often been identified based on the combination of species richness and threat information. With the development of the field of systematic conservation planning, more attention has been given to conservation costs. This leads to prioritizing developing countries, where costs are generally low and biodiversity is high. But many of these countries have poor governance, which may result in ineffective conservation or in larger costs than initially expected. We explore how the consideration of governance affects the selection of global conservation priorities for the world's mammals in a complementarity-based conservation prioritization. We use data on Control of Corruption (Worldwide Governance Indicators project) as an indicator of governance effectiveness, and gross domestic product per capita as an indicator of cost. We show that, while core areas with high levels of endemism are always selected as important regardless of governance and cost values, there are clear regional differences in selected sites when biodiversity, cost or governance are taken into account separately. Overall, the analysis supports the concentration of conservation efforts in most of the regions generally considered of high priority, but stresses the need for different conservation approaches in different continents owing to spatial patterns of governance and economic development.

Community Markets for Conservation (COMACO) links biodiversity conservation with sustainable improvements in livelihoods and food production.

Science.gov (United States)

Lewis, Dale; Bell, Samuel D; Fay, John; Bothi, Kim L; Gatere, Lydiah; Kabila, Makando; Mukamba, Mwangala; Matokwani, Edwin; Mushimbalume, Matthews; Moraru, Carmen I; Lehmann, Johannes; Lassoie, James; Wolfe, David; Lee, David R; Buck, Louise; Travis, Alexander J

2011-08-23

In the Luangwa Valley, Zambia, persistent poverty and hunger present linked challenges to rural development and biodiversity conservation. Both household coping strategies and larger-scale economic development efforts have caused severe natural resource degradation that limits future economic opportunities and endangers ecosystem services. A model based on a business infrastructure has been developed to promote and maintain sustainable agricultural and natural resource management practices, leading to direct and indirect conservation outcomes. The Community Markets for Conservation (COMACO) model operates primarily with communities surrounding national parks, strengthening conservation benefits produced by these protected areas. COMACO first identifies the least food-secure households and trains them in sustainable agricultural practices that minimize threats to natural resources while meeting household needs. In addition, COMACO identifies people responsible for severe natural resource depletion and trains them to generate alternative income sources. In an effort to maintain compliance with these practices, COMACO provides extension support and access to high-value markets that would otherwise be inaccessible to participants. Because the model is continually evolving via adaptive management, success or failure of the model as a whole is difficult to quantify at this early stage. We therefore test specific hypotheses and present data documenting the stabilization of previously declining wildlife populations; the meeting of thresholds of productivity that give COMACO access to stable, high-value markets and progress toward economic self-sufficiency; and the adoption of sustainable agricultural practices by participants and other community members. Together, these findings describe a unique, business-oriented model for poverty alleviation, food production, and biodiversity conservation.

Thermal characterization of Ag and Ag + N ion implanted ultra-high molecular weight polyethylene (UHMWPE)

Energy Technology Data Exchange (ETDEWEB)

Sokullu Urkac, E. [Department of Materials Science, Izmir High Technology Institute, Gulbahcekoyu Urla, Izmir (Turkey)]. E-mail: emelsu@gmail.com; Oztarhan, A. [Bioengineering Department, Ege University, Bornova, Izmir 35100 (Turkey); Tihminlioglu, F. [Department of Chemical Engineering, Izmir High Technology Institute, Gulbahcekoyu Urla, Izmir (Turkey); Kaya, N. [Bioengineering Department, Ege University, Bornova, Izmir 35100 (Turkey); Ila, D. [Center for Irradiation of Materials, Alabama A and M University, Normal AL 35762 (United States); Muntele, C. [Center for Irradiation of Materials, Alabama A and M University, Normal AL 35762 (United States); Budak, S. [Center for Irradiation of Materials, Alabama A and M University, Normal AL 35762 (United States); Oks, E. [H C Electronics Institute, Tomsk (Russian Federation); Nikolaev, A. [H C Electronics Institute, Tomsk (Russian Federation); Ezdesir, A. [R and D Department, PETKIM Holding A.S., Aliaga, Izmir 35801 (Turkey); Tek, Z. [Department of Physics, Celal Bayar University, Manisa (Turkey)

2007-08-15

Most of total hip joints are composed of ultra-high molecular weight polyethylene (UHMWPE ). However, as ultra-high molecular weight polyethylene is too stable in a body, wear debris may accumulate and cause biological response such as bone absorption and loosening of prosthesis. In this study, ultra-high molecular weight polyethylene samples were Ag and Ag + N hybrid ion implanted by using MEVVA ion implantation technique to improve its surface properties. Samples were implanted with a fluence of 10{sup 17} ion/cm{sup 2} and extraction voltage of 30 kV. Implanted and unimplanted samples were investigated by thermo-gravimetry analysis (TGA), differential scanning calorimetry (DSC), X-ray diffraction (XRD) analysis, scanning electron microscopy (SEM), optical microscopy (OM) and contact Angle measurement. Thermal characterization results showed that the ion bombardment induced an increase in the % crystallinity, onset and termination degradation temperatures of UHMWPE.

[Development of indel markers for molecular authentication of Panax ginseng and P. quinquefolius].

Science.gov (United States)

Wang, Rong-Bo; Tian, Hui-Li; Wang, Hong-Tao; Li, Gui-Sheng

2018-04-01

Panax ginseng and P. quinquefolius are two kinds of important medicinal herbs. They are morphologically similar but have different pharmacological effects. Therefore, botanical origin authentication of these two ginsengs is of great importance for ensuring pharmaceutical efficacy and food safety. Based on the fact that intron position in orthologous genes is highly conserved across plant species, intron length polymorphisms were exploited from unigenes of ginseng. Specific primers were respectively designed for these two species based on their insertion/deletion sequences of cytochrome P450 and glyceraldehyde 3-phosphate dehydrogenase, and multiplex PCR was conducted for molecular authentication of P.ginseng and P. quinquefolius. The results showed that the developed multiplex PCR assay was effective for molecular authentication of P.ginseng and P. quinquefolius without strict PCR condition and the optimization of reaction system.This study provides a preferred ideal marker system for molecular authentication of ginseng,and the presented method can be employed in origin authentication of other herbal preparations. Copyright© by the Chinese Pharmaceutical Association.

Massively parallel computation of conservation laws

Energy Technology Data Exchange (ETDEWEB)

Garbey, M [Univ. Claude Bernard, Villeurbanne (France); Levine, D [Argonne National Lab., IL (United States)

1990-01-01

The authors present a new method for computing solutions of conservation laws based on the use of cellular automata with the method of characteristics. The method exploits the high degree of parallelism available with cellular automata and retains important features of the method of characteristics. It yields high numerical accuracy and extends naturally to adaptive meshes and domain decomposition methods for perturbed conservation laws. They describe the method and its implementation for a Dirichlet problem with a single conservation law for the one-dimensional case. Numerical results for the one-dimensional law with the classical Burgers nonlinearity or the Buckley-Leverett equation show good numerical accuracy outside the neighborhood of the shocks. The error in the area of the shocks is of the order of the mesh size. The algorithm is well suited for execution on both massively parallel computers and vector machines. They present timing results for an Alliant FX/8, Connection Machine Model 2, and CRAY X-MP.

Integrating agricultural expansion into conservation biogeography: conflicts and priorities

Directory of Open Access Journals (Sweden)

Ricardo Dobrovolski

2014-06-01

Full Text Available Increasing food production without compromising biodiversity is one of the great challenges for humanity. The aims of my thesis were to define spatial priorities for biodiversity conservation and to evaluate conservation conflicts considering agricultural expansion in the 21st century. I also tested the effect of globalizing conservation efforts on both food production and biodiversity conservation. I found spatial conflicts between biodiversity conservation and agricultural expansion. However, incorporating agricultural expansion data into the spatial prioritization process can significantly alleviate conservation conflicts, by reducing spatial correlation between the areas under high impact of agriculture and the priority areas for conservation. Moreover, developing conservation blueprints at the global scale, instead of the usual approach based on national boundaries, can benefit both food production and biodiversity. Based on these findings I conclude that the incorporation of agricultural expansion as a key component for defining global conservation strategies should be added to the list of solutions for our cultivated planet.

Application of radiation grafting techniques to prepare the high molecular weight water-soluble polymer

International Nuclear Information System (INIS)

Le Hai; Nguyen Quoc Hien; Nguyen Tan Man; Truong Thi Hanh; Le Huu Tu; Tran Thi Tam; Pham Thi Sam; Pham Anh Tuan; Le Dinh Lang

2003-01-01

The results of the study on the preparation of the high molecular weight water-soluble polymers by radiation grafting and their properties is presented as follows: 1/ by radiation grafting, the molecular weight of PVA was increased 20 times and PAM was increased only 3 times; 2/ the thermal and medium stability of poly(vinyl alcohol) grafted with acrylamide was obviously improved. (LH)

Ultra-Fast RAFT-HDA Click Conjugation: An Efficient Route to High Molecular Weight Block Copolymers.

Science.gov (United States)

Inglis, Andrew J; Stenzel, Martina H; Barner-Kowollik, Christopher

2009-11-02

The use of the reversible addition fragmentation chain transfer-hetero Diels-Alder (RAFT-HDA) click reaction for the modular construction of block copolymers is extended to the generation of high molecular weight materials. Cyclopentadienyl end-functionalized polystyrene (PS-Cp) prepared via both atom transfer radical polymerization (ATRP) and the RAFT process are conjugated to poly(isobornyl acrylate) (PiBoA) (also prepared via RAFT polymerization) to achieve well-defined block copolymers with molecular weights ranging from 34 000 to over 100 000 g · mol(-1) and with small polydispersities (PDI HDA click chemistry can provide access to high molecular weight block copolymers in a simple and straight-forward fashion. Copyright © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular design toward highly efficient photovoltaic polymers based on two-dimensional conjugated benzodithiophene.

Science.gov (United States)

Ye, Long; Zhang, Shaoqing; Huo, Lijun; Zhang, Maojie; Hou, Jianhui

2014-05-20

As researchers continue to develop new organic materials for solar cells, benzo[1,2-b:4,5-b']dithiophene (BDT)-based polymers have come to the fore. To improve the photovoltaic properties of BDT-based polymers, researchers have developed and applied various strategies leading to the successful molecular design of highly efficient photovoltaic polymers. Novel polymer materials composed of two-dimensional conjugated BDT (2D-conjugated BDT) have boosted the power conversion efficiency of polymer solar cells (PSCs) to levels that exceed 9%. In this Account, we summarize recent progress related to the design and synthesis of 2D-conjugated BDT-based polymers and discuss their applications in highly efficient photovoltaic devices. We introduce the basic considerations for the construction of 2D-conjugated BDT-based polymers and systematic molecular design guidelines. For example, simply modifying an alkoxyl-substituted BDT to form an alkylthienyl-substituted BDT can improve the polymer hole mobilities substantially with little effect on their molecular energy level. Secondly, the addition of a variety of chemical moieties to the polymer can produce a 2D-conjugated BDT unit with more functions. For example, the introduction of a conjugated side chain with electron deficient groups (such as para-alkyl-phenyl, meta-alkoxyl-phenyl, and 2-alkyl-3-fluoro-thienyl) allowed us to modulate the molecular energy levels of 2D-conjugated BDT-based polymers. Through the rational design of BDT analogues such as dithienobenzodithiophene (DTBDT) or the insertion of larger π bridges, we can tune the backbone conformations of these polymers and modulate their photovoltaic properties. We also discuss the influence of 2D-conjugated BDT on polymer morphology and the blends of these polymers with phenyl-C61 (or C71)-butyric acid methyl ester (PCBM). Finally, we summarize the various applications of the 2D-conjugated BDT-based polymers in highly efficient PSC devices. Overall, this Account

Enzymatic and acidic degradation of high molecular weight dextran into low molecular weight and its characterizations using novel Diffusion-ordered NMR spectroscopy.

Science.gov (United States)

Iqbal, Samina; Marchetti, Roberta; Aman, Afsheen; Silipo, Alba; Qader, Shah Ali Ul; Molinaro, Antonio

2017-10-01

Low molecular weight fractions were derived from native high molecular weight dextran produced by Leuconostoc mesenteroides KIBGE-IB26. Structural characterization of native and low molecular weight fractions obtained after acidic and enzymatic hydrolysis was done using FTIR and NMR spectroscopy. The molecular weight was estimated using Diffusion Ordered NMR spectroscopy. Native dextran (892kDa) is composed of α-(1→6) glycosidic linkage along with α-(1→3) branching. Major proportion of 528kDa dextran was obtained after prolong enzymatic hydrolysis however, an effective acidic treatment at pH-1.4 up to 02 and 04h of exposure resulted in the formation of 77kDa and 57kDa, respectively. The increment in pH from 1.4 to 1.8 lowered the hydrolysis efficiency and resulted in the formation of 270kDa dextran fraction. The results suggest that derived low molecular weight water soluble fractions can be utilized as a drug delivery carrier along with multiple application relating pharmaceutical industries. Copyright © 2017 Elsevier B.V. All rights reserved.

Conserving GW scheme for nonequilibrium quantum transport in molecular contacts

DEFF Research Database (Denmark)

Thygesen, Kristian Sommer; Rubio, Angel

2008-01-01

We give a detailed presentation of our recent scheme to include correlation effects in molecular transport calculations using the nonequilibrium Keldysh formalism. The scheme is general and can be used with any quasiparticle self-energy, but for practical reasons, we mainly specialize to the so......-called GW self-energy, widely used to describe the quasiparticle band structures and spectroscopic properties of extended and low-dimensional systems. We restrict the GW self-energy to a finite, central region containing the molecule, and we describe the leads by density functional theory (DFT). A minimal...

Conservation inequality and the charismatic cat: Felis felicis

Directory of Open Access Journals (Sweden)

E.A. Macdonald

2015-01-01

Full Text Available Conservation resources are limited, making it impossible to invest equally in all threatened species. One way to maximise conservation gains is to focus upon those species with particular public appeal, using them to generate funding and support that could also benefit less charismatic species. Although this approach is already used by many conservation organisations, no reliable metrics currently exist to determine the likely charisma of a given species, and therefore identify the most appropriate targets for such campaigns. Here we use market research techniques on over 1500 people from five continents to assess the relative charisma of different mammals, which factors appear to drive it, and how these patterns vary between countries. Felids and primates emerged as highly favoured species for conservation, with the tiger (Panthera tigris the top species by a wide margin. Using an information theoretic approach we develop models that successfully predict respondents’ preferences across the entire sample, suggesting global commonalities in the attributes that people prefer for conservation. However, by analysing each country separately we are able to improve our models, thus highlighting the importance of identifying locally specific flagships for conservation. The most important attributes were body size and IUCN status, although the extent of baldness, whether the species was a potential threat to humans and whether the eyes were forward or side facing were also widely important. Several of the key attributes revealed in this study could be extrapolated to nearly all terrestrial mammals, paving the way for a standardised global identification of species likely to prove effective for future conservation campaigns. The public preferred species with which they had affinity and familiarity, and we discuss how these aspects could be increased to promote the under-achievers, whilst maximising the funding potential of the highly charismatic mammals

Solvent extraction of cerium (III) with high molecular weight amines

International Nuclear Information System (INIS)

Chatterjee, A.; Basu, S.

1992-01-01

The use of high molecular weight amines in the extraction of cerium (III) as EDTA complex from neutral aqueous medium is reported. The extraction condition was optimised from the study of effects of several variables like concentration of amine and EDTA pH nature of diluents etc. The method has been applied for the determination of cerium in few mineral samples. (author). 7 refs., 5 tabs

Mercury-free high pressure discharge lamps dominated by molecular radiation

International Nuclear Information System (INIS)

Kaening, M; Hitzschke, L; Berger, M; Schalk, B; Franke, St; Methling, R

2011-01-01

High intensity discharge (HID) lamps dominated by molecular radiation offer a very promising alternative for use in future light sources. They are able to deliver competitive efficacies of about 110 lm W -1 and higher, excellent colour rendering index above 90 and a correlated colour temperature in the 3000-4000 K region at the operating point near the Planckian locus. Moreover, these lamps are opening up the possibility of dimming. Due to the fact that they are able to omit mercury they are environmentally friendly. The emission spectra generated by these HID lamps differ significantly from those of conventional lamps. The reason for this is the dominance of molecular radiation processes. In comparison with conventional HID lamps atomic contributions are usually rather small. In the present case they amount to less than about 10% of the total intensity in the visible range.

Mercury-free high pressure discharge lamps dominated by molecular radiation

Energy Technology Data Exchange (ETDEWEB)

Kaening, M; Hitzschke, L; Berger, M [Research Europe, OSRAM GmbH, Werner-von-Siemens Strasse 6, 86159 Augsburg (Germany); Schalk, B [Vitec Group Videocom Division, Erfurter Strasse 16, 85386 Eching (Germany); Franke, St; Methling, R, E-mail: m.kaening@osram.de [INP, Leibniz-Institut fuer Plasmaforschung und Technologie e. V., Felix-Hausdorff-Strasse 2, 17489 Greifswald (Germany)

2011-06-08

High intensity discharge (HID) lamps dominated by molecular radiation offer a very promising alternative for use in future light sources. They are able to deliver competitive efficacies of about 110 lm W{sup -1} and higher, excellent colour rendering index above 90 and a correlated colour temperature in the 3000-4000 K region at the operating point near the Planckian locus. Moreover, these lamps are opening up the possibility of dimming. Due to the fact that they are able to omit mercury they are environmentally friendly. The emission spectra generated by these HID lamps differ significantly from those of conventional lamps. The reason for this is the dominance of molecular radiation processes. In comparison with conventional HID lamps atomic contributions are usually rather small. In the present case they amount to less than about 10% of the total intensity in the visible range.

77 FR 59712 - Energy Conservation Program: Energy Conservation Standards for Dishwashers

Science.gov (United States)

2012-10-01

... amended energy conservation standards, DOE conducted a market survey using all available public... Energy Conservation Program: Energy Conservation Standards for Dishwashers AGENCY: Office of Energy... establish amended energy conservation standards for dishwashers in the Federal Register on May 30, 2012. DOE...

Understanding conservationists' perspectives on the new-conservation debate.

Science.gov (United States)

Holmes, George; Sandbrook, Chris; Fisher, Janet A

2017-04-01

A vibrant debate about the future direction of biodiversity conservation centers on the merits of the so-called new conservation. Proponents of the new conservation advocate a series of positions on key conservation ideas, such as the importance of human-dominated landscapes and conservation's engagement with capitalism. These have been fiercely contested in a debate dominated by a few high-profile individuals, and so far there has been no empirical exploration of existing perspectives on these issues among a wider community of conservationists. We used Q methodology to examine empirically perspectives on the new conservation held by attendees at the 2015 International Congress for Conservation Biology (ICCB). Although we identified a consensus on several key issues, 3 distinct positions emerged: in favor of conservation to benefit people but opposed to links with capitalism and corporations, in favor of biocentric approaches but with less emphasis on wilderness protection than prominent opponents of new conservation, and in favor of the published new conservation perspective but with less emphasis on increasing human well-being as a goal of conservation. Our results revealed differences between the debate on the new conservation in the literature and views held within a wider, but still limited, conservation community and demonstrated the existence of at least one viewpoint (in favor of conservation to benefit people but opposed to links with capitalism and corporations) that is almost absent from the published debate. We hope the fuller understanding we present of the variety of views that exist but have not yet been heard, will improve the quality and tone of debates on the subject. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Molecular Aspects of H. pylori-Related MALT Lymphoma

Directory of Open Access Journals (Sweden)

Scott R. Owens

2011-01-01

Full Text Available Helicobacter pylori-related extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue is a paradigm for malignancy arising in an inflammatory background. While the diagnosis of H. pylori gastritis is often straightforward, distinction between severe gastritis and early lymphoma can be difficult and requires careful assessment of clinical findings in addition to histological features and immunohistochemical results. A number of cytogenetic abnormalities have been discovered in H. pylori-related lymphomas and several have clinical importance, related to the responsiveness of lymphoma to H. pylori eradication therapy, but routine molecular studies are not widely utilized. While molecular methods may be used in equivocal cases, a trial of conservative therapy is warranted given the propensity for these lymphomas to regress with eradication of the organism. Once therapy is initiated, care must be taken to avoid a premature assignment of disease refractoriness because complete response can take several months to more than a year. Cases truly refractory to H. pylori eradication therapy may be treated with adjuvant chemoradiation with a high response rate.

Development of gel-filter method for high enrichment of low-molecular weight proteins from serum.

Directory of Open Access Journals (Sweden)

Lingsheng Chen

Full Text Available The human serum proteome has been extensively screened for biomarkers. However, the large dynamic range of protein concentrations in serum and the presence of highly abundant and large molecular weight proteins, make identification and detection changes in the amount of low-molecular weight proteins (LMW, molecular weight ≤ 30kDa difficult. Here, we developed a gel-filter method including four layers of different concentration of tricine SDS-PAGE-based gels to block high-molecular weight proteins and enrich LMW proteins. By utilizing this method, we identified 1,576 proteins (n = 2 from 10 μL serum. Among them, 559 (n = 2 proteins belonged to LMW proteins. Furthermore, this gel-filter method could identify 67.4% and 39.8% more LMW proteins than that in representative methods of glycine SDS-PAGE and optimized-DS, respectively. By utilizing SILAC-AQUA approach with labeled recombinant protein as internal standard, the recovery rate for GST spiked in serum during the treatment of gel-filter, optimized-DS, and ProteoMiner was 33.1 ± 0.01%, 18.7 ± 0.01% and 9.6 ± 0.03%, respectively. These results demonstrate that the gel-filter method offers a rapid, highly reproducible and efficient approach for screening biomarkers from serum through proteomic analyses.

Changes in permittivity and density of molecular liquids under high pressure.

Science.gov (United States)

Kiselev, Vladimir D; Kornilov, Dmitry A; Konovalov, Alexander I

2014-04-03

We collected and analyzed the density and permittivity of 57 nonpolar and dipolar molecular liquids at different temperatures (143 sets) and pressures (555 sets). No equation was found that could accurately predict the change to polar liquid permittivity by the change of its density in the range of the pressures and temperatures tested. Consequently, the influence of high hydrostatic pressure and temperature on liquid permittivity may be a more complicated process compared to density changes. The pressure and temperature coefficients of permittivity can be drastically larger than the pressure and temperature coefficients of density, indicating that pressure and particularly temperature significantly affect the structure of molecular liquids. These changes have less influence on the density change but can strongly affect the permittivity change. The clear relationship between the tangent and secant moduli of the permittivity curvatures under pressure for various molecular liquids at different temperatures was obtained, from which one can calculate the Tait equation coefficients from the experimental values of the pressure influence on the permittivity at ambient pressure.

Conserving Earth's Biodiversity. [CD-ROM and] Instructor's Manual.

Science.gov (United States)

2000

This CD-ROM is designed as an interactive learning tool to support teaching in highly interdisciplinary fields such as conservation of biodiversity. Topics introduced in the software include the impact of humans on natural landscapes, threats to biodiversity, methods and theories of conservation biology, environmental laws, and relevant economic…

RAPD-PCR molecular analysis of the threatened Cabrera's vole ...

African Journals Online (AJOL)

Optimal management and conservation programs of the threatened Cabrera's vole require investigating potential molecular genetic markers in the genomic background, if the few remaining fragile populations are to ... The results described Cabrera's vole populations as a single genetic unit with slightly restricted gene flow.

MOUNTAIN NATURAL BIODIVERSITY CONSERVATION IN RUSSIA

Directory of Open Access Journals (Sweden)

Arkady Tishkov

2012-01-01

Full Text Available High biodiversity and degree of endemism of mountain biota strengthen the mountain regions’ status for the territorial nature conservation. Analysis of the protected areas’ representativeness in various mountain regions of Russia shows some discrepancy between their quantity, square and regional biodiversity originality. The biggest divergences are marked for the Northern Caucasus. The main problems: small area of the protected territories and also cluster character of their spatial distribution, mostly in the high mountains are not supposed to conform with the highest values of the regional flora’s and fauna’s uniqueness, to compensate representativeness of the protected biota and, in anyway, to correspond with the purpose of nature protection frame—the protected territories ecologic network’s forming. The situation in the Urals, Siberia and the Far East seems to be better. The large areas of the protected territories are in general agreement with the high originality of the nature ecosystems. Nevertheless each concrete case needs analysis of the regional biota’s and ecosystems’ biodiversity distribution within the protected areas, including character and (or unique elements of the regional biodiversity to be held. The development of the effectual territorial conservation of mountain regions needs differential approach. The creation of the large representative parcels of nature landscapes in the key-areas has the considerable meaning in the low-developed regions, difficult to access. And well-developed regions have the necessity of nature protected territories’ network development and the planning of the ecological frame’s forming. The territorial biodiversity conservation, including the system of federal, regional and local levels with protective conservation of the rare species has to be combined with ecosystem’s restoration, especially in the zones disturbed by erosion, recreation and military actions. Also it is

The relationship of protein conservation and sequence length

Directory of Open Access Journals (Sweden)

Panchenko Anna R

2002-11-01

Full Text Available Abstract Background In general, the length of a protein sequence is determined by its function and the wide variance in the lengths of an organism's proteins reflects the diversity of specific functional roles for these proteins. However, additional evolutionary forces that affect the length of a protein may be revealed by studying the length distributions of proteins evolving under weaker functional constraints. Results We performed sequence comparisons to distinguish highly conserved and poorly conserved proteins from the bacterium Escherichia coli, the archaeon Archaeoglobus fulgidus, and the eukaryotes Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. For all organisms studied, the conserved and nonconserved proteins have strikingly different length distributions. The conserved proteins are, on average, longer than the poorly conserved ones, and the length distributions for the poorly conserved proteins have a relatively narrow peak, in contrast to the conserved proteins whose lengths spread over a wider range of values. For the two prokaryotes studied, the poorly conserved proteins approximate the minimal length distribution expected for a diverse range of structural folds. Conclusions There is a relationship between protein conservation and sequence length. For all the organisms studied, there seems to be a significant evolutionary trend favoring shorter proteins in the absence of other, more specific functional constraints.

Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library.

Directory of Open Access Journals (Sweden)

Alessia Cariani

Full Text Available Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera, including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions.

Molecular mechanisms of aging and immune system regulation in Drosophila.

Science.gov (United States)

Eleftherianos, Ioannis; Castillo, Julio Cesar

2012-01-01

Aging is a complex process that involves the accumulation of deleterious changes resulting in overall decline in several vital functions, leading to the progressive deterioration in physiological condition of the organism and eventually causing disease and death. The immune system is the most important host-defense mechanism in humans and is also highly conserved in insects. Extensive research in vertebrates has concluded that aging of the immune function results in increased susceptibility to infectious disease and chronic inflammation. Over the years, interest has grown in studying the molecular interaction between aging and the immune response to pathogenic infections. The fruit fly Drosophila melanogaster is an excellent model system for dissecting the genetic and genomic basis of important biological processes, such as aging and the innate immune system, and deciphering parallel mechanisms in vertebrate animals. Here, we review the recent advances in the identification of key players modulating the relationship between molecular aging networks and immune signal transduction pathways in the fly. Understanding the details of the molecular events involved in aging and immune system regulation will potentially lead to the development of strategies for decreasing the impact of age-related diseases, thus improving human health and life span.

A conserved regulatory mechanism in bifunctional biotin protein ligases.

Science.gov (United States)

Wang, Jingheng; Beckett, Dorothy

2017-08-01

Class II bifunctional biotin protein ligases (BirA), which catalyze post-translational biotinylation and repress transcription initiation, are broadly distributed in eubacteria and archaea. However, it is unclear if these proteins all share the same molecular mechanism of transcription regulation. In Escherichia coli the corepressor biotinoyl-5'-AMP (bio-5'-AMP), which is also the intermediate in biotin transfer, promotes operator binding and resulting transcription repression by enhancing BirA dimerization. Like E. coli BirA (EcBirA), Staphylococcus aureus, and Bacillus subtilis BirA (Sa and BsBirA) repress transcription in vivo in a biotin-dependent manner. In this work, sedimentation equilibrium measurements were performed to investigate the molecular basis of this biotin-responsive transcription regulation. The results reveal that, as observed for EcBirA, Sa, and BsBirA dimerization reactions are significantly enhanced by bio-5'-AMP binding. Thus, the molecular mechanism of the Biotin Regulatory System is conserved in the biotin repressors from these three organisms. © 2017 The Protein Society.

How conserved are the conserved 16S-rRNA regions?

Directory of Open Access Journals (Sweden)

Marcel Martinez-Porchas

2017-02-01

Full Text Available The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123 were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%. Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.

Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees.

Science.gov (United States)

Hollender, Courtney A; Pascal, Thierry; Tabb, Amy; Hadiarto, Toto; Srinivasan, Chinnathambi; Wang, Wanpeng; Liu, Zhongchi; Scorza, Ralph; Dardick, Chris

2018-05-15

Plant shoots typically grow upward in opposition to the pull of gravity. However, exceptions exist throughout the plant kingdom. Most conspicuous are trees with weeping or pendulous branches. While such trees have long been cultivated and appreciated for their ornamental value, the molecular basis behind the weeping habit is not known. Here, we characterized a weeping tree phenotype in Prunus persica (peach) and identified the underlying genetic mutation using a genomic sequencing approach. Weeping peach tree shoots exhibited a downward elliptical growth pattern and did not exhibit an upward bending in response to 90° reorientation. The causative allele was found to be an uncharacterized gene, Ppa013325 , having a 1.8-Kb deletion spanning the 5' end. This gene, dubbed WEEP , was predominantly expressed in phloem tissues and encodes a highly conserved 129-amino acid protein containing a sterile alpha motif (SAM) domain. Silencing WEEP in the related tree species Prunus domestica (plum) resulted in more outward, downward, and wandering shoot orientations compared to standard trees, supporting a role for WEEP in directing lateral shoot growth in trees. This previously unknown regulator of branch orientation, which may also be a regulator of gravity perception or response, provides insights into our understanding of how tree branches grow in opposition to gravity and could serve as a critical target for manipulating tree architecture for improved tree shape in agricultural and horticulture applications. Copyright © 2018 the Author(s). Published by PNAS.

Conservation

NARCIS (Netherlands)

Noteboom, H.P.

1985-01-01

The IUCN/WWF Plants Conservation Programme 1984 — 1985. World Wildlife Fund chose plants to be the subject of their fund-raising campaign in the period 1984 — 1985. The objectives were to: 1. Use information techniques to achieve the conservation objectives of the Plants Programme – to save plants;

Gas Source Techniques for Molecular Beam Epitaxy of Highly Mismatched Ge Alloys

Directory of Open Access Journals (Sweden)

Chad A. Stephenson

2016-12-01

Full Text Available Ge and its alloys are attractive candidates for a laser compatible with silicon integrated circuits. Dilute germanium carbide (Ge1−xCx offers a particularly interesting prospect. By using a precursor gas with a Ge4C core, C can be preferentially incorporated in substitutional sites, suppressing interstitial and C cluster defects. We present a method of reproducible and upscalable gas synthesis of tetrakis(germylmethane, or (H3Ge4C, followed by the design of a hybrid gas/solid-source molecular beam epitaxy system and subsequent growth of defect-free Ge1−xCx by molecular beam epitaxy (MBE. Secondary ion mass spectroscopy, transmission electron microscopy and contactless electroreflectance confirm the presence of carbon with very high crystal quality resulting in a decrease in the direct bandgap energy. This technique has broad applicability to growth of highly mismatched alloys by MBE.

Recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers

DEFF Research Database (Denmark)

Andersen, Lars Dyrskjøt; Zieger, Karsten; Ørntoft, Torben Falck

2007-01-01

individually contributed to the management of the disease. However, the development of high-throughput techniques for simultaneous assessment of a large number of markers has allowed classification of tumors into clinically relevant molecular subgroups beyond those possible by pathological classification. Here......Bladder cancer is the fifth most common neoplasm in industrialized countries. Due to frequent recurrences of the superficial form of this disease, bladder cancer ranks as one of the most common cancers. Despite the description of a large number of tumor markers for bladder cancers, none have......, we review the recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers....

Cross-cohort analysis identifies a TEAD4 ↔ MYCN positive-feedback loop as the core regulatory element of high-risk neuroblastoma. | Office of Cancer Genomics

Science.gov (United States)

High-risk neuroblastomas show a paucity of recurrent somatic mutations at diagnosis. As a result, the molecular basis for this aggressive phenotype remains elusive. Recent progress in regulatory network analysis helped us elucidate disease-driving mechanisms downstream of genomic alterations, including recurrent chromosomal alterations. Our analysis identified three molecular subtypes of high-risk neuroblastomas, consistent with chromosomal alterations, and identified subtype-specific master regulator (MR) proteins that were conserved across independent cohorts.

Determining the drivers of population structure in a highly urbanized landscape to inform conservation planning.

Science.gov (United States)

Thomassen, Henri A; Harrigan, Ryan J; Semple Delaney, Kathleen; Riley, Seth P D; Serieys, Laurel E K; Pease, Katherine; Wayne, Robert K; Smith, Thomas B

2018-02-01

Understanding the environmental contributors to population structure is of paramount importance for conservation in urbanized environments. We used spatially explicit models to determine genetic population structure under current and future environmental conditions across a highly fragmented, human-dominated environment in Southern California to assess the effects of natural ecological variation and urbanization. We focused on 7 common species with diverse habitat requirements, home-range sizes, and dispersal abilities. We quantified the relative roles of potential barriers, including natural environmental characteristics and an anthropogenic barrier created by a major highway, in shaping genetic variation. The ability to predict genetic variation in our models differed among species: 11-81% of intraspecific genetic variation was explained by environmental variables. Although an anthropogenically induced barrier (a major highway) severely restricted gene flow and movement at broad scales for some species, genetic variation seemed to be primarily driven by natural environmental heterogeneity at a local level. Our results show how assessing environmentally associated variation for multiple species under current and future climate conditions can help identify priority regions for maximizing population persistence under environmental change in urbanized regions. © 2017 Society for Conservation Biology.

The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD

Science.gov (United States)

Calmettes, Charles; Ing, Christopher; Buckwalter, Carolyn M.; El Bakkouri, Majida; Chieh-Lin Lai, Christine; Pogoutse, Anastassia; Gray-Owen, Scott D.; Pomès, Régis; Moraes, Trevor F.

2015-01-01

Invading bacteria from the Neisseriaceae, Acinetobacteriaceae, Bordetellaceae and Moraxellaceae families express the conserved outer-membrane zinc transporter zinc-uptake component D (ZnuD) to overcome nutritional restriction imposed by the host organism during infection. Here we demonstrate that ZnuD is required for efficient systemic infections by the causative agent of bacterial meningitis, Neisseria meningitidis, in a mouse model. We also combine X-ray crystallography and molecular dynamics simulations to gain insight into the mechanism of zinc recognition and transport across the bacterial outer-membrane by ZnuD. Because ZnuD is also considered a promising vaccine candidate against N. meningitidis, we use several ZnuD structural intermediates to map potential antigenic epitopes, and propose a mechanism by which ZnuD can maintain high sequence conservation yet avoid immune recognition by altering the conformation of surface-exposed loops. PMID:26282243

Comparing the cost-effectiveness of water conservation policies in a depleting aquifer:A dynamic analysis of the Kansas High Plains

Science.gov (United States)

This research analyzes two groundwater conservation policies in the Kansas High Plains located within the Ogallala aquifer: 1) cost-share assistance to increase irrigation efficiency; and 2) incentive payments to convert irrigated crop production to dryland crop production. To compare the cost-effec...

Conservation.

Science.gov (United States)

National Audubon Society, New York, NY.

This set of teaching aids consists of seven Audubon Nature Bulletins, providing the teacher and student with informational reading on various topics in conservation. The bulletins have these titles: Plants as Makers of Soil, Water Pollution Control, The Ground Water Table, Conservation--To Keep This Earth Habitable, Our Threatened Air Supply,…

Identification of evolutionarily conserved Momordica charantia microRNAs using computational approach and its utility in phylogeny analysis.

Science.gov (United States)

Thirugnanasambantham, Krishnaraj; Saravanan, Subramanian; Karikalan, Kulandaivelu; Bharanidharan, Rajaraman; Lalitha, Perumal; Ilango, S; HairulIslam, Villianur Ibrahim

2015-10-01

Momordica charantia (bitter gourd, bitter melon) is a monoecious Cucurbitaceae with anti-oxidant, anti-microbial, anti-viral and anti-diabetic potential. Molecular studies on this economically valuable plant are very essential to understand its phylogeny and evolution. MicroRNAs (miRNAs) are conserved, small, non-coding RNA with ability to regulate gene expression by bind the 3' UTR region of target mRNA and are evolved at different rates in different plant species. In this study we have utilized homology based computational approach and identified 27 mature miRNAs for the first time from this bio-medically important plant. The phylogenetic tree developed from binary data derived from the data on presence/absence of the identified miRNAs were noticed to be uncertain and biased. Most of the identified miRNAs were highly conserved among the plant species and sequence based phylogeny analysis of miRNAs resolved the above difficulties in phylogeny approach using miRNA. Predicted gene targets of the identified miRNAs revealed their importance in regulation of plant developmental process. Reported miRNAs held sequence conservation in mature miRNAs and the detailed phylogeny analysis of pre-miRNA sequences revealed genus specific segregation of clusters. Copyright © 2015 Elsevier Ltd. All rights reserved.

Persistent leatherback turtle migrations present opportunities for conservation.

Directory of Open Access Journals (Sweden)

George L Shillinger

2008-07-01

Full Text Available Effective transboundary conservation of highly migratory marine animals requires international management cooperation as well as clear scientific information about habitat use by these species. Populations of leatherback turtles (Dermochelys coriacea in the eastern Pacific have declined by >90% during the past two decades, primarily due to unsustainable egg harvest and fisheries bycatch mortality. While research and conservation efforts on nesting beaches are ongoing, relatively little is known about this population of leatherbacks' oceanic habitat use and migration pathways. We present the largest multi-year (2004-2005, 2005-2006, and 2007 satellite tracking dataset (12,095 cumulative satellite tracking days collected for leatherback turtles. Forty-six females were electronically tagged during three field seasons at Playa Grande, Costa Rica, the largest extant nesting colony in the eastern Pacific. After completing nesting, the turtles headed southward, traversing the dynamic equatorial currents with rapid, directed movements. In contrast to the highly varied dispersal patterns seen in many other sea turtle populations, leatherbacks from Playa Grande traveled within a persistent migration corridor from Costa Rica, past the equator, and into the South Pacific Gyre, a vast, low-energy, low-productivity region. We describe the predictable effects of ocean currents on a leatherback migration corridor and characterize long-distance movements by the turtles in the eastern South Pacific. These data from high seas habitats will also elucidate potential areas for mitigating fisheries bycatch interactions. These findings directly inform existing multinational conservation frameworks and provide immediate regions in the migration corridor where conservation can be implemented. We identify high seas locations for focusing future conservation efforts within the leatherback dispersal zone in the South Pacific Gyre.

Persistent Leatherback Turtle Migrations Present Opportunities for Conservation

Science.gov (United States)

Shillinger, George L; Palacios, Daniel M; Bailey, Helen; Bograd, Steven J; Swithenbank, Alan M; Gaspar, Philippe; Wallace, Bryan P; Spotila, James R; Paladino, Frank V; Piedra, Rotney; Eckert, Scott A; Block, Barbara A

2008-01-01

Effective transboundary conservation of highly migratory marine animals requires international management cooperation as well as clear scientific information about habitat use by these species. Populations of leatherback turtles (Dermochelys coriacea) in the eastern Pacific have declined by >90% during the past two decades, primarily due to unsustainable egg harvest and fisheries bycatch mortality. While research and conservation efforts on nesting beaches are ongoing, relatively little is known about this population of leatherbacks' oceanic habitat use and migration pathways. We present the largest multi-year (2004–2005, 2005–2006, and 2007) satellite tracking dataset (12,095 cumulative satellite tracking days) collected for leatherback turtles. Forty-six females were electronically tagged during three field seasons at Playa Grande, Costa Rica, the largest extant nesting colony in the eastern Pacific. After completing nesting, the turtles headed southward, traversing the dynamic equatorial currents with rapid, directed movements. In contrast to the highly varied dispersal patterns seen in many other sea turtle populations, leatherbacks from Playa Grande traveled within a persistent migration corridor from Costa Rica, past the equator, and into the South Pacific Gyre, a vast, low-energy, low-productivity region. We describe the predictable effects of ocean currents on a leatherback migration corridor and characterize long-distance movements by the turtles in the eastern South Pacific. These data from high seas habitats will also elucidate potential areas for mitigating fisheries bycatch interactions. These findings directly inform existing multinational conservation frameworks and provide immediate regions in the migration corridor where conservation can be implemented. We identify high seas locations for focusing future conservation efforts within the leatherback dispersal zone in the South Pacific Gyre. PMID:18630987

Molecular mechanism for inhibition of twinfilin by phosphoinositides

DEFF Research Database (Denmark)

Hakala, Markku; Kalimeri, Maria; Enkavi, Giray

2018-01-01

actin-depolymerizing factor (ADF)/cofilin-like ADF homology domains of twinfilin bind phosphoinositides only with low affinity. Mutagenesis and biochemical experiments combined with atomistic molecular dynamics simulations reveal that the C-terminal tail of twinfilin interacts with membranes through......Membrane phosphoinositides control organization and dynamics of the actin cytoskeleton by regulating the activities of several key actin-binding proteins. Twinfilin is an evolutionarily conserved protein that contributes to cytoskeletal dynamics by interacting with actin monomers, filaments......, and the heterodimeric capping protein. Twinfilin also binds phosphoinositides, which inhibit its interactions with actin, but the underlying mechanism has remained unknown. Here, we show that the high-affinity binding site of twinfilin for phosphoinositides is located at the C-terminal tail region, whereas the two...

Conservation Triage Falls Short Because Conservation Is Not Like Emergency Medicine

Directory of Open Access Journals (Sweden)

John A. Vucetich

2017-05-01

Full Text Available Conservation triage, as a concept, seems to have been born from analogizing circumstances that characterize conservation with triage, as the concept applies to emergency medicine. Careful consideration—facilitated through the aid of formal argumentation—demonstrates the critical limitations of the analogy. Those limitations reveal how the concept of conservation triage falls short. For example, medical triage presupposes that resources available for an emergency are limited and fixed. By contrast, the resources available for conservation are not fixed. Moreover, the ethics of prioritization in medical triage is characterized by there being universal agreement on the moral value of the patients. However, in conservation there is not universal agreement on the value of various objects of conservation concern. The looming importance of those features of conservation—disputed values and unfixed resources—make conservation triage a largely un-useful concept.

High-energy molecular lasers self-controlled volume-discharge lasers and applications

CERN Document Server

Apollonov, V V

2016-01-01

This book displays the physics and design of high-power molecular lasers. The lasers described are self-controlled volume-discharge lasers. The book explains self-sustained discharge lasers, self-initiated discharge lasers and technical approaches to laser design. Important topics discussed are laser efficiency, laser beam quality and electric field homogeneity. The book contains many new innovative applications.

Structure and properties of simple molecular systems at very high density

International Nuclear Information System (INIS)

LeSar, R.

1989-01-01

The use of computer simulations in the study of molecular systems at very high density is reviewed. Applications to the thermodynamics of dense fluid nitrogen and phase transitions in solid oxygen are presented. The effects of changes in the atomic electronic structure on the equation of state of very dense helium are discussed. 19 refs., 2 figs

Mechanisms of plastic deformation in highly cross-linked UHMWPE for total hip components--the molecular physics viewpoint.

Science.gov (United States)

Takahashi, Yasuhito; Shishido, Takaaki; Yamamoto, Kengo; Masaoka, Toshinori; Kubo, Kosuke; Tateiwa, Toshiyuki; Pezzotti, Giuseppe

2015-02-01

Plastic deformation is an unavoidable event in biomedical polymeric implants for load-bearing application during long-term in-vivo service life, which involves a mass transfer process, irreversible chain motion, and molecular reorganization. Deformation-induced microstructural alterations greatly affect mechanical properties and durability of implant devices. The present research focused on evaluating, from a molecular physics viewpoint, the impact of externally applied strain (or stress) in ultra-high molecular weight polyethylene (UHMWPE) prostheses, subjected to radiation cross-linking and subsequent remelting for application in total hip arthroplasty (THA). Two different types of commercial acetabular liners, which belong to the first-generation highly cross-linked UHMWPE (HXLPE), were investigated by means of confocal/polarized Raman microprobe spectroscopy. The amount of crystalline region and the spatial distribution of molecular chain orientation were quantitatively analyzed according to a combined theory including Raman selection rules for the polyethylene orthorhombic structure and the orientation distribution function (ODF) statistical approach. The structurally important finding was that pronounced recrystallization and molecular reorientation increasingly appeared in the near-surface regions of HXLPE liners with increasing the amount of plastic (compressive) deformation stored in the microstructure. Such molecular rearrangements, occurred in response to external strains, locally increase surface cross-shear (CS) stresses, which in turn trigger microscopic wear processes in HXLPE acetabular liners. Thus, on the basis of the results obtained at the molecular scale, we emphasize here the importance of minimizing the development of irrecoverable deformation strain in order to retain the pristine and intrinsically high wear performance of HXLPE components. Copyright © 2014 Elsevier Ltd. All rights reserved.

Increasing participation in incentive programs for biodiversity conservation.

Science.gov (United States)

Sorice, Michael G; Oh, Chi-Ok; Gartner, Todd; Snieckus, Mary; Johnson, Rhett; Donlan, C Josh

2013-07-01

Engaging private landowners in conservation activities for imperiled species is critical to maintaining and enhancing biodiversity. Market-based approaches can incentivize conservation behaviors on private lands by shifting the benefit-cost ratio of engaging in activities that result in net conservation benefits for target species. In the United States and elsewhere, voluntary conservation agreements with financial incentives are becoming an increasingly common strategy. While the influence of program design and delivery of voluntary conservation programs is often overlooked, these aspects are critical to achieving the necessary participation to attain landscape-scale outcomes. Using a sample of family-forest landowners in the southeast United States, we show how preferences for participation in a conservation program to protect an at-risk species, the gopher tortoise (Gopherus polyphemus), are related to program structure, delivery, and perceived efficacy. Landowners were most sensitive to programs that are highly controlling, require permanent conservation easements, and put landowners at risk for future regulation. Programs designed with greater levels of compensation and that support landowners' autonomy to make land management decisions can increase participation and increase landowner acceptance of program components that are generally unfavorable, like long-term contracts and permanent easements. There is an inherent trade-off between maximizing participation and maximizing the conservation benefits when designing a conservation incentive program. For conservation programs targeting private lands to achieve landscape-level benefits, they must attract a critical level of participation that creates a connected mosaic of conservation benefits. Yet, programs with attributes that strive to maximize conservation benefits within a single agreement (and reduce risks of failure) are likely to have lower participation, and thus lower landscape benefits. Achieving

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

Science.gov (United States)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

Intravascular near-infrared fluorescence molecular imaging of atherosclerosis: toward coronary arterial visualization of biologically high-risk plaques

Science.gov (United States)

Calfon, Marcella A.; Vinegoni, Claudio; Ntziachristos, Vasilis; Jaffer, Farouc A.

2010-01-01

New imaging methods are urgently needed to identify high-risk atherosclerotic lesions prior to the onset of myocardial infarction, stroke, and ischemic limbs. Molecular imaging offers a new approach to visualize key biological features that characterize high-risk plaques associated with cardiovascular events. While substantial progress has been realized in clinical molecular imaging of plaques in larger arterial vessels (carotid, aorta, iliac), there remains a compelling, unmet need to develop molecular imaging strategies targeted to high-risk plaques in human coronary arteries. We present recent developments in intravascular near-IR fluorescence catheter-based strategies for in vivo detection of plaque inflammation in coronary-sized arteries. In particular, the biological, light transmission, imaging agent, and engineering principles that underlie a new intravascular near-IR fluorescence sensing method are discussed. Intravascular near-IR fluorescence catheters appear highly translatable to the cardiac catheterization laboratory, and thus may offer a new in vivo method to detect high-risk coronary plaques and to assess novel atherosclerosis biologics.

Universal antibodies against the highly conserved influenza fusion peptide cross-neutralize several subtypes of influenza A virus

Energy Technology Data Exchange (ETDEWEB)

Hashem, Anwar M. [Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, HPFB, Health Canada, Ottawa, ON (Canada); Department of Microbiology, Faculty of Medicine, King Abdulaziz University, Jeddah (Saudi Arabia); Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON (Canada); Van Domselaar, Gary [National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB (Canada); Li, Changgui; Wang, Junzhi [National Institute for the Control of Pharmaceutical and Biological Products, Beijing (China); She, Yi-Min; Cyr, Terry D. [Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, HPFB, Health Canada, Ottawa, ON (Canada); Sui, Jianhua [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 44 Binney Street, Boston, MA 02115 (United States); He, Runtao [National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB (Canada); Marasco, Wayne A. [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 44 Binney Street, Boston, MA 02115 (United States); Li, Xuguang, E-mail: Sean.Li@hc-sc.gc.ca [Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, HPFB, Health Canada, Ottawa, ON (Canada); Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON (Canada)

2010-12-10

Research highlights: {yields} The fusion peptide is the only universally conserved epitope in all influenza viral hemagglutinins. {yields} Anti-fusion peptide antibodies are universal antibodies that cross-react with all influenza HA subtypes. {yields} The universal antibodies cross-neutralize different influenza A subtypes. {yields} The universal antibodies inhibit the fusion process between the viruses and the target cells. -- Abstract: The fusion peptide of influenza viral hemagglutinin plays a critical role in virus entry by facilitating membrane fusion between the virus and target cells. As the fusion peptide is the only universally conserved epitope in all influenza A and B viruses, it could be an attractive target for vaccine-induced immune responses. We previously reported that antibodies targeting the first 14 amino acids of the N-terminus of the fusion peptide could bind to virtually all influenza virus strains and quantify hemagglutinins in vaccines produced in embryonated eggs. Here we demonstrate that these universal antibodies bind to the viral hemagglutinins in native conformation presented in infected mammalian cell cultures and neutralize multiple subtypes of virus by inhibiting the pH-dependant fusion of viral and cellular membranes. These results suggest that this unique, highly-conserved linear sequence in viral hemagglutinin is exposed sufficiently to be attacked by the antibodies during the course of infection and merits further investigation because of potential importance in the protection against diverse strains of influenza viruses.

Universal antibodies against the highly conserved influenza fusion peptide cross-neutralize several subtypes of influenza A virus

International Nuclear Information System (INIS)

Hashem, Anwar M.; Van Domselaar, Gary; Li, Changgui; Wang, Junzhi; She, Yi-Min; Cyr, Terry D.; Sui, Jianhua; He, Runtao; Marasco, Wayne A.; Li, Xuguang

2010-01-01

Research highlights: → The fusion peptide is the only universally conserved epitope in all influenza viral hemagglutinins. → Anti-fusion peptide antibodies are universal antibodies that cross-react with all influenza HA subtypes. → The universal antibodies cross-neutralize different influenza A subtypes. → The universal antibodies inhibit the fusion process between the viruses and the target cells. -- Abstract: The fusion peptide of influenza viral hemagglutinin plays a critical role in virus entry by facilitating membrane fusion between the virus and target cells. As the fusion peptide is the only universally conserved epitope in all influenza A and B viruses, it could be an attractive target for vaccine-induced immune responses. We previously reported that antibodies targeting the first 14 amino acids of the N-terminus of the fusion peptide could bind to virtually all influenza virus strains and quantify hemagglutinins in vaccines produced in embryonated eggs. Here we demonstrate that these universal antibodies bind to the viral hemagglutinins in native conformation presented in infected mammalian cell cultures and neutralize multiple subtypes of virus by inhibiting the pH-dependant fusion of viral and cellular membranes. These results suggest that this unique, highly-conserved linear sequence in viral hemagglutinin is exposed sufficiently to be attacked by the antibodies during the course of infection and merits further investigation because of potential importance in the protection against diverse strains of influenza viruses.

Setting conservation priorities.

Science.gov (United States)

Wilson, Kerrie A; Carwardine, Josie; Possingham, Hugh P

2009-04-01

A generic framework for setting conservation priorities based on the principles of classic decision theory is provided. This framework encapsulates the key elements of any problem, including the objective, the constraints, and knowledge of the system. Within the context of this framework the broad array of approaches for setting conservation priorities are reviewed. While some approaches prioritize assets or locations for conservation investment, it is concluded here that prioritization is incomplete without consideration of the conservation actions required to conserve the assets at particular locations. The challenges associated with prioritizing investments through time in the face of threats (and also spatially and temporally heterogeneous costs) can be aided by proper problem definition. Using the authors' general framework for setting conservation priorities, multiple criteria can be rationally integrated and where, how, and when to invest conservation resources can be scheduled. Trade-offs are unavoidable in priority setting when there are multiple considerations, and budgets are almost always finite. The authors discuss how trade-offs, risks, uncertainty, feedbacks, and learning can be explicitly evaluated within their generic framework for setting conservation priorities. Finally, they suggest ways that current priority-setting approaches may be improved.

Conservation of biodiversity in mountain ecosystems -- At a glance

OpenAIRE

MacKinnon, K.

2002-01-01

Metadata only record Mountains are especially important for biodiversity conservation since many harbor unique assemblages of plants and animals, including high levels of endemic species. Mountain biodiversity and natural habitats bestow multiple ecosystem, soil conservation, and watershed benefits. Mountains are often centers of endemism, where species are prevalent in or peculiar to a particular region, and Pleistocene refuges, which are hypothesized to have high levels of diversity wher...

Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

Directory of Open Access Journals (Sweden)

Rangel-Figueiredo Teresa

2010-06-01

Full Text Available Abstract Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95. With breed information, 30 cows and three bulls were identified (q > 0.95 that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10 relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P st = 0.028, P > 0.05. Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50 to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that

HIGH-ENERGY COSMIC-RAY DIFFUSION IN MOLECULAR CLOUDS: A NUMERICAL APPROACH

International Nuclear Information System (INIS)

Fatuzzo, M.; Melia, F.; Todd, E.; Adams, F. C.

2010-01-01

The propagation of high-energy cosmic rays (CRs) through giant molecular clouds constitutes a fundamental process in astronomy and astrophysics. The diffusion of CRs through these magnetically turbulent environments is often studied through the use of energy-dependent diffusion coefficients, although these are not always well motivated theoretically. Now, however, it is feasible to perform detailed numerical simulations of the diffusion process computationally. While the general problem depends upon both the field structure and particle energy, the analysis may be greatly simplified by dimensionless analysis. That is, for a specified purely turbulent field, the analysis depends almost exclusively on a single parameter-the ratio of the maximum wavelength of the turbulent field cells to the particle gyration radius. For turbulent magnetic fluctuations superimposed over an underlying uniform magnetic field, particle diffusion depends on a second dimensionless parameter that characterizes the ratio of the turbulent to uniform magnetic field energy densities. We consider both of these possibilities and parametrize our results to provide simple quantitative expressions that suitably characterize the diffusion process within molecular cloud environments. Doing so, we find that the simple scaling laws often invoked by the high-energy astrophysics community to model CR diffusion through such regions appear to be fairly robust for the case of a uniform magnetic field with a strong turbulent component, but are only valid up to ∼50 TeV particle energies for a purely turbulent field. These results have important consequences for the analysis of CR processes based on TeV emission spectra associated with dense molecular clouds.

Molecular Dynamics Simulation of High Density DNA Arrays

Directory of Open Access Journals (Sweden)

Rudolf Podgornik

2018-01-01

Full Text Available Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and

Conservation investment for rare plants in urban environments.

Science.gov (United States)

Schwartz, Mark W; Smith, Lacy M; Steel, Zachary L

2013-01-01

Budgets for species conservation limit actions. Expending resources in areas of high human density is costly and generally considered less likely to succeed. Yet, coastal California contains both a large fraction of narrowly endemic at-risk plant species as well as the state's three largest metropolitan regions. Hence understanding the capacity to protect species along the highly urbanized coast is a conservation priority. We examine at-risk plant populations along California's coastline from San Diego to north of San Francisco to better understand whether there is a relationship between human population density and: i) performance of at-risk plant populations; and ii) conservation spending. Answering these questions can help focus appropriate strategic conservation investment. Rare plant performance was measured using the annualized growth rate estimate between census periods using the California Natural Diversity Database. Human density was estimated using Census Bureau statistics from the year 2000. We found strong evidence for a lack of a relationship between human population density and plant population performance in California's coastal counties. Analyzing US Endangered Species expenditure reports, we found large differences in expenditures among counties, with plants in San Diego County receiving much higher expenditures than other locations. We found a slight positive relationship between expenditures on behalf of endangered species and human density. Together these data support the argument that conservation efforts by protecting habitats within urban environments are not less likely to be successful than in rural areas. Expenditures on behalf of federally listed endangered and threatened plants do not appear to be related to proximity to human populations. Given the evidence of sufficient performance in urban environments, along with a high potential to leverage public support for nature in urban environments, expenditures in these areas appear to be an

Characterization of genetic diversity in chickpea using SSR markers, Start Codon Targeted Polymorphism (SCoT) and Conserved DNA-Derived Polymorphism (CDDP).

Science.gov (United States)

Hajibarat, Zahra; Saidi, Abbas; Hajibarat, Zohreh; Talebi, Reza

2015-07-01

To evaluate the genetic diversity among 48 genotypes of chickpea comprising cultivars, landraces and internationally developed improved lines genetic distances were evaluated using three different molecular marker techniques: Simple Sequence Repeat (SSR); Start Codon Targeted (SCoT) and Conserved DNA-derived Polymorphism (CDDP). Average polymorphism information content (PIC) for SSR, SCoT and CDDP markers was 0.47, 0.45 and 0.45, respectively, and this revealed that three different marker types were equal for the assessment of diversity amongst genotypes. Cluster analysis for SSR and SCoT divided the genotypes in to three distinct clusters and using CDDP markers data, genotypes grouped in to five clusters. There were positive significant correlation (r = 0.43, P SSR markers. These results suggest that efficiency of SSR, SCOT and CDDP markers was relatively the same in fingerprinting of chickpea genotypes. To our knowledge, this is the first detailed report of using targeted DNA region molecular marker (CDDP) for genetic diversity analysis in chickpea in comparison with SCoT and SSR markers. Overall, our results are able to prove the suitability of SCoT and CDDP markers for genetic diversity analysis in chickpea for their high rates of polymorphism and their potential for genome diversity and germplasm conservation.

The impact of computer science in molecular medicine: enabling high-throughput research.

Science.gov (United States)

de la Iglesia, Diana; García-Remesal, Miguel; de la Calle, Guillermo; Kulikowski, Casimir; Sanz, Ferran; Maojo, Víctor

2013-01-01

The Human Genome Project and the explosion of high-throughput data have transformed the areas of molecular and personalized medicine, which are producing a wide range of studies and experimental results and providing new insights for developing medical applications. Research in many interdisciplinary fields is resulting in data repositories and computational tools that support a wide diversity of tasks: genome sequencing, genome-wide association studies, analysis of genotype-phenotype interactions, drug toxicity and side effects assessment, prediction of protein interactions and diseases, development of computational models, biomarker discovery, and many others. The authors of the present paper have developed several inventories covering tools, initiatives and studies in different computational fields related to molecular medicine: medical informatics, bioinformatics, clinical informatics and nanoinformatics. With these inventories, created by mining the scientific literature, we have carried out several reviews of these fields, providing researchers with a useful framework to locate, discover, search and integrate resources. In this paper we present an analysis of the state-of-the-art as it relates to computational resources for molecular medicine, based on results compiled in our inventories, as well as results extracted from a systematic review of the literature and other scientific media. The present review is based on the impact of their related publications and the available data and software resources for molecular medicine. It aims to provide information that can be useful to support ongoing research and work to improve diagnostics and therapeutics based on molecular-level insights.

Molecular sensors and molecular logic gates

International Nuclear Information System (INIS)

Georgiev, N.; Bojinov, V.

2013-01-01

Full text: The rapid grow of nanotechnology field extended the concept of a macroscopic device to the molecular level. Because of this reason the design and synthesis of (supra)-molecular species capable of mimicking the functions of macroscopic devices are currently of great interest. Molecular devices operate via electronic and/or nuclear rearrangements and, like macroscopic devices, need energy to operate and communicate between their elements. The energy needed to make a device work can be supplied as chemical energy, electrical energy, or light. Luminescence is one of the most useful techniques to monitor the operation of molecular-level devices. This fact determinates the synthesis of novel fluorescence compounds as a considerable and inseparable part of nanoscience development. Further miniaturization of semiconductors in electronic field reaches their limit. Therefore the design and construction of molecular systems capable of performing complex logic functions is of great scientific interest now. In semiconductor devices the logic gates work using binary logic, where the signals are encoded as 0 and 1 (low and high current). This process is executable on molecular level by several ways, but the most common are based on the optical properties of the molecule switches encoding the low and high concentrations of the input guest molecules and the output fluorescent intensities with binary 0 and 1 respectively. The first proposal to execute logic operations at the molecular level was made in 1988, but the field developed only five years later when the analogy between molecular switches and logic gates was experimentally demonstrated by de Silva. There are seven basic logic gates: AND, OR, XOR, NOT, NAND, NOR and XNOR and all of them were achieved by molecules, the fluorescence switching as well. key words: fluorescence, molecular sensors, molecular logic gates

To what extent do potential conservation donors value community-aspects of conservation projects in low income countries?

Science.gov (United States)

Young, Richard P.; Gibbons, James M.; Jones, Julia P. G.

2018-01-01

There is a major gap in funding required for conservation, especially in low income countries. Given the significant contribution of taxpayers in industrialized countries to funding conservation overseas, and donations from membership organisation, understanding the preferences of ordinary people in a high income country for different attributes of conservation projects is valuable for future marketing of conservation. We conducted a discrete choice experiment with visitors to a UK zoo, while simultaneously conducting a revealed preference study through a real donation campaign on the same sample. Respondents showed the highest willingness to pay for projects that have local community involvement in management (95% confidence interval £9.82 to £15.83), and for improvement in threatened species populations (£2.97 - £13.87). Both of these were significantly larger than the willingness to pay for projects involving provision of alternative livelihoods, or improving the condition of conservation sites. Results of the simultaneous donation campaign showed that respondents were very willing to donate the suggested £1 or above donation (88% made a donation, n = 1798); there was no effect of which of the two campaigns they were exposed to (threatened species management or community involvement in management). The small number of people who did not make a donation had a higher stated willingness to pay within the choice experiment, which may suggest hypothetical bias. Conservationists increasingly argue that conservation should include local communities in management (for both pragmatic and moral reasons). It is heartening that potential conservation donors seem to agree. PMID:29451923

Conservation Value

OpenAIRE

Tisdell, Clement A.

2010-01-01

This paper outlines the significance of the concept of conservation value and discusses ways in which it is determined paying attention to views stemming from utilitarian ethics and from deontological ethics. The importance of user costs in relation to economic decisions about the conservation and use of natural resources is emphasised. Particular attention is given to competing views about the importance of conserving natural resources in order to achieve economic sustainability. This then l...

Removal of high-molecular weight polycyclic aromatic hydrocarbons

Directory of Open Access Journals (Sweden)

Ulrich Vasconcelos

2011-01-01

Full Text Available Alternatives for the removal of high-molecular weight polycyclic aromatic hydrocarbons (HWM-PAH from soil were tested by adding fertilizer or glycerol, as well as the combination of both. Experiments were carried out for 60 days in reactors containing a HWM-PAH-contaminated soil (8030 μg kg-1, accompanied by pH monitoring, humidity control and quantification of total heterotrophic bacteria and total fungus. Fertilizer addition removed 41.6% of HWM-PAH. Fertilizer and glycerol in combination removed 46.2%. When glycerol was added individually, degradation reached 50.4%. Glycerol also promoted the increase of degradation rate during the first 30 days suggesting the HMW-PAH removal occurred through cometabolic pathways.

The Implications of Breast Cancer Molecular Phenotype for Radiation Oncology

Energy Technology Data Exchange (ETDEWEB)

Sioshansi, Shirin [Department of Radiation Oncology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA (United States); Department of Radiation Oncology, Rhode Island Hospital, Warren Alpert School of Medicine at Brown University, Providence, RI (United States); Huber, Kathryn E. [Department of Radiation Oncology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA (United States); Wazer, David E., E-mail: dwazer@tuftsmedicalcenter.org [Department of Radiation Oncology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA (United States); Department of Radiation Oncology, Rhode Island Hospital, Warren Alpert School of Medicine at Brown University, Providence, RI (United States)

2011-06-28

The identification of distinct molecular subtypes of breast cancer has advanced the understanding and treatment of breast cancer by providing insight into prognosis, patterns of recurrence, and effectiveness of therapy. The prognostic significance of molecular phenotype with regard to distant recurrences and overall survival are well established in the literature and has been readily incorporated into systemic therapy management decisions. However, despite the accumulating data suggesting similar prognostic significance for locoregional recurrence, integration of molecular phenotype into local management decision making has lagged. Although there are some conflicting reports, collectively the literature supports a low risk of local recurrence (LR) in the hormone receptor (HR) positive luminal subtypes compared to HR negative subtypes [triple negative (TN) and HER2-enriched]. The development of targeted therapies, such as trastuzumab for the treatment of HER2-enriched subtype, has been shown to mitigate the increased risk of LR. Unfortunately, no such remedy exists to address the increased risk of LR for patients with TN tumors, making it a clinical challenge for radiation oncologists. In this review we discuss the correlation between molecular subtype and LR following either breast conservation therapy or mastectomy. We also explore the possible mechanisms for increased LR in TN breast cancer and radiotherapeutic implications for this population, such as the safety of breast conservation, consideration of dose escalation, and the appropriateness of accelerated partial breast irradiation.

The Implications of Breast Cancer Molecular Phenotype for Radiation Oncology

International Nuclear Information System (INIS)

Sioshansi, Shirin; Huber, Kathryn E.; Wazer, David E.

2011-01-01

The identification of distinct molecular subtypes of breast cancer has advanced the understanding and treatment of breast cancer by providing insight into prognosis, patterns of recurrence, and effectiveness of therapy. The prognostic significance of molecular phenotype with regard to distant recurrences and overall survival are well established in the literature and has been readily incorporated into systemic therapy management decisions. However, despite the accumulating data suggesting similar prognostic significance for locoregional recurrence, integration of molecular phenotype into local management decision making has lagged. Although there are some conflicting reports, collectively the literature supports a low risk of local recurrence (LR) in the hormone receptor (HR) positive luminal subtypes compared to HR negative subtypes [triple negative (TN) and HER2-enriched]. The development of targeted therapies, such as trastuzumab for the treatment of HER2-enriched subtype, has been shown to mitigate the increased risk of LR. Unfortunately, no such remedy exists to address the increased risk of LR for patients with TN tumors, making it a clinical challenge for radiation oncologists. In this review we discuss the correlation between molecular subtype and LR following either breast conservation therapy or mastectomy. We also explore the possible mechanisms for increased LR in TN breast cancer and radiotherapeutic implications for this population, such as the safety of breast conservation, consideration of dose escalation, and the appropriateness of accelerated partial breast irradiation.

Comparative profiling of miRNA expression in developing seeds of high linoleic and high oleic safflower (Carthamus tinctorius L. plants

Directory of Open Access Journals (Sweden)

Shijiang eCao

2013-12-01

Full Text Available Vegetable oils high in oleic acid are considered to be advantageous because of their better nutritional value and potential industrial applications. The oleic acid content in the classic safflower oil is normally 10-15% while a natural mutant (ol accumulates elevated oleic acid up to 70% in seed oil. As a part of our investigation into the molecular features of the high oleic (HO trait in safflower we have profiled the microRNA (miRNA populations in developing safflower seeds expressing the ol allele in comparison to the wild type high linoleic (HL safflower using deep sequencing technology. The small RNA populations of the mid-maturity developing embryos of homozygous ol HO and wild type HL safflower had a very similar size distribution pattern, however, only ~16.5% of the unique small RNAs were overlapping in these two genotypes. From these two small RNA populations we have found 55 known miRNAs and identified two candidate novel miRNA families to be likely unique to the developing safflower seeds. Target genes with conserved as well as novel functions were predicted for the conserved miRNAs. We have also identified 13 miRNAs differentially expressed between the HO and HL safflower genotypes. The results may lay a foundation for unravelling the miRNA-mediated molecular processes that regulate oleic acid accumulation in the HO safflower mutant and developmental processes in safflower embryos in general.

Molecular characterization of a rat α2B-adrenergic receptor

International Nuclear Information System (INIS)

Zeng, D.; Harrison, J.K.; D'Angelo, D.D.; Barber, C.M.; Tucker, A.L.; Lu, Z.; Lynch, K.R.

1990-01-01

α 2 -Adrenergic receptors comprise a heterogeneous population based on pharmacologic and molecular evidence. The authors have isolated a cDNA clone (pRNGα 2 ) encoding a rat α 2 -adrenergic receptor. A rat kidney cDNA library was screened with an oligonucleotide complementary to a highly conserved region found in all biogenic amine receptors described to date. The deduced amino acid sequence displays many features of guanyl nucleotide-binding protein-coupled receptors except it does not have a consensus N-linked glycosylation site near the amino terminus. Membranes prepared from COS cells transfected with pRNGα 2 DNA display high affinity an saturable binding to [ 3 H]rauwolscine. Competition curve data analysis shows that RNGα 2 protein binds to a variety of adrenergic drugs with the following rank order of potency: yohimbine ≥ chlorpromazine > prazosin ≥ clonidine > norepinephrine ≥ oxymetazoline. RNGα 2 RNA accumulates in both rat kidney and neonatal rat lung. When a cysteine residue (Cys-169) that is conserved among all members of the seven-transmembrane-region superfamily is changed to phenylalanine, the RNGα 2 protein fails to bind [ 3 H]rauwolscine after expression in COS cells. They conclude that pRNGα 2 likely represents a cDNA for a rat α 2B -adrenergic receptor

Direct Photolithography on Molecular Crystals for High Performance Organic Optoelectronic Devices.

Science.gov (United States)

Yao, Yifan; Zhang, Lei; Leydecker, Tim; Samorì, Paolo

2018-05-23

Organic crystals are generated via the bottom-up self-assembly of molecular building blocks which are held together through weak noncovalent interactions. Although they revealed extraordinary charge transport characteristics, their labile nature represents a major drawback toward their integration in optoelectronic devices when the use of sophisticated patterning techniques is required. Here we have devised a radically new method to enable the use of photolithography directly on molecular crystals, with a spatial resolution below 300 nm, thereby allowing the precise wiring up of multiple crystals on demand. Two archetypal organic crystals, i.e., p-type 2,7-diphenyl[1]benzothieno[3,2- b][1]benzothiophene (Dph-BTBT) nanoflakes and n-type N, N'-dioctyl-3,4,9,10-perylenedicarboximide (PTCDI-C8) nanowires, have been exploited as active materials to realize high-performance top-contact organic field-effect transistors (OFETs), inverter and p-n heterojunction photovoltaic devices supported on plastic substrate. The compatibility of our direct photolithography technique with organic molecular crystals is key for exploiting the full potential of organic electronics for sophisticated large-area devices and logic circuitries, thus paving the way toward novel applications in plastic (opto)electronics.

Unveiling the Structural Origin of the High Carrier Mobility of a Molecular Monolayer on Boron Nitride

OpenAIRE

Xu, Rui; He, Daowei; Zhang, Yuhan; Wu, Bing; Liu, Fengyuan; Meng, Lan; Liu, Jun-Fang; Wu, Qisheng; Shi, Yi; Wang, Jinlan; Nie, Jia-Cai; Wang, Xinran; He, Lin

2014-01-01

Very recently, it was demonstrated that the carrier mobility of a molecular monolayer dioctylbenzothienobenzothiophene (C8-BTBT) on boron nitride can reach 10 cm2/Vs, the highest among the previously reported monolayer molecular field-effect transistors. Here we show that the high-quality single crystal of the C8-BTBT monolayer may be the key origin of the record-high carrier mobility. We discover that the C8-BTBT molecules prefer layer-by-layer growth on both hexagonal boron nitride and grap...

Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals.

Science.gov (United States)

Davies, Kalina T J; Tsagkogeorga, Georgia; Rossiter, Stephen J

2014-12-19

The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes - such as those regulating sensory system development - suggests crucial roles in regulating gene expression and cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems. Phylogenetic reconstructions of concatenated CNEs broadly recovered accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that utilise

Restricted-range fishes and the conservation of Brazilian freshwaters.

Science.gov (United States)

Nogueira, Cristiano; Buckup, Paulo A; Menezes, Naercio A; Oyakawa, Osvaldo T; Kasecker, Thais P; Ramos Neto, Mario B; da Silva, José Maria C

2010-06-30

Freshwaters are the most threatened ecosystems on earth. Although recent assessments provide data on global priority regions for freshwater conservation, local scale priorities remain unknown. Refining the scale of global biodiversity assessments (both at terrestrial and freshwater realms) and translating these into conservation priorities on the ground remains a major challenge to biodiversity science, and depends directly on species occurrence data of high taxonomic and geographic resolution. Brazil harbors the richest freshwater ichthyofauna in the world, but knowledge on endemic areas and conservation in Brazilian rivers is still scarce. Using data on environmental threats and revised species distribution data we detect and delineate 540 small watershed areas harboring 819 restricted-range fishes in Brazil. Many of these areas are already highly threatened, as 159 (29%) watersheds have lost more than 70% of their original vegetation cover, and only 141 (26%) show significant overlap with formally protected areas or indigenous lands. We detected 220 (40%) critical watersheds overlapping hydroelectric dams or showing both poor formal protection and widespread habitat loss; these sites harbor 344 endemic fish species that may face extinction if no conservation action is in place in the near future. We provide the first analysis of site-scale conservation priorities in the richest freshwater ecosystems of the globe. Our results corroborate the hypothesis that freshwater biodiversity has been neglected in former conservation assessments. The study provides a simple and straightforward method for detecting freshwater priority areas based on endemism and threat, and represents a starting point for integrating freshwater and terrestrial conservation in representative and biogeographically consistent site-scale conservation strategies, that may be scaled-up following naturally linked drainage systems. Proper management (e. g. forestry code enforcement, landscape

A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.

Science.gov (United States)

Yu, Chenggang; Boutté, Angela; Yu, Xueping; Dutta, Bhaskar; Feala, Jacob D; Schmid, Kara; Dave, Jitendra; Tawa, Gregory J; Wallqvist, Anders; Reifman, Jaques

2015-02-01

The multifactorial nature of traumatic brain injury (TBI), especially the complex secondary tissue injury involving intertwined networks of molecular pathways that mediate cellular behavior, has confounded attempts to elucidate the pathology underlying the progression of TBI. Here, systems biology strategies are exploited to identify novel molecular mechanisms and protein indicators of brain injury. To this end, we performed a meta-analysis of four distinct high-throughput gene expression studies involving different animal models of TBI. By using canonical pathways and a large human protein-interaction network as a scaffold, we separately overlaid the gene expression data from each study to identify molecular signatures that were conserved across the different studies. At 24 hr after injury, the significantly activated molecular signatures were nonspecific to TBI, whereas the significantly suppressed molecular signatures were specific to the nervous system. In particular, we identified a suppressed subnetwork consisting of 58 highly interacting, coregulated proteins associated with synaptic function. We selected three proteins from this subnetwork, postsynaptic density protein 95, nitric oxide synthase 1, and disrupted in schizophrenia 1, and hypothesized that their abundance would be significantly reduced after TBI. In a penetrating ballistic-like brain injury rat model of severe TBI, Western blot analysis confirmed our hypothesis. In addition, our analysis recovered 12 previously identified protein biomarkers of TBI. The results suggest that systems biology may provide an efficient, high-yield approach to generate testable hypotheses that can be experimentally validated to identify novel mechanisms of action and molecular indicators of TBI. © 2014 The Authors. Journal of Neuroscience Research Published by Wiley Periodicals, Inc.

Radiation chemistry in high pressure paying attention to molecular motion and alignment

International Nuclear Information System (INIS)

Sasuga, Tsuneo

1978-01-01

Effects of high pressure or radiation-induced cross-linking of synthetic rubbers and polymerization of methacrylates and acrylonitrile (AN) have been studied paying attention to molecular motion and alignment. The following were revealed from radiation-induced crosslinking reaction, pressure-volume-temperature (P-V-T) measurement and chemical relaxation of polymer crosslinked at high pressure: (1) The rate of crosslinking is increased in compression especially in polymers containing double bonds, due to chain reaction through double bonds. (2) Crosslinking points of the polymer with double bonds crosslinked at high pressure are dispersed as cluster. (3) Crosslinking reaction is intimately related with change of the molecular motion in a polymer under pressure. Van't Hoff plots of methacrylates and AN breaked at a pressure depending on the monomer. The pressure giving the breaks depends on length of methacrylate. P-V curves of the polymer-monomer coexistence system as-polymerized exhibit peculiar behavior at the pressure giving the breaks. AN exhibits complicated polymerization behavior at a pressure changing compressibility of the monomer. From above results etc. it is concluded that monomer molecules are aligned in short range at a pressure corresponding to geometrical structure of the monomer molecules. (auth.)

A guide to calculating habitat-quality metrics to inform conservation of highly mobile species

Science.gov (United States)

Bieri, Joanna A.; Sample, Christine; Thogmartin, Wayne E.; Diffendorfer, James E.; Earl, Julia E.; Erickson, Richard A.; Federico, Paula; Flockhart, D. T. Tyler; Nicol, Sam; Semmens, Darius J.; Skraber, T.; Wiederholt, Ruscena; Mattsson, Brady J.

2018-01-01

Many metrics exist for quantifying the relative value of habitats and pathways used by highly mobile species. Properly selecting and applying such metrics requires substantial background in mathematics and understanding the relevant management arena. To address this multidimensional challenge, we demonstrate and compare three measurements of habitat quality: graph-, occupancy-, and demographic-based metrics. Each metric provides insights into system dynamics, at the expense of increasing amounts and complexity of data and models. Our descriptions and comparisons of diverse habitat-quality metrics provide means for practitioners to overcome the modeling challenges associated with management or conservation of such highly mobile species. Whereas previous guidance for applying habitat-quality metrics has been scattered in diversified tracks of literature, we have brought this information together into an approachable format including accessible descriptions and a modeling case study for a typical example that conservation professionals can adapt for their own decision contexts and focal populations.Considerations for Resource ManagersManagement objectives, proposed actions, data availability and quality, and model assumptions are all relevant considerations when applying and interpreting habitat-quality metrics.Graph-based metrics answer questions related to habitat centrality and connectivity, are suitable for populations with any movement pattern, quantify basic spatial and temporal patterns of occupancy and movement, and require the least data.Occupancy-based metrics answer questions about likelihood of persistence or colonization, are suitable for populations that undergo localized extinctions, quantify spatial and temporal patterns of occupancy and movement, and require a moderate amount of data.Demographic-based metrics answer questions about relative or absolute population size, are suitable for populations with any movement pattern, quantify demographic

Molecular phylogeny of mangroves IV. nature and extent of intra-specific genetic variation and species diversity in mangroves

International Nuclear Information System (INIS)

Parida, A.; Parani, M.; Lakshmi, M.; Elango, S.; Ram, N.; Anuratha, C.S.

1998-01-01

Mangroves occupy estuarine ecosystems in the tropical regions of the world. Despite their highly productive nature and the protective roles they play in the coastal region, the ecosystem as a whole is under severe threat due to various climatic and anthropogenic factors. Therefore, the need for conservation of mangroves is widely emphasised. However, information on existing genetic diversity based on which a strategy for genetic conservation is to be drawn is not available for mangroves. This is primarily because conventional genetic analysis is difficult in these species for various reasons. Therefore, as an aid to our on-going conservation programme, efforts were made to assess the nature and extent of diversity in a number of mangrove species of the Indian coast using molecular markers. The nature and extent of intra-population diversity in sixteen mangrove species and detailed analysis of inter-population genetic polymorphism in four species, Acanthus ilicifolius, Excoecaria agallocha, Avicennia spp and Rhizophora (species and hybrid), is reported in the present communication. (author)

Interaction of MYC with host cell factor-1 is mediated by the evolutionarily conserved Myc box IV motif.

Science.gov (United States)

Thomas, L R; Foshage, A M; Weissmiller, A M; Popay, T M; Grieb, B C; Qualls, S J; Ng, V; Carboneau, B; Lorey, S; Eischen, C M; Tansey, W P

2016-07-07

The MYC family of oncogenes encodes a set of three related transcription factors that are overexpressed in many human tumors and contribute to the cancer-related deaths of more than 70,000 Americans every year. MYC proteins drive tumorigenesis by interacting with co-factors that enable them to regulate the expression of thousands of genes linked to cell growth, proliferation, metabolism and genome stability. One effective way to identify critical co-factors required for MYC function has been to focus on sequence motifs within MYC that are conserved throughout evolution, on the assumption that their conservation is driven by protein-protein interactions that are vital for MYC activity. In addition to their DNA-binding domains, MYC proteins carry five regions of high sequence conservation known as Myc boxes (Mb). To date, four of the Mb motifs (MbI, MbII, MbIIIa and MbIIIb) have had a molecular function assigned to them, but the precise role of the remaining Mb, MbIV, and the reason for its preservation in vertebrate Myc proteins, is unknown. Here, we show that MbIV is required for the association of MYC with the abundant transcriptional coregulator host cell factor-1 (HCF-1). We show that the invariant core of MbIV resembles the tetrapeptide HCF-binding motif (HBM) found in many HCF-interaction partners, and demonstrate that MYC interacts with HCF-1 in a manner indistinguishable from the prototypical HBM-containing protein VP16. Finally, we show that rationalized point mutations in MYC that disrupt interaction with HCF-1 attenuate the ability of MYC to drive tumorigenesis in mice. Together, these data expose a molecular function for MbIV and indicate that HCF-1 is an important co-factor for MYC.

Effects of preference heterogeneity among landowners on spatial conservation prioritization

DEFF Research Database (Denmark)

Nielsen, Anne Sofie Elberg; Strange, Niels; Bruun, Hans Henrik

2017-01-01

The participation of private landowners in conservation is crucial to efficient biodiversity conservation. This is especially the case in settings where the share of private ownership is large and the economic costs associated with land acquisition are high. We used probit regression analysis...... into a spatial prioritization for conservation of unmanaged forests. The choice models are based on sociodemographic data on the entire population of Danish forest owners and historical data on their participation in conservation schemes. Inclusion in the model of information on private landowners' willingness...... to supply land for conservation yielded at intermediate budget levels up to 30% more expected species coverage than the uninformed prioritization scheme. Our landowner-choice model provides an example of moving toward more implementable conservation planning....

Chemistry of the High-mass Protostellar Molecular Clump IRAS 16562–3959

Science.gov (United States)

Guzmán, Andrés E.; Guzmán, Viviana V.; Garay, Guido; Bronfman, Leonardo; Hechenleitner, Federico

2018-06-01

We present molecular line observations of the high-mass molecular clump IRAS 16562‑3959 taken at 3 mm using the Atacama Large Millimeter/submillimeter Array at 1.″7 angular resolution (0.014 pc spatial resolution). This clump hosts the actively accreting high-mass young stellar object (HMYSO) G345.4938+01.4677, which is associated with a hypercompact H II region. We identify and analyze emission lines from 22 molecular species (encompassing 34 isomers) and classify them into two groups, depending on their spatial distribution within the clump. One of these groups gathers shock tracers (e.g., SiO, SO, HNCO) and species formed in dust grains like methanol (CH3OH), ethenone or ketene (H2CCO), and acetaldehyde (CH3CHO). The second group collects species closely resembling the dust continuum emission morphology and are formed mainly in the gas phase, like hydrocarbons (CCH, c-C3H2, CH3CCH), cyanopolyynes (HC3N and HC5N), and cyanides (HCN and CH3C3N). Emission from complex organic molecules (COMs) like CH3OH, propanenitrile (CH3CH2CN), and methoxymethane (CH3OCH3) arise from gas in the vicinity of a hot molecular core (T ≳ 100 K) associated with the HMYSO. Other COMs such as propyne (CH3CCH), acrylonitrile (CH2CHCN), and acetaldehyde seem to better trace warm (T ≲ 80 K) dense gas. In addition, deuterated ammonia (NH2D) is detected mostly in the outskirts of IRAS 16562‑3959 and associated with near-infrared dark globules, probably gaseous remnants of the clump’s prestellar phase. The spatial distribution of molecules in IRAS 16562‑3959 supports the view that in protostellar clumps, chemical tracers associated with different evolutionary stages—starless to hot cores/H II regions—exist coevally.

Gene pool conservation and tree improvement in Serbia

Directory of Open Access Journals (Sweden)

Isajev Vasilije

2009-01-01

Full Text Available This paper presents the concepts applied in the gene pool conservation and tree improvement in Serbia. Gene pool conservation of tree species in Serbia includes a series of activities aiming at the sustainability and protection of genetic and species variability. This implies the investigation of genetic resources and their identification through the research of the genetic structure and the breeding system of individual species. Paper also includes the study of intra- and inter-population variability in experiments - provenance tests, progeny tests, half- and full-sib lines, etc. The increased use of the genetic potential in tree improvement in Serbia should be intensified by the following activities: improvement of production of normal forest seed, application of the concept of new selections directed primarily to the improvement of only one character, because in that case the result would be certain, establishment and management of seed orchards as specialized plantations for long-term production of genetically good-quality forest seeds, and the shortening of the improvement process by introducing new techniques and methods (molecular markers, somaclonal variation, genetic engineering, protoplast fusion, micropropagation, etc..

Cosmetic results in early stage breast cancer patients with high-dose brachytherapy after conservative surgery

International Nuclear Information System (INIS)

Torres, Felipe; Pineda, Beatriz E

2004-01-01

Purpose: to reveal cosmetic results in patients at early stages of low risk breast cancer treated with partial accelerated radiotherapy using high dose rate brachytherapy. Methods and materials: from March 2001 to July 2003,14 stages l and ll breast cancer patients were treated at the Colombian national cancer institute in Bogota with conservative surgery and radiotherapy upon the tumor bed (partial accelerated radiotherapy), using interstitial implants with iridium 192 (high dose rate brachytherapy) with a dose of 32 Gys, over 4 days, at 8 fractions twice a day. Results: with an average follow up of 17.7 months, good cosmetic results were found among 71.4 % of patients and excellent results among 14.3% of patients, furthermore none of the patients neither local nor regional or distant relapses. Conclusion: among patients who suffer from breast cancer at early stages, it showed is possible to apply partial accelerated radiotherapy upon the tumor bed with high doses over 4 days with good to excellent cosmetic results

Cooperative light-induced molecular movements of highly ordered azobenzene self-assembled monolayers.

Science.gov (United States)

Pace, Giuseppina; Ferri, Violetta; Grave, Christian; Elbing, Mark; von Hänisch, Carsten; Zharnikov, Michael; Mayor, Marcel; Rampi, Maria Anita; Samorì, Paolo

2007-06-12

Photochromic systems can convert light energy into mechanical energy, thus they can be used as building blocks for the fabrication of prototypes of molecular devices that are based on the photomechanical effect. Hitherto a controlled photochromic switch on surfaces has been achieved either on isolated chromophores or within assemblies of randomly arranged molecules. Here we show by scanning tunneling microscopy imaging the photochemical switching of a new terminally thiolated azobiphenyl rigid rod molecule. Interestingly, the switching of entire molecular 2D crystalline domains is observed, which is ruled by the interactions between nearest neighbors. This observation of azobenzene-based systems displaying collective switching might be of interest for applications in high-density data storage.

Advancing Treatment of Pituitary Adenomas through Targeted Molecular Therapies: The Acromegaly & Cushing Disease Paradigms

Directory of Open Access Journals (Sweden)

Michael Anthony Mooney

2016-07-01

Full Text Available The current treatment of pituitary adenomas requires a balance of conservative management, surgical resection, and in select tumor types, molecular therapy. Acromegaly treatment is an evolving field where our understanding of molecular targets and drug therapies has improved treatment options for patients with excess growth hormone levels. We highlight the use of molecular therapies in this disease process and advances in this field, which may represent a paradigm shift for the future of pituitary adenoma treatment.

Molecular gated-AlGaN/GaN high electron mobility transistor for pH detection.

Science.gov (United States)

Ding, Xiangzhen; Yang, Shuai; Miao, Bin; Gu, Le; Gu, Zhiqi; Zhang, Jian; Wu, Baojun; Wang, Hong; Wu, Dongmin; Li, Jiadong

2018-04-18

A molecular gated-AlGaN/GaN high electron mobility transistor has been developed for pH detection. The sensing surface of the sensor was modified with 3-aminopropyltriethoxysilane to provide amphoteric amine groups, which would play the role of receptors for pH detection. On modification with 3-aminopropyltriethoxysilane, the transistor exhibits good chemical stability in hydrochloric acid solution and is sensitive for pH detection. Thus, our molecular gated-AlGaN/GaN high electron mobility transistor acheived good electrical performances such as chemical stability (remained stable in hydrochloric acid solution), good sensitivity (37.17 μA/pH) and low hysteresis. The results indicate a promising future for high-quality sensors for pH detection.

Impending conservation crisis for Southeast Asian amphibians.

Science.gov (United States)

Rowley, Jodi; Brown, Rafe; Bain, Raoul; Kusrini, Mirza; Inger, Robert; Stuart, Bryan; Wogan, Guin; Thy, Neang; Chan-Ard, Tanya; Trung, Cao Tien; Diesmos, Arvin; Iskandar, Djoko T; Lau, Michael; Ming, Leong Tzi; Makchai, Sunchai; Truong, Nguyen Quang; Phimmachak, Somphouthone

2010-06-23

With an understudied amphibian fauna, the highest deforestation rate on the planet and high harvesting pressures, Southeast Asian amphibians are facing a conservation crisis. Owing to the overriding threat of habitat loss, the most critical conservation action required is the identification and strict protection of habitat assessed as having high amphibian species diversity and/or representing distinctive regional amphibian faunas. Long-term population monitoring, enhanced survey efforts, collection of basic biological and ecological information, continued taxonomic research and evaluation of the impact of commercial trade for food, medicine and pets are also needed. Strong involvement of regional stakeholders, students and professionals is essential to accomplish these actions.

Crosstalk between Apoptosis and Autophagy: Molecular Mechanisms and Therapeutic Strategies in Cancer

Directory of Open Access Journals (Sweden)

Abdelouahid El-Khattouti

2013-01-01

Full Text Available Both apoptosis and autophagy are highly conserved processes that besides their role in the maintenance of the organismal and cellular homeostasis serve as a main target of tumor therapeutics. Although their important roles in the modulation of tumor therapeutic strategies have been widely reported, the molecular actions of both apoptosis and autophagy are counteracted by cancer protective mechanisms. While apoptosis is a tightly regulated process that is implicated in the removal of damaged or unwanted cells, autophagy is a cellular catabolic pathway that is involved in lysosomal degradation and recycling of proteins and organelles, and thereby is considered an important survival/protective mechanism for cancer cells in response to metabolic stress or chemotherapy. Although the relationship between autophagy and cell death is very complicated and has not been characterized in detail, the molecular mechanisms that control this relationship are considered to be a relevant target for the development of a therapeutic strategy for tumor treatment. In this review, we focus on the molecular mechanisms of apoptosis, autophagy, and those of the crosstalk between apoptosis and autophagy in order to provide insight into the molecular mechanisms that may be essential for the balance between cell survival and death as well as their role as targets for the development of novel therapeutic approaches.

Constraints of philanthropy on determining the distribution of biodiversity conservation funding.

Science.gov (United States)

Larson, Eric R; Howell, Stephen; Kareiva, Peter; Armsworth, Paul R

2016-02-01

Caught between ongoing habitat destruction and funding shortfalls, conservation organizations are using systematic planning approaches to identify places that offer the highest biodiversity return per dollar invested. However, available tools do not account for the landscape of funding for conservation or quantify the constraints this landscape imposes on conservation outcomes. Using state-level data on philanthropic giving to and investments in land conservation by a large nonprofit organization, we applied linear regression to evaluate whether the spatial distribution of conservation philanthropy better explained expenditures on conservation than maps of biodiversity priorities, which were derived from a planning process internal to the organization and return on investment (ROI) analyses based on data on species richness, land costs, and existing protected areas. Philanthropic fund raising accounted for considerably more spatial variation in conservation spending (r(2) = 0.64) than either of the 2 systematic conservation planning approaches (r(2) = 0.08-0.21). We used results of one of the ROI analyses to evaluate whether increases in flexibility to reallocate funding across space provides conservation gains. Small but plausible "tax" increments of 1-10% on states redistributed to the optimal funding allocation from the ROI analysis could result in gains in endemic species protected of 8.5-80.2%. When such increases in spatial flexibility are not possible, conservation organizations should seek to cultivate increased support for conservation in priority locations. We used lagged correlations of giving to and spending by the organization to evaluate whether investments in habitat protection stimulate future giving to conservation. The most common outcome at the state level was that conservation spending quarters correlated significantly and positively with lagged fund raising quarters. In effect, periods of high fund raising for biodiversity followed (rather than

Data Mining FAERS to Analyze Molecular Targets of Drugs Highly Associated with Stevens-Johnson Syndrome.

Science.gov (United States)

Burkhart, Keith K; Abernethy, Darrell; Jackson, David

2015-06-01

Drug features that are associated with Stevens-Johnson syndrome (SJS) have not been fully characterized. A molecular target analysis of the drugs associated with SJS in the FDA Adverse Event Reporting System (FAERS) may contribute to mechanistic insights into SJS pathophysiology. The publicly available version of FAERS was analyzed to identify disproportionality among the molecular targets, metabolizing enzymes, and transporters for drugs associated with SJS. The FAERS in-house version was also analyzed for an internal comparison of the drugs most highly associated with SJS. Cyclooxygenases 1 and 2, carbonic anhydrase 2, and sodium channel 2 alpha were identified as disproportionately associated with SJS. Cytochrome P450 (CYPs) 3A4 and 2C9 are disproportionately represented as metabolizing enzymes of the drugs associated with SJS adverse event reports. Multidrug resistance protein 1 (MRP-1), organic anion transporter 1 (OAT1), and PEPT2 were also identified and are highly associated with the transport of these drugs. A detailed review of the molecular targets identifies important roles for these targets in immune response. The association with CYP metabolizing enzymes suggests that reactive metabolites and oxidative stress may have a contributory role. Drug transporters may enhance intracellular tissue concentrations and also have vital physiologic roles that impact keratinocyte proliferation and survival. Data mining FAERS may be used to hypothesize mechanisms for adverse drug events by identifying molecular targets that are highly associated with drug-induced adverse events. The information gained may contribute to systems biology disease models.

Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species.

Science.gov (United States)

Khan, Suliman; Nabi, Ghulam; Ullah, Muhammad Wajid; Yousaf, Muhammad; Manan, Sehrish; Siddique, Rabeea; Hou, Hongwei

2016-01-01

In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a "sixth" mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species.

Speeding up Monte Carlo molecular simulation by a non-conservative early rejection scheme

KAUST Repository

Kadoura, Ahmad Salim; Salama, Amgad; Sun, Shuyu

2015-01-01

Monte Carlo (MC) molecular simulation describes fluid systems with rich information, and it is capable of predicting many fluid properties of engineering interest. In general, it is more accurate and representative than equations of state

Glade/woodland restoration in the St. Francis Mountain Bird Conservation Area

Science.gov (United States)

David A. Hasenbeck

2007-01-01

The Missouri Department of Conservation (MDC), the Missouri Department of Natural Resources, the U.S. Forest Service, and American Bird Conservancy, share goals to restore and manage high quality glade, savanna, and woodland habitats within the Saint Francis Bird Conservation Area. The partnership endeavors to maintain and enhance an ecosystem with native glade and...

Reversible, high molecular weight palladium and platinum coordination polymers based on phosphorus ligands

NARCIS (Netherlands)

Paulusse, J.M.J.; Huijbers, J.P.J.; Sijbesma, R.P.

2005-01-01

A general strategy for the preparation and characterization of high molecular weight coordination polymers based on bifunctional phosphorus ligands and palladium or platinum dichloride is described. Metal-to-ligand stoichiometry is of key importance for the formation of linear coordination polymers

Reversible, High Molecular Weight Palladium and Platinum Coordination Polymers Based on Phosphorus Ligands

NARCIS (Netherlands)

Paulusse, Jos Marie Johannes; Huijbers, Jeroen P.J.; Sijbesma, Rint P.

2005-01-01

A general strategy for the preparation and characterization of high molecular weight coordination polymers based on bifunctional phosphorus ligands and palladium or platinum dichloride is described. Metal-to-ligand stoichiometry is of key importance for the formation of linear coordination polymers

Detection of high molecular weight proteins by MALDI imaging mass spectrometry.

Science.gov (United States)

Mainini, Veronica; Bovo, Giorgio; Chinello, Clizia; Gianazza, Erica; Grasso, Marco; Cattoretti, Giorgio; Magni, Fulvio

2013-06-01

MALDI imaging mass spectrometry (IMS) is a unique technology to explore the spatial distribution of biomolecules directly on tissues. It allows the in situ investigation of a large number of small proteins and peptides. Detection of high molecular weight proteins through MALDI IMS still represents an important challenge, as it would allow the direct investigation of the distribution of more proteins involved in biological processes, such as cytokines, enzymes, neuropeptide precursors and receptors. In this work we compare the traditional method performed with sinapinic acid with a comparable protocol using ferulic acid as the matrix. Data show a remarkable increase of signal acquisition in the mass range of 20k to 150k Th. Moreover, we report molecular images of biomolecules above 70k Th, demonstrating the possibility of expanding the application of this technology both in clinical investigations and basic science.

Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE

Directory of Open Access Journals (Sweden)

Constantinos Yeles

2017-11-01

Full Text Available Ionizing radiation-induced bystander effects (RIBE encompass a number of effects with potential for a plethora of damages in adjacent non-irradiated tissue. The cascade of molecular events is initiated in response to the exposure to ionizing radiation (IR, something that may occur during diagnostic or therapeutic medical applications. In order to better investigate these complex response mechanisms, we employed a unified framework integrating statistical microarray analysis, signal normalization, and translational bioinformatics functional analysis techniques. This approach was applied to several microarray datasets from Gene Expression Omnibus (GEO related to RIBE. The analysis produced lists of differentially expressed genes, contrasting bystander and irradiated samples versus sham-irradiated controls. Furthermore, comparative molecular analysis through BioInfoMiner, which integrates advanced statistical enrichment and prioritization methodologies, revealed discrete biological processes, at the cellular level. For example, the negative regulation of growth, cellular response to Zn2+-Cd2+, and Wnt and NIK/NF-kappaB signaling, thus refining the description of the phenotypic landscape of RIBE. Our results provide a more solid understanding of RIBE cell-specific response patterns, especially in the case of high-LET radiations, like α-particles and carbon-ions.

Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance

Energy Technology Data Exchange (ETDEWEB)

Rushton, Phillip S.; Olek, Anna T.; Makowski, Lee; Badger, John; Steussy, C. Nicklaus; Carpita, Nicholas C.; Stauffacher, Cynthia V. (NEU); (Purdue)

2016-11-22

The crystallographic structure of a rice (Oryza sativa) cellulose synthase, OsCesA8, plant-conserved region (P-CR), one of two unique domains in the catalytic domain of plant CesAs, was solved to 2.4 Å resolution. Two antiparallel α-helices form a coiled-coil domain linked by a large extended connector loop containing a conserved trio of aromatic residues. The P-CR structure was fit into a molecular envelope for the P-CR domain derived from small-angle X-ray scattering data. The P-CR structure and molecular envelope, combined with a homology-based chain trace of the CesA8 catalytic core, were modeled into a previously determined CesA8 small-angle X-ray scattering molecular envelope to produce a detailed topological model of the CesA8 catalytic domain. The predicted position for the P-CR domain from the molecular docking models places the P-CR connector loop into a hydrophobic pocket of the catalytic core, with the coiled-coil aligned near the entrance of the substrate UDP-glucose into the active site. In this configuration, the P-CR coiled-coil alone is unlikely to regulate substrate access to the active site, but it could interact with other domains of CesA, accessory proteins, or other CesA catalytic domains to control substrate delivery.

Probing two-centre interference in molecular high harmonic generation

International Nuclear Information System (INIS)

Vozzi, C; Calegari, F; Benedetti, E; Berlasso, R; Sansone, G; Stagira, S; Nisoli, M; Altucci, C; Velotta, R; Torres, R; Heesel, E; Kajumba, N; Marangos, J P

2006-01-01

Two-centre interference in the recombination step of molecular high harmonic generation (HHG) has been probed in CO 2 and O 2 . We report the order dependence of characteristic enhancements or suppressions of high harmonic production in aligned samples of both molecules. In CO 2 , a robust destructive interference was seen consistent with the known separation of the oxygen atoms that are active in HHG. In O 2 , a harmonic enhancement was found indicating constructive interference. A good agreement was found with a simple two-centre interference model that includes the angular distribution function of the sample. The effective momentum of the electron wave was determined from the spectral position of these interferences. Ellipticity-dependent studies in CO 2 clearly show how the destructive interference can be 'switched off' by increasing the degree of ellipticity and thus shifting the effective resonance condition

Molecular cloning, characterization, and overexpression of a novel [Fe]-hydrogenase isolated from a high rate of hydrogen producing Enterobacter cloacae IIT-BT 08

International Nuclear Information System (INIS)

Mishra, Jayshree; Khurana, Seema; Kumar, Narendra; Ghosh, Ananta K.; Das, Debabrata

2004-01-01

Degenerate primers were designed from the conserved zone of hydA structural gene encoding for catalytic subunit of [Fe]-hydrogenase of different hydrogen producing bacteria. A 750 bp of PCR product was amplified by using the above-mentioned degenerate primers and genomic DNA of Enterobacter cloacae IIT-BT 08 as template. The amplified PCR product was cloned and sequenced. The sequence showed the presence of an ORF of 450 bp with significant similarity (40%) with C-terminal end of the conserved zone (H-cluster) of [Fe]- hydrogenase. hydA ORF was then amplified and cloned in-frame with GST in pGEX4T-1 and overexpressed in a non-hydrogen producing Escherichia coli BL-21 to produce a GST-fusion protein of a calculated molecular mass of about 42.1 kDa. Recombinant protein was purified and specifically recognized by anti-GST monoclonal antibody through Western blot. Southern hybridization confirmed the presence of this gene in E. cloacae IIT-BT 08 genome. In vitro hydrogenase assay with the overexpressed hydrogenase enzyme showed that it is catalytically active upon anaerobic adaptation. In vivo hydrogenase assay confirmed the presence of H 2 gas in the gas mixture obtained from the batch culture of recombinant E. coli BL-21. A tentative molecular mechanism has been proposed about the transfer of electron from electron donor to H-cluster without the mediation of the F-cluster

High-Performance Modeling of Carbon Dioxide Sequestration by Coupling Reservoir Simulation and Molecular Dynamics

KAUST Repository

Bao, Kai; Yan, Mi; Allen, Rebecca; Salama, Amgad; Lu, Ligang; Jordan, Kirk E.; Sun, Shuyu; Keyes, David E.

2015-01-01

The present work describes a parallel computational framework for carbon dioxide (CO2) sequestration simulation by coupling reservoir simulation and molecular dynamics (MD) on massively parallel high-performance-computing (HPC) systems

Assessing Date Palm Genetic Diversity Using Different Molecular Markers.

Science.gov (United States)

Atia, Mohamed A M; Sakr, Mahmoud M; Adawy, Sami S

2017-01-01

Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.

Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

Institute of Scientific and Technical Information of China (English)

Chengzhen Sun; Bofeng Bai

2017-01-01

Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

Conservation without borders: building communication and action across disciplinary boundaries for effective conservation.

Science.gov (United States)

Margles, Shawn W; Peterson, Richard B; Ervin, Jamison; Kaplin, Beth A

2010-01-01

Interdisciplinary approaches to conservation research and environmental management continue to garner interest among practitioners, academics, and students. Yet, cases of practitioners and researchers from different disciplines successfully working in concert towards an integrated conservation approach are rare. What is preventing practitioners of multiple disciplines from harmoniously working together? Why are practitioners and academics struggling to apply their graduate training to real world conservation? What is preventing the benefits of cooperation and partnerships between different disciplines addressing conservation from being realized? This special issue "Conservation without Borders: Building Communication and Action across Disciplinary Boundaries for Effective Conservation" asks readers to consider the numerous interpretations and implications of the phrase "Conservation without Borders" and to reflect on how different academic and disciplinary lenses can contribute to a more integrated approach to tackling conservation challenges. The articles that comprise this special issue offer readers insights into the ways in which different disciplines view conservation work and interdisciplinary approaches to environmental problems. Bringing these perspectives and approaches together in one place is a step towards improving communication across disciplines for the purpose of achieving more successful biodiversity conservation.

78 FR 73589 - Energy Conservation Program: Energy Conservation Standards for Commercial and Industrial Electric...

Science.gov (United States)

2013-12-06

... Conservation Program: Energy Conservation Standards for Commercial and Industrial Electric Motors; Proposed... Conservation Program: Energy Conservation Standards for Commercial and Industrial Electric Motors AGENCY... proposes energy conservation standards for a number of different groups of electric motors that DOE has not...

On the interconnection of stable protein complexes: inter-complex hubs and their conservation in Saccharomyces cerevisiae and Homo sapiens networks.

Science.gov (United States)

Guerra, Concettina

2015-01-01

Protein complexes are key molecular entities that perform a variety of essential cellular functions. The connectivity of proteins within a complex has been widely investigated with both experimental and computational techniques. We developed a computational approach to identify and characterise proteins that play a role in interconnecting complexes. We computed a measure of inter-complex centrality, the crossroad index, based on disjoint paths connecting proteins in distinct complexes and identified inter-complex hubs as proteins with a high value of the crossroad index. We applied the approach to a set of stable complexes in Saccharomyces cerevisiae and in Homo sapiens. Just as done for hubs, we evaluated the topological and biological properties of inter-complex hubs addressing the following questions. Do inter-complex hubs tend to be evolutionary conserved? What is the relation between crossroad index and essentiality? We found a good correlation between inter-complex hubs and both evolutionary conservation and essentiality.

High-energy, stable and recycled molecular solar thermal storage materials using AZO/graphene hybrids by optimizing hydrogen bonds.

Science.gov (United States)

Luo, Wen; Feng, Yiyu; Qin, Chengqun; Li, Man; Li, Shipei; Cao, Chen; Long, Peng; Liu, Enzuo; Hu, Wenping; Yoshino, Katsumi; Feng, Wei

2015-10-21

An important method for establishing a high-energy, stable and recycled molecular solar heat system is by designing and preparing novel photo-isomerizable molecules with a high enthalpy and a long thermal life by controlling molecular interactions. A meta- and ortho-bis-substituted azobenzene chromophore (AZO) is covalently grafted onto reduced graphene oxide (RGO) for solar thermal storage materials. High grafting degree and close-packed molecules enable intermolecular hydrogen bonds (H-bonds) for both trans-(E) and cis-(Z) isomers of AZO on the surface of nanosheets, resulting in a dramatic increase in enthalpy and lifetime. The metastable Z-form of AZO on RGO is thermally stabilized with a half-life of 52 days by steric hindrance and intermolecular H-bonds calculated using density functional theory (DFT). The AZO-RGO fuel shows a high storage capacity of 138 Wh kg(-1) by optimizing intermolecular H-bonds with a good cycling stability for 50 cycles induced by visible light at 520 nm. Our work opens up a new method for making advanced molecular solar thermal storage materials by tuning molecular interactions on a nano-template.

A 7-d exercise program increases high-molecular weight adiponectin in obese adults

DEFF Research Database (Denmark)

Kelly, Karen R; Blaszczak, Alecia; Haus, Jacob M

2012-01-01

High-molecular weight (HMW) adiponectin is the biologically active form of adiponectin and is related to enhanced insulin sensitivity and metabolic function. Previously, we found that 7 d of exercise improves insulin sensitivity in obese subjects; however, whether short-term exercise training...

Molecular evidence for increased regulatory conservation during metamorphosis, and against deleterious cascading effects of hybrid breakdown in Drosophila

Directory of Open Access Journals (Sweden)

Artieri Carlo G

2010-03-01

circuits during morphogenesis may lead to it being more refractory to divergence of underlying gene regulatory mechanisms - more than that suggested by the conservation of gene expression levels between species during earlier stages. This provides support for a 'developmental hourglass' model of divergence of gene expression in Drosophila resulting in a highly conserved pupal stage.

Molecular structure and thermodynamic predictions to create highly sensitive microRNA biosensors

International Nuclear Information System (INIS)

Larkey, Nicholas E.; Brucks, Corinne N.; Lansing, Shan S.; Le, Sophia D.; Smith, Natasha M.; Tran, Victoria; Zhang, Lulu; Burrows, Sean M.

2016-01-01

Many studies have established microRNAs (miRNAs) as post-transcriptional regulators in a variety of intracellular molecular processes. Abnormal changes in miRNA have been associated with several diseases. However, these changes are sometimes subtle and occur at nanomolar levels or lower. Several biosensing hurdles for in situ cellular/tissue analysis of miRNA limit detection of small amounts of miRNA. Of these limitations the most challenging are selectivity and sensor degradation creating high background signals and false signals. Recently we developed a reporter+probe biosensor for let-7a that showed potential to mitigate false signal from sensor degradation. Here we designed reporter+probe biosensors for miR-26a-2-3p and miR-27a-5p to better understand the effect of thermodynamics and molecular structures of the biosensor constituents on the analytical performance. Signal changes from interactions between Cy3 and Cy5 on the reporters were used to understand structural aspects of the reporter designs. Theoretical thermodynamic values, single stranded conformations, hetero- and homodimerization structures, and equilibrium concentrations of the reporters and probes were used to interpret the experimental observations. Studies of the sensitivity and selectivity revealed 5–9 nM detection limits in the presence and absence of interfering off-analyte miRNAs. These studies will aid in determining how to rationally design reporter+probe biosensors to overcome hurdles associated with highly sensitive miRNA biosensing. - Highlights: • Challenges facing highly sensitive miRNA biosensor designs are addressed. • Thermodynamic and molecular structure design metrics for reporter+probe biosensors are proposed. • The influence of ideal and non-ideal reporter hairpin structures on reporter+probe formation and signal change are discussed. • 5–9 nM limits of detection were observed with no interference from off-analytes.

Molecular structure and thermodynamic predictions to create highly sensitive microRNA biosensors

Energy Technology Data Exchange (ETDEWEB)

Larkey, Nicholas E.; Brucks, Corinne N.; Lansing, Shan S.; Le, Sophia D.; Smith, Natasha M.; Tran, Victoria; Zhang, Lulu; Burrows, Sean M., E-mail: sean.burrows@oregonstate.edu

2016-02-25

Many studies have established microRNAs (miRNAs) as post-transcriptional regulators in a variety of intracellular molecular processes. Abnormal changes in miRNA have been associated with several diseases. However, these changes are sometimes subtle and occur at nanomolar levels or lower. Several biosensing hurdles for in situ cellular/tissue analysis of miRNA limit detection of small amounts of miRNA. Of these limitations the most challenging are selectivity and sensor degradation creating high background signals and false signals. Recently we developed a reporter+probe biosensor for let-7a that showed potential to mitigate false signal from sensor degradation. Here we designed reporter+probe biosensors for miR-26a-2-3p and miR-27a-5p to better understand the effect of thermodynamics and molecular structures of the biosensor constituents on the analytical performance. Signal changes from interactions between Cy3 and Cy5 on the reporters were used to understand structural aspects of the reporter designs. Theoretical thermodynamic values, single stranded conformations, hetero- and homodimerization structures, and equilibrium concentrations of the reporters and probes were used to interpret the experimental observations. Studies of the sensitivity and selectivity revealed 5–9 nM detection limits in the presence and absence of interfering off-analyte miRNAs. These studies will aid in determining how to rationally design reporter+probe biosensors to overcome hurdles associated with highly sensitive miRNA biosensing. - Highlights: • Challenges facing highly sensitive miRNA biosensor designs are addressed. • Thermodynamic and molecular structure design metrics for reporter+probe biosensors are proposed. • The influence of ideal and non-ideal reporter hairpin structures on reporter+probe formation and signal change are discussed. • 5–9 nM limits of detection were observed with no interference from off-analytes.

Energy conservation opportunities: audit vis-a-vis mine productivity

Energy Technology Data Exchange (ETDEWEB)

Iyer, G.H.

2009-07-01

Mining operation, whether opencast or underground, with modern equipment is highly energy intensive, needing energy conservation and management to ensure efficiency, cost effectiveness, and overall productivity. Exhaustible primary energy resources such as coal, lignite, oil, and nuclear fuels are being mined out to meet our energy needs. An attempt has been made in this paper to highlight the energy conservation opportunities, energy audit, the relevant Energy Conservation Act 2001 and certain energy saving measures leading to higher productivity followed by a few case study examples. 3 refs.

Fixism and conservation science.

Science.gov (United States)

Robert, Alexandre; Fontaine, Colin; Veron, Simon; Monnet, Anne-Christine; Legrand, Marine; Clavel, Joanne; Chantepie, Stéphane; Couvet, Denis; Ducarme, Frédéric; Fontaine, Benoît; Jiguet, Frédéric; le Viol, Isabelle; Rolland, Jonathan; Sarrazin, François; Teplitsky, Céline; Mouchet, Maud

2017-08-01

The field of biodiversity conservation has recently been criticized as relying on a fixist view of the living world in which existing species constitute at the same time targets of conservation efforts and static states of reference, which is in apparent disagreement with evolutionary dynamics. We reviewed the prominent role of species as conservation units and the common benchmark approach to conservation that aims to use past biodiversity as a reference to conserve current biodiversity. We found that the species approach is justified by the discrepancy between the time scales of macroevolution and human influence and that biodiversity benchmarks are based on reference processes rather than fixed reference states. Overall, we argue that the ethical and theoretical frameworks underlying conservation research are based on macroevolutionary processes, such as extinction dynamics. Current species, phylogenetic, community, and functional conservation approaches constitute short-term responses to short-term human effects on these reference processes, and these approaches are consistent with evolutionary principles. © 2016 Society for Conservation Biology.

Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters

Energy Technology Data Exchange (ETDEWEB)

Santini, Simona; Boore, Jeffrey L.; Meyer, Axel

2003-12-31

Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involved in the regulation of Hox genes, while several others are new elements that might have regulatory functions. The majority of these newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac). The conserved intergenic regions located between the most rostrally expressed genes in the developing embryo are longer and better retained through evolution. We document that presumed regulatory sequences are retained differentially in either A or A clusters resulting from a genome duplication in the fish lineage. This observation supports both the hypothesis that the conserved elements are involved in gene regulation and the Duplication-Deletion-Complementation model.

Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation

DEFF Research Database (Denmark)

Czaban, Adrian; Sharma, Sapna; Byrne, Stephen

2015-01-01

species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family...... clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity...... enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some...

Identifying ambassador species for conservation marketing

Directory of Open Access Journals (Sweden)

E.A. Macdonald

2017-10-01

Full Text Available Conservation relies heavily on external funding, much of it from a supportive public. Therefore it is important to know which species are most likely to catalyse such funding. Whilst previous work has looked at the physical attributes that contribute to a species' appeal, no previous studies have tried to examine the extent to which a species' sympatriots might contribute to it's potential as flagship for wider conservation. Therefore, here we estimate ‘flexibility’ and ‘appeal’ scores for all terrestrial mammals (n = 4320 and identify which of these might serve as ambassadors (defined as both highly appealing and flexible. Relatively few mammals (between 240 and 331 emerged as ambassadors, with carnivores featuring heavily in this group (representing 5% of terrestrial mammals but 39% of ambassadors. ‘Top ambassadors’ were defined as those with both flexibility and appeal scores greater than 1 standard deviation above the mean. Less than a quarter of the 20 most endangered and evolutionary distinct species in this study were classed as ambassadors, highlighting the need for surrogate species to catalyse conservation effort in areas with such priority species. This is the first global analysis bringing together flexibility and appeal for all terrestrial mammals, and demonstrates an approach for determining how best to market species in order to achieve maximal conservation gain in a world with urgent conservation need but limited resources.

Advances in the Application of Genetics in Marine Turtle Biology and Conservation

Directory of Open Access Journals (Sweden)

Lisa M. Komoroske

2017-06-01

Full Text Available Marine turtles migrate across long distances, exhibit complex life histories, and occupy habitats that are difficult to observe. These factors present substantial challenges to understanding fundamental aspects of their biology or assessing human impacts, many of which are important for the effective conservation of these threatened and endangered species. The early development and application of genetic tools made important contributions to understanding marine turtle population and evolutionary biology, such as providing evidence of regional natal homing by breeding adults, establishing connectivity between rookeries and foraging habitats, and determining phylogeography and broad scale stock structure for most marine turtle species. Recent innovations in molecular technologies, statistical methods, and creative application of genetic tools have significantly built upon this knowledge to address key questions in marine turtle biology and conservation management. Here, we evaluate the latest major advances and potential of marine turtle genetic applications, including improved resolution and large-scale syntheses of population structure, connectivity and phylogeography, estimation of key demographic rates such as age to maturity and operational or breeding sex ratios, insight into reproductive strategies and behavior, and assessment of differential human impacts among populations. We then discuss remaining challenges and emerging capabilities, such as rapid, multiplexed genotyping, and investigation of the genomic underpinnings of adaptive variation afforded by high-throughput sequencing technologies.

High rate of destruction of molecular clouds by hot stars

International Nuclear Information System (INIS)

Heydari-Malayeri, M.; Lortet, M.C.; Deharveng, L.

1980-01-01

Tenorio-Tagle (1979) first proposed the idea of a third dynamical phase, the champagne phase, following the formation and expansion phases of an HII region. The champagne phase begins when the high pressure gas of an HII region formed inside a molecular cloud reaches the edge of the cloud and bursts into the lower pressure, low density, intercloud medium. One important implication of the model is the prediction of an enormous enhancement of the rate of erosion of the molecular cloud by the ionising radiation of hot stars, which begins as soon as the process of the decrease of the gas density between the star and the cloud is started. The proportion of hydrogen molecules eroded by ionising photons may reach about 10 -2 . The mass eroded may exceed the mass of the ionised gas in the case where the ionisation front reaching the edge of the cloud is of D-type. Additional mechanisms (for instance stellar winds), if at work, may even increase the efficiency of the mechanism. (Auth.)

Molecular fingerprint of high fat diet induced urinary bladder metabolic dysfunction in a rat model.

Directory of Open Access Journals (Sweden)

Andreas Oberbach

Full Text Available AIMS/HYPOTHESIS: Diabetic voiding dysfunction has been reported in epidemiological dimension of individuals with diabetes mellitus. Animal models might provide new insights into the molecular mechanisms of this dysfunction to facilitate early diagnosis and to identify new drug targets for therapeutic interventions. METHODS: Thirty male Sprague-Dawley rats received either chow or high-fat diet for eleven weeks. Proteomic alterations were comparatively monitored in both groups to discover a molecular fingerprinting of the urinary bladder remodelling/dysfunction. Results were validated by ELISA, Western blotting and immunohistology. RESULTS: In the proteome analysis 383 proteins were identified and canonical pathway analysis revealed a significant up-regulation of acute phase reaction, hypoxia, glycolysis, β-oxidation, and proteins related to mitochondrial dysfunction in high-fat diet rats. In contrast, calcium signalling, cytoskeletal proteins, calpain, 14-3-3η and eNOS signalling were down-regulated in this group. Interestingly, we found increased ubiquitin proteasome activity in the high-fat diet group that might explain the significant down-regulation of eNOS, 14-3-3η and calpain. CONCLUSIONS/INTERPRETATION: Thus, high-fat diet is sufficient to induce significant remodelling of the urinary bladder and alterations of the molecular fingerprint. Our findings give new insights into obesity related bladder dysfunction and identified proteins that may indicate novel pathophysiological mechanisms and therefore constitute new drug targets.

Advancing Treatment of Pituitary Adenomas through Targeted Molecular Therapies: The Acromegaly and Cushing Disease Paradigms.

Science.gov (United States)

Mooney, Michael A; Simon, Elias D; Little, Andrew S

2016-01-01

The current treatment of pituitary adenomas requires a balance of conservative management, surgical resection, and in select tumor types, molecular therapy. Acromegaly treatment is an evolving field where our understanding of molecular targets and drug therapies has improved treatment options for patients with excess growth hormone levels. We highlight the use of molecular therapies in this disease process and advances in this field, which may represent a paradigm shift for the future of pituitary adenoma treatment.

The implications of breast cancer molecular phenotype for radiation oncology

Directory of Open Access Journals (Sweden)

Shirin eSioshansi

2011-06-01

Full Text Available The identification of distinct molecular subtypes of breast cancer has advanced the understanding and treatment of breast cancer by providing insight into prognosis, patterns of recurrence and effectiveness of therapy. The prognostic significance of molecular phenotype with regard to distant recurrences and overall survival are well established in the literature and has been readily incorporated into systemic therapy management decisions. However, despite the accumulating data suggesting similar prognostic significance for locoregional recurrence, integration of molecular phenotype into local management decision making has lagged. Although there are some conflicting reports, collectively the literature supports a low risk of local recurrence in the hormone receptor positive luminal subtypes compared to hormone receptor negative subtypes (triple negative and HER2-enriched. The development of targeted therapies, such as trastuzumab for the treatment of HER2-enriched subtype, has been shown to mitigate the increased risk of local recurrence. Unfortunately, no such remedy exists to address the increased risk of local recurrence for patients with triple negative tumors, making it a clinical challenge for radiation oncologists. In this review we discuss the correlation between molecular subtype and local recurrence following either breast conservation therapy or mastectomy. We also explore the possible mechanisms for increased local recurrence in triple negative breast cancer and radiotherapeutic implications for this population, such as the safety of breast conservation, consideration of dose escalation and the appropriateness of accelerated partial breast irradiation.

Molecular Characterization of the Skate Peripherin/rds Gene: Relationship to Its Orthologues and Paralogues

Science.gov (United States)

Li, Chibo; Ding, Xi-Qin; O’Brien, John; Al-Ubaidi, Muayyad R.

2010-01-01

PURPOSE A great deal of information about functionally significant domains of a protein may be obtained by comparison of primary sequences of gene homologues over a broad phylogenetic base. This study was designed to identify evolutionarily conserved domains of the photoreceptor disc membrane protein peripherin/rds by analysis of the homologue in a primitive vertebrate, the skate. METHODS A skate retinal cDNA library was screened using a mouse peripherin/rds clone. The 5′ and 3′ untranslated regions of the skate peripherin/rds (srds) cDNA were isolated by the rapid amplification of cDNA ends (RACE) approach. The gene structure was characterized by PCR amplification and sequencing of genomic fragments. Northern and Western blot analyses were used to identify srds transcript and protein, respectively. RESULTS A new homologue of peripherin/rds was identified from the skate retinal cDNA library. SRDS is a glycoprotein with a predicted molecular mass of 40.2 kDa. The srds gene consists of two exons and one small intron and transcribes into a single 6-kb message. Phylogenetic analysis places SRDS at the base of peripherin/rds family and near the division of that group and the branch leading to rds-like and rom-1 genes. SRDS protein is 54.5% identical with peripherin/rds across species. Identity is significantly higher (73%) in the intradiscal domains. Sequence comparison revealed the conservation of all residues that have been shown, on mutation, to associate with retinitis pigmentosa and showed conservation of most residues associated with macular dystrophies. Comparison with ROM-1 and other rds-like proteins revealed the presence of a highly conserved domain in the large intradiscal loop. CONCLUSIONS Srds represents the skate orthologue of mammalian peripherin/rds genes. Conservation of most of the residues associated with human retinal diseases indicates that these residues serve important functional roles. The high degree of conservation of a short stretch within

Molecular classification of fatty liver by high-throughput profiling of protein post-translational modifications.

Science.gov (United States)

Urasaki, Yasuyo; Fiscus, Ronald R; Le, Thuc T

2016-04-01

We describe an alternative approach to classifying fatty liver by profiling protein post-translational modifications (PTMs) with high-throughput capillary isoelectric focusing (cIEF) immunoassays. Four strains of mice were studied, with fatty livers induced by different causes, such as ageing, genetic mutation, acute drug usage, and high-fat diet. Nutrient-sensitive PTMs of a panel of 12 liver metabolic and signalling proteins were simultaneously evaluated with cIEF immunoassays, using nanograms of total cellular protein per assay. Changes to liver protein acetylation, phosphorylation, and O-N-acetylglucosamine glycosylation were quantified and compared between normal and diseased states. Fatty liver tissues could be distinguished from one another by distinctive protein PTM profiles. Fatty liver is currently classified by morphological assessment of lipid droplets, without identifying the underlying molecular causes. In contrast, high-throughput profiling of protein PTMs has the potential to provide molecular classification of fatty liver. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Restricted-range fishes and the conservation of Brazilian freshwaters.

Directory of Open Access Journals (Sweden)

Cristiano Nogueira

Full Text Available BACKGROUND: Freshwaters are the most threatened ecosystems on earth. Although recent assessments provide data on global priority regions for freshwater conservation, local scale priorities remain unknown. Refining the scale of global biodiversity assessments (both at terrestrial and freshwater realms and translating these into conservation priorities on the ground remains a major challenge to biodiversity science, and depends directly on species occurrence data of high taxonomic and geographic resolution. Brazil harbors the richest freshwater ichthyofauna in the world, but knowledge on endemic areas and conservation in Brazilian rivers is still scarce. METHODOLOGY/PRINCIPAL FINDINGS: Using data on environmental threats and revised species distribution data we detect and delineate 540 small watershed areas harboring 819 restricted-range fishes in Brazil. Many of these areas are already highly threatened, as 159 (29% watersheds have lost more than 70% of their original vegetation cover, and only 141 (26% show significant overlap with formally protected areas or indigenous lands. We detected 220 (40% critical watersheds overlapping hydroelectric dams or showing both poor formal protection and widespread habitat loss; these sites harbor 344 endemic fish species that may face extinction if no conservation action is in place in the near future. CONCLUSIONS/SIGNIFICANCE: We provide the first analysis of site-scale conservation priorities in the richest freshwater ecosystems of the globe. Our results corroborate the hypothesis that freshwater biodiversity has been neglected in former conservation assessments. The study provides a simple and straightforward method for detecting freshwater priority areas based on endemism and threat, and represents a starting point for integrating freshwater and terrestrial conservation in representative and biogeographically consistent site-scale conservation strategies, that may be scaled-up following naturally linked

Molecular Simulation towards Efficient and Representative Subsurface Reservoirs Modeling

KAUST Repository

Kadoura, Ahmad

2016-09-01

This dissertation focuses on the application of Monte Carlo (MC) molecular simulation and Molecular Dynamics (MD) in modeling thermodynamics and flow of subsurface reservoir fluids. At first, MC molecular simulation is proposed as a promising method to replace correlations and equations of state in subsurface flow simulators. In order to accelerate MC simulations, a set of early rejection schemes (conservative, hybrid, and non-conservative) in addition to extrapolation methods through reweighting and reconstruction of pre-generated MC Markov chains were developed. Furthermore, an extensive study was conducted to investigate sorption and transport processes of methane, carbon dioxide, water, and their mixtures in the inorganic part of shale using both MC and MD simulations. These simulations covered a wide range of thermodynamic conditions, pore sizes, and fluid compositions shedding light on several interesting findings. For example, the possibility to have more carbon dioxide adsorbed with more preadsorbed water concentrations at relatively large basal spaces. The dissertation is divided into four chapters. The first chapter corresponds to the introductory part where a brief background about molecular simulation and motivations are given. The second chapter is devoted to discuss the theoretical aspects and methodology of the proposed MC speeding up techniques in addition to the corresponding results leading to the successful multi-scale simulation of the compressible single-phase flow scenario. In chapter 3, the results regarding our extensive study on shale gas at laboratory conditions are reported. At the fourth and last chapter, we end the dissertation with few concluding remarks highlighting the key findings and summarizing the future directions.

Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project

DEFF Research Database (Denmark)

Pundhir, Sachin; Hannibal, Tine Dahlbæk; Bang-Berthelsen, Claus Heiner

2014-01-01

. In this study, we have utilized the wealth of high-throughput sequencing data produced during the Encyclopedia of DNA Elements (ENCODE) project to identify spatially conserved regulatory elements within the Cd247 gene from human and mouse. We show the presence of two transcription factor binding sites...

Ethics of conservation triage

Directory of Open Access Journals (Sweden)

Kerrie A Wilson

2016-09-01

Full Text Available Conservation triage seems to be at a stalemate between those who accept triage based on utilitarian rationalization, and those that reject it based on a number of ethical principles. We argue that without considered attention to the ethics of conservation triage we risk further polarization in the field of conservation. We draw lessons from the medical sector, where triage is more intuitive and acceptable, and also from disaster planning, to help navigate the challenges that triage entails for conservation science, practice, and policy. We clarify the consequentialist, deontological, and virtue ethical stances that influence the level of acceptance of triage. We emphasize the ethical dimensions of conservation triage in principle and in practice, particularly in the context of stakeholder diversity, a wide range of possible objectives and actions, broader institutions, and significant uncertainties. A focus on a more diverse set of ethics, more considered choice of triage as a conservation tool, open communication of triage objectives and protocols, greater consideration of risk preferences, and regular review and adaptation of triage protocols is required for conservation triage to become more acceptable among diverse conservation practitioners, institutions, and the general public. Accepting conservation triage as fundamentally an ethical problem would foster more open dialogue and constructive debate about the role of conservation triage in a wider system of care.

Next Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue Specimens for Enhanced Clinical Guidance

Science.gov (United States)

2016-07-01

AWARD NUMBER: W81XWH- 14-1-0192 TITLE: Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer...DATES COVERED 4. TITLE AND SUBTITLE Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue

Evolution of cell cycle control: same molecular machines, different regulation

DEFF Research Database (Denmark)

de Lichtenberg, Ulrik; Jensen, Thomas Skøt; Brunak, Søren

2007-01-01

Decades of research has together with the availability of whole genomes made it clear that many of the core components involved in the cell cycle are conserved across eukaryotes, both functionally and structurally. These proteins are organized in complexes and modules that are activated or deacti......Decades of research has together with the availability of whole genomes made it clear that many of the core components involved in the cell cycle are conserved across eukaryotes, both functionally and structurally. These proteins are organized in complexes and modules that are activated...... for assembling the same molecular machines just in time for action....

Key interactions by conserved polar amino acids located at the transmembrane helical boundaries in Class B GPCRs modulate activation, effector specificity and biased signalling in the glucagon-like peptide-1 receptor

OpenAIRE

Wootten, Denise; Reynolds, Christopher A.; Smith, Kevin J.; Mobarec, Juan C.; Furness, Sebastian G.B.; Miller, Laurence J.; Christopoulos, Arthur; Sexton, Patrick M.

2016-01-01

Class B GPCRs can activate multiple signalling effectors with the potential to exhibit biased agonism in response to ligand stimulation. Previously, we highlighted key TM domain polar amino acids that were crucial for the function of the GLP-1 receptor, a key therapeutic target for diabetes and obesity. Using a combination of mutagenesis, pharmacological characterisation, mathematical and computational molecular modelling, this study identifies additional highly conserved polar residues locat...

Conserved gene regulatory module specifies lateral neural borders across bilaterians.

Science.gov (United States)

Li, Yongbin; Zhao, Di; Horie, Takeo; Chen, Geng; Bao, Hongcun; Chen, Siyu; Liu, Weihong; Horie, Ryoko; Liang, Tao; Dong, Biyu; Feng, Qianqian; Tao, Qinghua; Liu, Xiao

2017-08-01

The lateral neural plate border (NPB), the neural part of the vertebrate neural border, is composed of central nervous system (CNS) progenitors and peripheral nervous system (PNS) progenitors. In invertebrates, PNS progenitors are also juxtaposed to the lateral boundary of the CNS. Whether there are conserved molecular mechanisms determining vertebrate and invertebrate lateral neural borders remains unclear. Using single-cell-resolution gene-expression profiling and genetic analysis, we present evidence that orthologs of the NPB specification module specify the invertebrate lateral neural border, which is composed of CNS and PNS progenitors. First, like in vertebrates, the conserved neuroectoderm lateral border specifier Msx/vab-15 specifies lateral neuroblasts in Caenorhabditis elegans Second, orthologs of the vertebrate NPB specification module ( Msx/vab-15 , Pax3/7/pax-3 , and Zic/ref-2 ) are significantly enriched in worm lateral neuroblasts. In addition, like in other bilaterians, the expression domain of Msx/vab-15 is more lateral than those of Pax3/7/pax-3 and Zic/ref- 2 in C. elegans Third, we show that Msx/vab-15 regulates the development of mechanosensory neurons derived from lateral neural progenitors in multiple invertebrate species, including C. elegans , Drosophila melanogaster , and Ciona intestinalis We also identify a novel lateral neural border specifier, ZNF703/tlp-1 , which functions synergistically with Msx/vab- 15 in both C. elegans and Xenopus laevis These data suggest a common origin of the molecular mechanism specifying lateral neural borders across bilaterians.

Position sensitive detection coupled to high-resolution time-of-flight mass spectrometry: Imaging for molecular beam deflection experiments

International Nuclear Information System (INIS)

Abd El Rahim, M.; Antoine, R.; Arnaud, L.; Barbaire, M.; Broyer, M.; Clavier, Ch.; Compagnon, I.; Dugourd, Ph.; Maurelli, J.; Rayane, D.

2004-01-01

We have developed and tested a high-resolution time-of-flight mass spectrometer coupled to a position sensitive detector for molecular beam deflection experiments. The major achievement of this new spectrometer is to provide a three-dimensional imaging (X and Y positions and time-of-flight) of the ion packet on the detector, with a high acquisition rate and a high resolution on both the mass and the position. The calibration of the experimental setup and its application to molecular beam deflection experiments are discussed

Indian energy conservation- status and strategies

International Nuclear Information System (INIS)

Dharmalingam, P.

1996-01-01

High rates of inflation combined with social justice against a backdrop of ever increasing population- this is a challenge which the Government of India is facing today. It is evident that the annual growth rate of 5.6% as envisaged for the VIIIth five year plan can never be met unless conscious efforts are made to augment energy supplies by energy demand management through energy conservation. In this context, a review of the energy consuming sectors in terms of their consumption trends, energy efficiencies or intensities, energy conservation opportunities, technologies used and energy investment programmes would prove useful and informative. (author). 10 tabs

Developmental evolutionary biology of the vertebrate ear: conserving mechanoelectric transduction and developmental pathways in diverging morphologies

Science.gov (United States)

Fritzsch, B.; Beisel, K. W.; Bermingham, N. A.

2000-01-01

This brief overview shows that a start has been made to molecularly dissect vertebrate ear development and its evolutionary conservation to the development of the insect hearing organ. However, neither the patterning process of the ear nor the patterning process of insect sensory organs is sufficiently known at the moment to provide more than a first glimpse. Moreover, hardly anything is known about otocyst development of the cephalopod molluscs, another triploblast lineage that evolved complex 'ears'. We hope that the apparent conserved functional and cellular components present in the ciliated sensory neurons/hair cells will also be found in the genes required for vertebrate ear and insect sensory organ morphogenesis (Fig. 3). Likewise, we expect that homologous pre-patterning genes will soon be identified for the non-sensory cell development, which is more than a blocking of neuronal development through the Delta/Notch signaling system. Generation of the apparently unique ear could thus represent a multiplication of non-sensory cells by asymmetric and symmetric divisions as well as modification of existing patterning process by implementing novel developmental modules. In the final analysis, the vertebrate ear may come about by increasing the level of gene interactions in an already existing and highly conserved interactive cascade of bHLH genes. Since this was apparently achieved in all three lineages of triploblasts independently (Fig. 3), we now need to understand how much of the morphogenetic cascades are equally conserved across phyla to generate complex ears. The existing mutations in humans and mice may be able to point the direction of future research to understand the development of specific cell types and morphologies in the formation of complex arthropod, cephalopod, and vertebrate 'ears'.

Spatially Extended and High-Velocity Dispersion Molecular Component in Spiral Galaxies: Single-Dish Versus Interferometric Observations

Science.gov (United States)

Caldú-Primo, Anahi; Schruba, Andreas; Walter, Fabian; Leroy, Adam; Bolatto, Alberto D.; Vogel, Stuart

2015-02-01

Recent studies of the molecular medium in nearby galaxies have provided mounting evidence that the molecular gas can exist in two phases: one that is clumpy and organized as molecular clouds and another one that is more diffuse. This last component has a higher velocity dispersion than the clumpy one. In order to investigate these two molecular components further, we compare the fluxes and line widths of CO in NGC 4736 and NGC 5055, two nearby spiral galaxies for which high-quality interferometric as well as single-dish data sets are available. Our analysis leads to two main results: (1) employing three different methods, we determine the flux recovery of the interferometer as compared to the single-dish to be within a range of 35%-74% for NGC 4736 and 81%-92% for NGC 5055, and (2) when focusing on high (S/N ≥ 5) lines of sight (LOSs), the single-dish line widths are larger by ˜(40 ± 20)% than the ones derived from interferometric data, which is in agreement with stacking all LOSs. These results point to a molecular gas component that is distributed over spatial scales larger than 30″(˜1 kpc), and is therefore filtered out by the interferometer. The available observations do not allow us to distinguish between a truly diffuse gas morphology and a uniform distribution of small clouds that are separated by less than the synthesized beam size (˜3″ or ˜100 pc), as they would both be invisible for the interferometer. This high velocity dispersion component has a dispersion similar to what is found in the atomic medium, as traced through observations of the H i line.

Mitochondrial C4375T mutation might be a molecular risk factor in a maternal Chinese hypertensive family under haplotype C.

Science.gov (United States)

Chen, Hong; Sun, Min; Fan, Zhen; Tong, Maoqing; Chen, Guodong; Li, Danhui; Ye, Jihui; Yang, Yumin; Zhu, Yongding; Zhu, Jianhua

2017-12-04

Here, we reported a Han Chinese essential hypertensive pedigree based on clinical hereditary and molecular data. To know the molecular basis on this family, mitochondrial genome of one proband from the family was identified through direct sequencing analysis. The age of onset year and affected degree of patients are different in this family. And matrilineal family members carrying C4375T mutation and belong to Eastern Asian halopgroup C. Phylogenetic analysis shows 4375C is highly conservative in 17 species. It is suggested that these mutations might participate in the development of hypertension in this family. And halopgroup C might play a modifying role on the phenotype in this Chinese hypertensive family.

Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.

Science.gov (United States)

Varadi, Mihaly; Zsolyomi, Fruzsina; Guharoy, Mainak; Tompa, Peter

2015-01-01

Proteins form large macromolecular assemblies with RNA that govern essential molecular processes. RNA-binding proteins have often been associated with conformational flexibility, yet the extent and functional implications of their intrinsic disorder have never been fully assessed. Here, through large-scale analysis of comprehensive protein sequence and structure datasets we demonstrate the prevalence of intrinsic structural disorder in RNA-binding proteins and domains. We addressed their functionality through a quantitative description of the evolutionary conservation of disordered segments involved in binding, and investigated the structural implications of flexibility in terms of conformational stability and interface formation. We conclude that the functional role of intrinsically disordered protein segments in RNA-binding is two-fold: first, these regions establish extended, conserved electrostatic interfaces with RNAs via induced fit. Second, conformational flexibility enables them to target different RNA partners, providing multi-functionality, while also ensuring specificity. These findings emphasize the functional importance of intrinsically disordered regions in RNA-binding proteins.

Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.

Directory of Open Access Journals (Sweden)

Mihaly Varadi

Full Text Available Proteins form large macromolecular assemblies with RNA that govern essential molecular processes. RNA-binding proteins have often been associated with conformational flexibility, yet the extent and functional implications of their intrinsic disorder have never been fully assessed. Here, through large-scale analysis of comprehensive protein sequence and structure datasets we demonstrate the prevalence of intrinsic structural disorder in RNA-binding proteins and domains. We addressed their functionality through a quantitative description of the evolutionary conservation of disordered segments involved in binding, and investigated the structural implications of flexibility in terms of conformational stability and interface formation. We conclude that the functional role of intrinsically disordered protein segments in RNA-binding is two-fold: first, these regions establish extended, conserved electrostatic interfaces with RNAs via induced fit. Second, conformational flexibility enables them to target different RNA partners, providing multi-functionality, while also ensuring specificity. These findings emphasize the functional importance of intrinsically disordered regions in RNA-binding proteins.

Effectiveness of amphibians as biodiversity surrogates in pond conservation.

Science.gov (United States)

Ilg, Christiane; Oertli, Beat

2017-04-01

Amphibian decline has led to worldwide conservation efforts, including the identification and designation of sites for their protection. These sites could also play an important role in the conservation of other freshwater taxa. In 89 ponds in Switzerland, we assessed the effectiveness of amphibians as a surrogate for 4 taxonomic groups that occur in the same freshwater ecosystems as amphibians: dragonflies, aquatic beetles, aquatic gastropods, and aquatic plants. The ponds were all of high value for amphibian conservation. Cross-taxon correlations were tested for species richness and conservation value, and Mantel tests were used to investigate community congruence. Species richness, conservation value, and community composition of amphibians were weakly congruent with these measures for the other taxonomic groups. Paired comparisons for the 5 groups considered showed that for each metric, amphibians had the lowest degree of congruence. Our results imply that site designation for amphibian conservation will not necessarily provide protection for freshwater biodiversity as a whole. To provide adequate protection for freshwater species, we recommend other taxonomic groups be considered in addition to amphibians in the prioritization and site designation process. © 2016 Society for Conservation Biology.

ADM pseudotensors, conserved quantities and covariant conservation laws in general relativity