WorldWideScience

Sample records for conservative fragmentation chains

  1. Single chain Fab (scFab fragment

    Directory of Open Access Journals (Sweden)

    Brenneis Mariam

    2007-03-01

    Full Text Available Abstract Background The connection of the variable part of the heavy chain (VH and and the variable part of the light chain (VL by a peptide linker to form a consecutive polypeptide chain (single chain antibody, scFv was a breakthrough for the functional production of antibody fragments in Escherichia coli. Being double the size of fragment variable (Fv fragments and requiring assembly of two independent polypeptide chains, functional Fab fragments are usually produced with significantly lower yields in E. coli. An antibody design combining stability and assay compatibility of the fragment antigen binding (Fab with high level bacterial expression of single chain Fv fragments would be desirable. The desired antibody fragment should be both suitable for expression as soluble antibody in E. coli and antibody phage display. Results Here, we demonstrate that the introduction of a polypeptide linker between the fragment difficult (Fd and the light chain (LC, resulting in the formation of a single chain Fab fragment (scFab, can lead to improved production of functional molecules. We tested the impact of various linker designs and modifications of the constant regions on both phage display efficiency and the yield of soluble antibody fragments. A scFab variant without cysteins (scFabΔC connecting the constant part 1 of the heavy chain (CH1 and the constant part of the light chain (CL were best suited for phage display and production of soluble antibody fragments. Beside the expression system E. coli, the new antibody format was also expressed in Pichia pastoris. Monovalent and divalent fragments (DiFabodies as well as multimers were characterised. Conclusion A new antibody design offers the generation of bivalent Fab derivates for antibody phage display and production of soluble antibody fragments. This antibody format is of particular value for high throughput proteome binder generation projects, due to the avidity effect and the possible use of

  2. Production of a phage-displayed single chain variable fragment ...

    African Journals Online (AJOL)

    Purpose: To develop specific single chain variable fragments (scFv) against infectious bursal disease virus (IBDV) via phage display technology. Methods: Purified viruses were initially applied for iterative panning rounds of scFv phage display libraries. The binding ability of the selected scFv antibody fragments against the ...

  3. Who wants to conserve remaining forest fragments in the ...

    African Journals Online (AJOL)

    Contiguous forests in Madagascar are continuously converted into forest fragments due to deforestation, and dispersed into landscape mosaics dominated by agriculture. These fragments are of increasing importance for biodiversity conservation as well as for the well being of rural inhabitants, providing a high diversity of ...

  4. Production of a phage-displayed single chain variable fragment ...

    African Journals Online (AJOL)

    Purpose: To develop specific single chain variable fragments (scFv) against infectious bursal disease ... application of vitamins as well as antibiotics can .... D in. 4. 0. 5 n m. Clone number. 1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70 73 76 79 82 85 88 91 94. Figure 1: Indirect ELISA analysis for ...

  5. Mutagenicity Assessment of Organophosphates using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Assay

    National Research Council Canada - National Science Library

    Bhinder, Preety; Chaudhry, Asha

    2013-01-01

    In this study we have evaluated the mutagenicity of organophosphate pesticides acephate, chlorpyrifos, and profenofos using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP...

  6. Fenced and Fragmented: Conservation Value of Managed Metapopulations.

    Directory of Open Access Journals (Sweden)

    Susan M Miller

    Full Text Available Population fragmentation is threatening biodiversity worldwide. Species that once roamed vast areas are increasingly being conserved in small, isolated areas. Modern management approaches must adapt to ensure the continued survival and conservation value of these populations. In South Africa, a managed metapopulation approach has been adopted for several large carnivore species, all protected in isolated, relatively small, reserves that are fenced. As far as possible these approaches are based on natural metapopulation structures. In this network, over the past 25 years, African lions (Panthera leo were reintroduced into 44 fenced reserves with little attention given to maintaining genetic diversity. To examine the situation, we investigated the current genetic provenance and diversity of these lions. We found that overall genetic diversity was similar to that in a large national park, and included a mixture of four different southern African evolutionarily significant units (ESUs. This mixing of ESUs, while not ideal, provides a unique opportunity to study the impact of mixing ESUs over the long term. We propose a strategic managed metapopulation plan to ensure the maintenance of genetic diversity and improve the long-term conservation value of these lions. This managed metapopulation approach could be applied to other species under similar ecological constraints around the globe.

  7. Fenced and Fragmented: Conservation Value of Managed Metapopulations.

    Science.gov (United States)

    Miller, Susan M; Harper, Cindy K; Bloomer, Paulette; Hofmeyr, Jennifer; Funston, Paul J

    2015-01-01

    Population fragmentation is threatening biodiversity worldwide. Species that once roamed vast areas are increasingly being conserved in small, isolated areas. Modern management approaches must adapt to ensure the continued survival and conservation value of these populations. In South Africa, a managed metapopulation approach has been adopted for several large carnivore species, all protected in isolated, relatively small, reserves that are fenced. As far as possible these approaches are based on natural metapopulation structures. In this network, over the past 25 years, African lions (Panthera leo) were reintroduced into 44 fenced reserves with little attention given to maintaining genetic diversity. To examine the situation, we investigated the current genetic provenance and diversity of these lions. We found that overall genetic diversity was similar to that in a large national park, and included a mixture of four different southern African evolutionarily significant units (ESUs). This mixing of ESUs, while not ideal, provides a unique opportunity to study the impact of mixing ESUs over the long term. We propose a strategic managed metapopulation plan to ensure the maintenance of genetic diversity and improve the long-term conservation value of these lions. This managed metapopulation approach could be applied to other species under similar ecological constraints around the globe.

  8. Expression and production of llama variable heavy-chain antibody fragments (VHHs) by Aspergillus awamori

    NARCIS (Netherlands)

    Joosten, V.; Gouka, R.J.; Hondel, C.A.M.J.J. van den; Verrips, C.T.; Lokman, B.C.

    2005-01-01

    We report the expression and production of llama variable heavy-chain antibody fragments (VHHs) by Aspergillus awamori. Fragments encoding VHHs were cloned in a suitable Aspergillus expression vector and transformants secreting VHH fragments were analysed for integrated gene copy-numbers, mRNA

  9. Fragments of the constant region of immunoglobulin light chains are constituents of AL-amyloid proteins

    DEFF Research Database (Denmark)

    Olsen, K E; Sletten, K; Westermark, Per

    1998-01-01

    Immunoglobulin light chains are the precursor proteins of AL-amyloidosis. In the fibril formation process properties of the variable part of the immunoglobulin light chains are believed to be of major importance. In this work it is shown that fragments of the constant part of the immunoglobulin l...... light chain are a constituent of the AL-amyloid proteins of kappa type. A specific antiserum has identified these fragments in gel filtration fractions where the absorbance approached the base line after the main retarded peak. The fragments are small and have been overlooked previously...

  10. Stability of llama heavy chain antibody fragments under extreme conditions

    NARCIS (Netherlands)

    Dolk, E.

    2004-01-01

    Camelids have next to their normal antibodies, a unique subset of antibodies lacking light chains. The resulting single binding domain, VHH, of these heavy chain antibodies consequently have unique properties. A high stability is one of these properties, which was investigated in this thesis. The

  11. Stress Relaxation by Addition-Fragmentation Chain Transfer in Highly Crosslinked Thiol-Yne Networks

    OpenAIRE

    Park, Hee Young; Kloxin, Christopher J.; Scott, Timothy F.; Bowman, Christopher N.

    2010-01-01

    Radical mediated addition-fragmentation chain transfer of mid-chain allyl sulfide functional groups was utilized to reduce polymerization-induced shrinkage stress in thiol-yne step-growth photopolymerization reactions. In previous studies, the addition-fragmentation of allyl sulfide during the polymerization of a step-growth thiol-ene network demonstrated reduced polymerization stress; however, the glass transition temperature of the material was well below room temperature (~ −20°C). Many ap...

  12. Improved production and function of llama heavy chain antibody fragments by molecular evolution

    NARCIS (Netherlands)

    Linden, van der R.H.; Geus, de B.; Frenken, G.J.; Peters, H.; Verrips, C.T.

    2000-01-01

    The aim of this study was to improve production level of llama heavy chain antibody fragments (V (HH)) in Saccharomyces cerevisiae while retaining functional characteristics. For this purpose, the DNA shuffling technique was used on llama V (HH) fragments specific for the azo-dye reactive red-6. In

  13. (DNA) fragment using two-step polymerase chain reaction (PCR)

    African Journals Online (AJOL)

    Polymerase chain reaction (PCR), an essential tool in many fields such as molecular biology, normally comprises three steps: denaturation at a high temperature, annealing at a low temperature and elongation at a moderate temperature. Here, we report a two-step PCR method which incorporates annealing and elongation ...

  14. Biodiversity conservation across taxa and landscapes requires many small as well as single large habitat fragments.

    Science.gov (United States)

    Rösch, Verena; Tscharntke, Teja; Scherber, Christoph; Batáry, Péter

    2015-09-01

    Agricultural intensification has been shown to reduce biodiversity through processes such as habitat degradation and fragmentation. We tested whether several small or single large habitat fragments (re-visiting the 'single large or several small' debate) support more species across a wide range of taxonomic groups (plants, leafhoppers, true bugs, snails). Our study comprised 14 small (fragments of calcareous grassland in Central Germany along orthogonal gradients of landscape complexity and habitat connectivity. Each taxon was sampled on six plots per fragment. Across taxa, species richness did not differ between large and small fragments, whereas species-area accumulation curves showed that both overall and specialist species richness was much higher on several small fragments of calcareous grassland than on few large fragments. On average, 85% of the overall species richness was recorded on all small fragments taken together (4.6 ha), whereas the two largest ones (15.1 ha) only accounted for 37% of the species. This could be due to the greater geographic extent covered by many small fragments. However, community composition differed strongly between large and small fragments, and some of the rarest specialist species appeared to be confined to large fragments. The surrounding landscape did not show any consistent effects on species richness and community composition. Our results show that both single large and many small fragments are needed to promote landscape-wide biodiversity across taxa. We therefore question the focus on large fragments only and call for a new diversified habitat fragmentation strategy for biodiversity conservation.

  15. On the fragmentation of biomolecules: fragmentation of alanine dipeptide along the polypeptide chain

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander; Solov'yov, Andrey

    2006-01-01

    The interaction potential between amino acids in alanine dipeptide has been studied for the first time taking into account exact molecular geometry. Ab initio calculation has been performed in the framework of density functional theory taking into account all electrons in the system. The fragment...

  16. Flagships and fragments — perspectives on the conservation of ...

    African Journals Online (AJOL)

    The Clanwilliam yellowfish population has declined markedly over the past fifty years. Efforts to conserve the species illustrate the changing directions, frustrations and problems of riverine conservation in recent times. The illusions and problems of alien fish introductions provide a third dramatic example to illustrate the state ...

  17. Variable fragments of heavy chain antibodies (VHHs): a new magic bullet molecule of medicine?

    Science.gov (United States)

    Smolarek, Dorota; Bertrand, Olivier; Czerwinski, Marcin

    2012-06-14

     Serum of animals belonging to the Camelidae family (camels and llamas) contains fully active antibodies that are naturally devoid of light chains. Variable domains derived from heavy chain antibodies (hcAb) called VHHs or nanobodies™ can bind antigens as effectively as full-length antibodies and are easy to clone and express. Because of their potential, VHHs are being intensively studied as potential therapeutic, diagnostic and imaging tools. The paper reviews the molecular background of heavy chain antibodies and describes methods of obtaining recombinant fragments of heavy chain antibodies as well as their therapeutic, diagnostic and other applications.

  18.  Variable fragments of heavy chain antibodies (VHHs: a new magic bullet molecule of medicine?

    Directory of Open Access Journals (Sweden)

    Dorota Smolarek

    2012-06-01

    Full Text Available  Serum of animals belonging to the Camelidae family (camels and llamas contains fully active antibodies that are naturally devoid of light chains. Variable domains derived from heavy chain antibodies (hcAb called VHHs or nanobodies™ can bind antigens as effectively as full-length antibodies and are easy to clone and express. Because of their potential, VHHs are being intensively studied as potential therapeutic, diagnostic and imaging tools. The paper reviews the molecular background of heavy chain antibodies and describes methods of obtaining recombinant fragments of heavy chain antibodies as well as their therapeutic, diagnostic and other applications.

  19. Anchor side chains of short peptide fragments trigger ligand-exchange of class II MHC molecules.

    Directory of Open Access Journals (Sweden)

    Shashank Gupta

    Full Text Available Class II MHC molecules display peptides on the cell surface for the surveillance by CD4+ T cells. To ensure that these ligands accurately reflect the content of the intracellular MHC loading compartment, a complex processing pathway has evolved that delivers only stable peptide/MHC complexes to the surface. As additional safeguard, MHC molecules quickly acquire a 'non-receptive' state once they have lost their ligand. Here we show now that amino acid side chains of short peptides can bypass these safety mechanisms by triggering the reversible ligand-exchange. The catalytic activity of dipeptides such as Tyr-Arg was stereo-specific and could be enhanced by modifications addressing the conserved H-bond network near the P1 pocket of the MHC molecule. It affected both antigen-loading and ligand-release and strictly correlated with reported anchor preferences of P1, the specific target site for the catalytic side chain of the dipeptide. The effect was evident also in CD4+ T cell assays, where the allele-selective influence of the dipeptides translated into increased sensitivities of the antigen-specific immune response. Molecular dynamic calculations support the hypothesis that occupation of P1 prevents the 'closure' of the empty peptide binding site into the non-receptive state. During antigen-processing and -presentation P1 may therefore function as important "sensor" for peptide-load. While it regulates maturation and trafficking of the complex, on the cell surface, short protein fragments present in blood or lymph could utilize this mechanism to alter the ligand composition on antigen presenting cells in a catalytic way.

  20. Artificial Synthesis of Conserved Segment S Gene Fragment of Rift ...

    African Journals Online (AJOL)

    Methods: According to the reference sequences of RVFV published in GenBank, nine overlapping polymerase chain reaction (PCR) primers and four specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) primers were designed using DNAStar and LAMP primer design software, respectively.

  1. FragKB: structural and literature annotation resource of conserved peptide fragments and residues.

    Directory of Open Access Journals (Sweden)

    Ashish V Tendulkar

    Full Text Available BACKGROUND: FragKB (Fragment Knowledgebase is a repository of clusters of structurally similar fragments from proteins. Fragments are annotated with information at the level of sequence, structure and function, integrating biological descriptions derived from multiple existing resources and text mining. METHODOLOGY: FragKB contains approximately 400,000 conserved fragments from 4,800 representative proteins from PDB. Literature annotations are extracted from more than 1,700 articles and are available for over 12,000 fragments. The underlying systematic annotation workflow of FragKB ensures efficient update and maintenance of this database. The information in FragKB can be accessed through a web interface that facilitates sequence and structural visualization of fragments together with known literature information on the consequences of specific residue mutations and functional annotations of proteins and fragment clusters. FragKB is accessible online at http://ubio.bioinfo.cnio.es/biotools/fragkb/. SIGNIFICANCE: The information presented in FragKB can be used for modeling protein structures, for designing novel proteins and for functional characterization of related fragments. The current release is focused on functional characterization of proteins through inspection of conservation of the fragments.

  2. Polymerase chain reaction-restriction fragment length polymorphism analysis: a simple method for species identification in food.

    Science.gov (United States)

    Meyer, R; Höfelein, C; Lüthy, J; Candrian, U

    1995-01-01

    The polymerase chain reaction (PCR) technique was applied to meat species identification in marinated and heat-treated or fermented products and to the differentiation of closely related species. DNA was isolated from meat samples by using a DNA-binding resin and was subjected to PCR analysis. Primers used were complementary to conserved areas of the vertebrate mitochondrial cytochrome b (cytb) gene and yielded a 359 base-pair (bp) fragment, including a variable 307 bp region. Restriction endonuclease analysis based on sequence data of those fragments was used for differentiation among species. Restriction fragment length polymorphisms (RFLPs) were detected when pig, cattle, wild boar, buffalo, sheep, goat, horse, chicken, and turkey amplicons were cut with AluI, RsaI, TaqI, and HinfI. Analysis of sausages indicates the applicability of this approach to food products containing meat from 3 different species. The PCR-RFLP analytical method detected pork in heated meat mixtures with beef at levels below 1%, and the method was confirmed with porcine- and bovine-specific PCR assays by amplifying fragments of their growth hormone genes. Inter- and intraspecific differences of more than 22 animal species with nearly unknown cytb DNA sequences, including hoofed mammals (ungulates), and poultry were determined with PCR-RFLP typing by using 20 different endonucleases. This typing method allowed the discrimination of game meats, including stag, roe deer, chamois, moose, reindeer, kangaroo, springbok, and other antelopes in marinated and heat-treated products.

  3. Identification of screwworm species by polymerase chain reaction-restriction fragment length polymorphism.

    Science.gov (United States)

    Taylor, D B; Szalanski, A L; Peterson, R D

    1996-01-01

    Restriction fragment length polymorphisms in polymerase chain reaction amplified fragments (PCR-RFLP) of mitochondrial DNA were used to differentiate species of New World screwworms (Diptera: Calliphoridae). Twenty-seven restriction enzymes were screened on five regions of mtDNA. Eleven restriction fragment length patterns differentiated New World screwworm, Cochliomyia hominivorax (Coquerel), from secondary screwworm, Cochliomyia macellaria (F.). Five restriction fragment length patterns were polymorphic in C.hominivorax while all fragment patterns were fixed in C.macellaria. Diagnostic restriction fragment length patterns were used for species diagnosis, whereas intraspecific variable patterns were used to characterize field samples and laboratory strains. The PCR-RFLP technique is flexible with regard to developmental stage of the sample and method of preservation. We were able to characterize specimens of all life stages from egg to adult including larvae preserved in alcohol and pinned adults. PCR-RFLP is rapid and inexpensive, enabling specimens to be characterized within 24 h for less than $2.50.

  4. Wildlife conservation in fragmented tropical forests: A case of South Garo Hills, Meghalaya, North East India

    Science.gov (United States)

    Ashish. Kumar; Bruce G. Marcot; Rohitkumar. Patel

    2017-01-01

    This volume presents findings on, and implications for, wildlife conservation in the tropical forests in Garo Hills of Meghalaya state in the North East India. A companion volume presented the findings on forest fragmentation due to practice of slash and burn agriculture in the region. Both of the volumes summarize work completed over more than a decade on...

  5. Isolation, purification, and characterization of fragment B, the NH2-terminal half of the heavy chain of tetanus toxin.

    OpenAIRE

    Matsuda, M; Lei, D L; N. Sugimoto; Ozutsumi, K; Okabe, T.

    1989-01-01

    Fragment B, the N-terminal half of the heavy chain, an important domain of the tetanus neurotoxin molecule, was isolated for the first time. Tetanus toxin (composed of three domains, A, B, and C) was prepared from culture filtrates. Fragment A-B, derived from the toxin treated mildly with papain, was used for the isolation of fragment B. Fragment A-B obtained was dissociated into fragments A and B by reduction with 100 mM dithiothreitol and treatment with 2 M urea. Fragment B was separated fr...

  6. Fast local fragment chaining using sum-of-pair gap costs

    DEFF Research Database (Denmark)

    Otto, Christian; Hoffmann, Steve; Gorodkin, Jan

    2011-01-01

    Background: Fast seed-based alignment heuristics such as BLAST and BLAT have become indispensable tools in comparative genomics for all studies aiming at the evolutionary relations of proteins, genes, and non-coding RNAs. This is true in particular for the large mammalian genomes. The sensitivity......, and rank the fragments to improve the specificity. Results: Here we present a fast and flexible fragment chainer that for the first time also supports a sum-of-pair gap cost model. This model has proven to achieve a higher accuracy and sensitivity in its own field of application. Due to a highly time......-efficient index structure our method outperforms the only existing tool for fragment chaining under the linear gap cost model. It can easily be applied to the output generated by alignment tools such as segemehl or BLAST. As an example we consider homology-based searches for human and mouse snoRNAs demonstrating...

  7. The Technology Introduction of Chain Boiler Energy Conservation Transformation

    Science.gov (United States)

    Li, Henan; Liu, Xiwen; Yuan, Hong; Lin, Jiadai; Zhang, Yu

    2017-12-01

    Introduced the present status of chain boiler efficiency is low, the system analysis of the chain boiler optimization and upgrading of technology, for the whole progress of chain boiler to provide some ideas and reference.

  8. Incorporating fragmentation and non-native species into distribution models to inform fluvial fish conservation.

    Science.gov (United States)

    Taylor, Andrew T; Papeş, Monica; Long, James M

    2018-02-01

    Fluvial fishes face increased imperilment from anthropogenic activities, but the specific factors contributing most to range declines are often poorly understood. For example, the range of the fluvial-specialist shoal bass (Micropterus cataractae) continues to decrease, yet how perceived threats have contributed to range loss is largely unknown. We used species distribution models to determine which factors contributed most to shoal bass range loss. We estimated a potential distribution based on natural abiotic factors and a series of currently occupied distributions that incorporated variables characterizing land cover, non-native species, and river fragmentation intensity (no fragmentation, dams only, and dams and large impoundments). We allowed interspecific relationships between non-native congeners and shoal bass to vary across fragmentation intensities. Results from the potential distribution model estimated shoal bass presence throughout much of their native basin, whereas models of currently occupied distribution showed that range loss increased as fragmentation intensified. Response curves from models of currently occupied distribution indicated a potential interaction between fragmentation intensity and the relationship between shoal bass and non-native congeners, wherein non-natives may be favored at the highest fragmentation intensity. Response curves also suggested that >100 km of interconnected, free-flowing stream fragments were necessary to support shoal bass presence. Model evaluation, including an independent validation, suggested that models had favorable predictive and discriminative abilities. Similar approaches that use readily available, diverse, geospatial data sets may deliver insights into the biology and conservation needs of other fluvial species facing similar threats. © 2017 Society for Conservation Biology.

  9. Cloning approach and functional analysis of anti-intimin single-chain variable fragment (scFv

    Directory of Open Access Journals (Sweden)

    Elias Waldir P

    2011-02-01

    Full Text Available Abstract Background Intimin is an important virulence factor involved in the pathogenesis of enteropathogenic Escherichia coli (EPEC and enterohemorrhagic Escherichia coli (EHEC. Both pathogens are still important causes of diarrhea in children and adults in many developing and industrialized countries. Considering the fact that antibodies are important tools in the detection of various pathogens, an anti-intimin IgG2b monoclonal antibody was previously raised in immunized mice with the conserved sequence of the intimin molecule (int388-667. In immunoblotting assays, this monoclonal antibody showed excellent specificity. Despite good performance, the monoclonal antibody failed to detect some EPEC and EHEC isolates harboring variant amino acids within the 338-667 regions of intimin molecules. Consequently, motivated by its use for diagnosis purposes, in this study we aimed to the cloning and expression of the single-chain variable fragment from this monoclonal antibody (scFv. Findings Anti-intimin hybridoma mRNA was extracted and reversely transcripted to cDNA, and the light and heavy chains of the variable fragment of the antibody were amplified using commercial primers. The amplified chains were cloned into pGEM-T Easy vector. Specific primers were designed and used in an amplification and chain linkage strategy, obtaining the scFv, which in turn was cloned into pAE vector. E. coli BL21(DE3pLys strain was transformed with pAE scFv-intimin plasmid and subjected to induction of protein expression. Anti-intimin scFv, expressed as inclusion bodies (insoluble fraction, was denatured, purified and submitted to refolding. The protein yield was 1 mg protein per 100 mL of bacterial culture. To test the functionality of the scFv, ELISA and immunofluorescence assays were performed, showing that 275 ng of scFv reacted with 2 mg of purified intimin, resulting in an absorbance of 0.75 at 492 nm. The immunofluorescence assay showed a strong reactivity with

  10. Diverse responses of species to landscape fragmentation in a simple food chain.

    Science.gov (United States)

    Liao, Jinbao; Bearup, Daniel; Blasius, Bernd

    2017-09-01

    Habitat destruction, characterized by habitat loss and fragmentation, is a key driver of species extinction in spatial extended communities. Recently, there has been some progress in the theory of spatial food webs, however to date practically little is known about how habitat configurational fragmentation influences multi-trophic food web dynamics. To explore how habitat fragmentation affects species persistence in food webs, we introduce a modelling framework that describes the site occupancy of species in a tri-trophic system. We assume that species dispersal range increases with trophic level, exploiting pair-approximation techniques to describe the effect of habitat clustering. In accordance with the trophic rank hypothesis, both habitat loss and fragmentation generally cause species extinction, with stronger effects occurring at higher trophic levels. However, species display diverse responses (negative, neutral or positive) to habitat loss and fragmentation separately, depending on their dispersal range and trophic position. Counter-intuitively, prey species may benefit from habitat loss due to a release in top-down control. Similarly, habitat fragmentation has almost no influence on the site occupancy of the intermediate consumer in the tri-trophic system, though it decreases those of both basal species and top predator. Consequently, species' responses to habitat destruction vary as other species become extinct. Our results reiterate the importance of the interplay between bottom-up and top-down control in trophically linked communities, and highlight the complex responses occurring in even a simple food chain. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

  11. Regularity and mass conservation for discrete coagulation–fragmentation equations with diffusion

    KAUST Repository

    Cañizo, J.A.

    2010-03-01

    We present a new a priori estimate for discrete coagulation-fragmentation systems with size-dependent diffusion within a bounded, regular domain confined by homogeneous Neumann boundary conditions. Following from a duality argument, this a priori estimate provides a global L2 bound on the mass density and was previously used, for instance, in the context of reaction-diffusion equations. In this paper we demonstrate two lines of applications for such an estimate: On the one hand, it enables to simplify parts of the known existence theory and allows to show existence of solutions for generalised models involving collision-induced, quadratic fragmentation terms for which the previous existence theory seems difficult to apply. On the other hand and most prominently, it proves mass conservation (and thus the absence of gelation) for almost all the coagulation coefficients for which mass conservation is known to hold true in the space homogeneous case. © 2009 Elsevier Masson SAS. All rights reserved.

  12. Selecting a Conservation Surrogate Species for Small Fragmented Habitats Using Ecological Niche Modelling

    Science.gov (United States)

    Nekaris, K. Anne-Isola; Arnell, Andrew P.; Svensson, Magdalena S.

    2015-01-01

    Simple Summary Large “charismatic” animals (with widespread popular appeal) are often used as flagship species to raise awareness for conservation. Deforestation and forest fragmentation are among the main threats to biodiversity, and in many places such species are disappearing. In this paper we aim to find a suitable species among the less charismatic animal species left in the fragmented forests of South-western Sri Lanka. We selected ten candidates, using a questionnaire survey along with computer modelling of their distributions. The red slender loris and the fishing cat came out as finalists as they were both appealing to local people, and fulfilled selected ecological criteria. Abstract Flagship species are traditionally large, charismatic animals used to rally conservation efforts. Accepted flagship definitions suggest they need only fulfil a strategic role, unlike umbrella species that are used to shelter cohabitant taxa. The criteria used to select both flagship and umbrella species may not stand up in the face of dramatic forest loss, where remaining fragments may only contain species that do not suit either set of criteria. The Cinderella species concept covers aesthetically pleasing and overlooked species that fulfil the criteria of flagships or umbrellas. Such species are also more likely to occur in fragmented habitats. We tested Cinderella criteria on mammals in the fragmented forests of the Sri Lankan Wet Zone. We selected taxa that fulfilled both strategic and ecological roles. We created a shortlist of ten species, and from a survey of local perceptions highlighted two finalists. We tested these for umbrella characteristics against the original shortlist, utilizing Maximum Entropy (MaxEnt) modelling, and analysed distribution overlap using ArcGIS. The criteria highlighted Loris tardigradus tardigradus and Prionailurus viverrinus as finalists, with the former having highest flagship potential. We suggest Cinderella species can be effective

  13. Classification of integrable hydrodynamic chains and generating functions of conservation laws

    OpenAIRE

    Pavlov, Maxim V.

    2006-01-01

    New approach to classification of integrable hydrodynamic chains is established. Generating functions of conservation laws are classified by the method of hydrodynamic reductions. N parametric family of explicit hydrodynamic reductions allows to reconstruct corresponding hydrodynamic chains. Plenty new hydrodynamic chains are found.

  14. Selecting a Conservation Surrogate Species for Small Fragmented Habitats Using Ecological Niche Modelling

    Directory of Open Access Journals (Sweden)

    K. Anne-Isola Nekaris

    2015-01-01

    Full Text Available Flagship species are traditionally large, charismatic animals used to rally conservation efforts. Accepted flagship definitions suggest they need only fulfil a strategic role, unlike umbrella species that are used to shelter cohabitant taxa. The criteria used to select both flagship and umbrella species may not stand up in the face of dramatic forest loss, where remaining fragments may only contain species that do not suit either set of criteria. The Cinderella species concept covers aesthetically pleasing and overlooked species that fulfil the criteria of flagships or umbrellas. Such species are also more likely to occur in fragmented habitats. We tested Cinderella criteria on mammals in the fragmented forests of the Sri Lankan Wet Zone. We selected taxa that fulfilled both strategic and ecological roles. We created a shortlist of ten species, and from a survey of local perceptions highlighted two finalists. We tested these for umbrella characteristics against the original shortlist, utilizing Maximum Entropy (MaxEnt modelling, and analysed distribution overlap using ArcGIS. The criteria highlighted Loris tardigradus tardigradus and Prionailurus viverrinus as finalists, with the former having highest flagship potential. We suggest Cinderella species can be effective conservation surrogates especially in habitats where traditional flagship species have been extirpated.

  15. Geospatial characterization of deforestation, fragmentation and forest fires in Telangana state, India: conservation perspective.

    Science.gov (United States)

    Sudhakar Reddy, C; Vazeed Pasha, S; Jha, C S; Dadhwal, V K

    2015-07-01

    Conservation of biodiversity has been put to the highest priority throughout the world. The process of identifying threatened ecosystems will search for different drivers related to biodiversity loss. The present study aimed to generate spatial information on deforestation and ecological degradation indicators of fragmentation and forest fires using systematic conceptual approach in Telangana state, India. Identification of ecosystems facing increasing vulnerability can help to safeguard the extinctions of species and useful for conservation planning. The technological advancement of satellite remote sensing and Geographical Information System has increased greatly in assessment and monitoring of ecosystem-level changes. The areas of threat were identified by creating grid cells (5 × 5 km) in Geographical Information System (GIS). Deforestation was assessed using multi-source data of 1930, 1960, 1975, 1985, 1995, 2005 and 2013. The forest cover of 40,746 km(2), 29,299 km(2), 18,652 km(2), 18,368 km(2), 18,006 km(2), 17,556 km(2) and 17,520 km(2) was estimated during 1930, 1960, 1975, 1985, 1995, 2005 and 2013, respectively. Historical evaluation of deforestation revealed that major changes had occurred in forests of Telangana and identified 1095 extinct, 397 critically endangered, 523 endangered and 311 vulnerable ecosystem grid cells. The fragmentation analysis has identified 307 ecosystem grid cells under critically endangered status. Forest burnt area information was extracted using AWiFS data of 2005 to 2014. Spatial analysis indicates total fire-affected forest in Telangana as 58.9% in a decadal period. Conservation status has been recorded depending upon values of threat for each grid, which forms the basis for conservation priority hotspots. Of existing forest, 2.1% grids had severe ecosystem collapse and had been included under the category of conservation priority hotspot-I, followed by 27.2% in conservation priority hotspot-II and 51.5% in conservation

  16. The catabolism of human γG immunoglobulins of different heavy chain subclasses. III. The catabolism of heavy chain disease proteins and of Fc fragments of myeloma proteins

    Science.gov (United States)

    Spiegelberg, H. L.; Fishkin, B. G.

    1972-01-01

    The catabolism of 131I and 125I paired labelled Fc fragments of myeloma proteins and of H chain disease proteins of different heavy chain subclasses was studied in men and monkeys. In contrast to the previously demonstrated catabolic heterogeneity of intact γG immunoglobulins, the Fc fragments and H chain disease proteins of all subclasses tested were catabolized at a similar rate. These data suggest that structures not present on the Fc fragments are responsible for the faster turnover rate of γG3 immunoglobulins and for the differences in half-lives of myeloma proteins within a given subclass. The catabolic features of the H chain disease proteins differed from those of intact γG. Although the whole body half-lives of the two proteins were similar, the fractional turnover rate of the H chain disease proteins was higher than that of γG, on the average 8% of the intravascular pool/day as compared to 4% for γG. One-half to 1% of the intravascular pool of the H chain disease protein and less than 0·1% of the γG was excreted into the urine. An average of 24% of the H chain disease proteins and 44% of the γG equilibrated into the intravascular compartment. PMID:4624553

  17. Reversible Addition-Fragmentation Chain Transfer Polymerization of Acrylonitrile under Irradiation of Blue LED Light

    Directory of Open Access Journals (Sweden)

    Zhicheng Huang

    2016-12-01

    Full Text Available Compared to unhealthy UV or γ-ray and high-energy-consumption thermal external stimuli, the promising light emitting diode (LED external stimulus has some outstanding technological merits such as narrow wavelength distribution, low heat generation and energy consumption, and safety for human beings. In this work, a novel reversible addition-fragmentation transfer (RAFT polymerization system for acrylonitrile (AN was developed under the irradiation of blue LED light at room temperature, using 1,2,3,5-tetrakis(carbazol-9-yl-4,6-dicyanobenzene (4CzIPN as a novel radical initiator and 2-cyanoprop-2-yl-1-dithionaphthalate (CPDN as the typical chain transfer agent. Well-defined polyacrylonitrile (PAN with a controlled molecular weight and narrow molecular weight distribution was successfully synthesized. This strategy may provide another effective method for scientific researchers or the industrial community to synthesize a PAN-based precursor of carbon fibers.

  18. Construction and molecular characterization of mouse single-chain variable fragment antibodies against Burkholderia mallei and Burkholderia pseudomallei.

    Science.gov (United States)

    Kim, Ho San; Tsai, Shien; Zou, Nianxiang; Lo, Shyh-Ching; Wear, Douglas J; Izadjoo, Mina J

    2011-02-28

    We have selected two lipopolysaccharide (LPS) specific Burkholderia mallei mouse monoclonal antibodies (mAbs) and four anti-capsular B. pseudomallei-specific mAbs to generate mouse single-chain variable fragment (scFv) antibodies. This selection was made through extensive in vitro and in vivo assay from our library of mAbs against B. mallei and B. pseudomallei. We initially generated the mouse immunoglobulin variable heavy chain (VH) and light chain (VL) regions from each of these six selected mAbs using a phage display scFv technology. We determined the coding sequences of the VH and VL regions and successfully constructed two B. mallei-specific scFv phage antibodies consisting of two different VH (VH1 and VH2) and one Vλ1 families. Four scFvs constructed against B. pseudomallei had two VH (VH1 and VH6) and two VL (Vκ4/5 and Vκ21) families. All of six scFv antibodies constructed demonstrated good binding activity without any rounds of biopanning against B. mallei (M5D and M18F were 0.425 and 0.480 at OD405nm) and B. pseudomallei (P1E7, P2I67, P7C6, and P7F4 were 0.523, 0.859, 0.775, and 0.449 at OD405nm) by ELISA, respectively. A comparison of the immunoglobulin gene segments revealed that the gene sequences in complementarity-determining regions (CDRs) of three out of four B. pseudomallei-specific scFvs are highly conserved. We determined that the two B. mallei-specific scFvs have different CDRs in the VH, but the amino acid sequences of CDRs in the VL are conserved. This high sequence homology found in CDRs of VH or VL of these mAbs contributes to our better understanding and determination of binding to the specific antigenic epitope(s). The scFv phage display technology may be a valuable tool to develop and engineer mAbs with improved antigen-binding affinity. Copyright © 2010 Elsevier B.V. All rights reserved.

  19. Differential binding of heavy chain variable domain 3 antigen binding fragments to protein A chromatography resins.

    Science.gov (United States)

    Bach, Julia; Lewis, Nathaniel; Maggiora, Kathy; Gillespie, Alison J; Connell-Crowley, Lisa

    2015-08-28

    This work examines the binding of 15 different VH3 IgGs and their corresponding F(ab')2 fragments to two different protein A chromatography resins: MabSelect(®), which utilizes a recombinant protein A ligand, and MabSelect SuRe(®) (SuRe), which utilizes a tetrameric Z domain ligand. The results show that VH3 F(ab')2 fragments can exhibit a variety of binding behaviours for the two resins. Contrary to previously published data, a subset of these molecules show strong interaction with the Z domain of SuRe(®). Furthermore, the results show that sequence variability of residue 57 in the VH3 heavy chain CDR2 domain correlates with binding behaviour on MabSelect(®) and SuRe(®). Site-directed mutagenesis of this residue confers gain or loss of VH3 F(ab')2 binding to these resins in 3 mAbs, demonstrating that it plays a key role in both recombinant protein A and Z domain interaction. A fourth mAb with a longer CDR2 loop was not affected by mutation of residue 57, indicating that CDR2 domain length may alter the binding interface and lead to the involvement of other residues in protein A binding. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Generation of human antibody fragments against Streptococcus mutans using a phage display chain shuffling approach

    Directory of Open Access Journals (Sweden)

    Barth Stefan

    2005-01-01

    Full Text Available Abstract Background Common oral diseases and dental caries can be prevented effectively by passive immunization. In humans, passive immunotherapy may require the use of humanized or human antibodies to prevent adverse immune responses against murine epitopes. Therefore we generated human single chain and diabody antibody derivatives based on the binding characteristics of the murine monoclonal antibody Guy's 13. The murine form of this antibody has been used successfully to prevent Streptococcus mutans colonization and the development of dental caries in non-human primates, and to prevent bacterial colonization in human clinical trials. Results The antibody derivatives were generated using a chain-shuffling approach based on human antibody variable gene phage-display libraries. Like the parent antibody, these derivatives bound specifically to SAI/II, the surface adhesin of the oral pathogen S. mutans. Conclusions Humanization of murine antibodies can be easily achieved using phage display libraries. The human antibody fragments bind the antigen as well as the causative agent of dental caries. In addition the human diabody derivative is capable of aggregating S. mutans in vitro, making it a useful candidate passive immunotherapeutic agent for oral diseases.

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

    Science.gov (United States)

    Shuey, John A.

    2013-01-01

    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. PMID:26462535

  2. Expression of recombinant antibody (single chain antibody fragment) in transgenic plant Nicotiana tabacum cv. Xanthi.

    Science.gov (United States)

    Dobhal, S; Chaudhary, V K; Singh, A; Pandey, D; Kumar, A; Agrawal, S

    2013-12-01

    Plants offer an alternative inexpensive and convenient technology for large scale production of recombinant proteins especially recombinant antibodies (plantibodies). In this paper, we describe the expression of a model single chain antibody fragment (B6scFv) in transgenic tobacco. Four different gene constructs of B6scFv with different target signals for expression in different compartments of a tobacco plant cell with and without endoplasmic reticulum (ER) retention signal were used. Agrobacterium mediated plant transformation of B6scFv gene was performed with tobacco leaf explants and the gene in regenerated plants was detected using histochemical GUS assay and PCR. The expression of B6scFv gene was detected by western blotting and the recombinant protein was purified from putative transgenic tobacco plants using metal affinity chromatography. The expression level of recombinant protein was determined by indirect enzyme-linked immunosorbent assay. The highest accumulation of protein was found up to 3.28 % of the total soluble protein (TSP) in plants expressing B6scFv 1003 targeted to the ER, and subsequently expression of 2.9 % of TSP in plants expressing B6scFv 1004 (with target to apoplast with ER retention signal). In contrast, lower expression of 0.78 and 0.58 % of TSP was found in plants expressing antibody fragment in cytosol and apoplast, without ER retention signal. The described method/system could be used in the future for diverse applications including expression of other recombinant molecules in plants for immunomodulation, obtaining pathogen resistance against plant pathogens, altering metabolic pathways and also for the expression of different antibodies of therapeutic and diagnostic uses.

  3. Amino and Acetamide Functional Group Effects on the Ionization and Fragmentation of Sugar Chains in Positive-Ion Mass Spectrometry

    Science.gov (United States)

    Yamagaki, Tohru; Sugahara, Kohtaro; Watanabe, Takehiro

    2014-01-01

    To elucidate the influence of amino (-NH2) and acetamide (-NHCOCH3, -NAc) groups in sugar chains on their ionization and fragmentation, cycloamyloses (cyclodextrins, CyDs) and lacto-oligosaccharide are analyzed by MALDI TOF/TOF and ESI Q-TOF mass spectrometry. CyD derivatives substituted by amino or acetamide groups are ideal analytes to extract the function group effects, which are amino-CyD with one hexosamine (HexNH2) and acetamide-CyD with one N-acetyl hexosamine (HexNAc). Interestingly, the relative ion intensities and isotope-like patterns in their product ion spectra depend on the functional groups and ion forms of sugar chains. Consequently, the results indicate that a proton (H+) localizes on the amino group of the amino sugar, and that the proton (H+) induces their fragmentation. Sodium cation (Na+) attachment is independent from amino group and exerts no influence on their fragmentation patterns in amino group except for mono- and disaccharide fragment ions because there is the possibility of the reducing end effect. In contrast, a sodium cation localizes much more frequently on the acetamide group in acetamide-CyDs because the chemical species with HexNAc are stable. Thus, their ions with HexNAc are abundant. These results are consistent with the fragmentation of lacto-neo- N-tetraose and maltotetraose, suggesting that a sodium cation generally localizes much more frequently on the acetamide group in sugar chains.

  4. Isolation, purification, and characterization of fragment B, the NH2-terminal half of the heavy chain of tetanus toxin.

    Science.gov (United States)

    Matsuda, M; Lei, D L; Sugimoto, N; Ozutsumi, K; Okabe, T

    1989-11-01

    Fragment B, the N-terminal half of the heavy chain, an important domain of the tetanus neurotoxin molecule, was isolated for the first time. Tetanus toxin (composed of three domains, A, B, and C) was prepared from culture filtrates. Fragment A-B, derived from the toxin treated mildly with papain, was used for the isolation of fragment B. Fragment A-B obtained was dissociated into fragments A and B by reduction with 100 mM dithiothreitol and treatment with 2 M urea. Fragment B was separated from fragment A by ion-exchange column chromatography on a Mono Q column equilibrated with 20 mM Tris hydrochloride buffer (pH 7.6), containing 1 mM dithiothreitol and 2 M urea, in a fast-protein liquid chromatography system by elution with a linear gradient of 0 to 0.5 M NaCl. Fragment B was obtained in two forms having molecular weights of 48,000 +/- 2,000, which were indistinguishable by sodium dodecyl sulfate-gel electrophoresis or antigenic specificity, but distinguishable on polyacrylamide gel electrophoresis without sodium dodecyl sulfate and on isoelectric focusing (pI 6.7 and 7.3). The recovery of fragment B was 50 to 72% of that of fragment A-B on a molar basis. Purified fragment B was not toxic to mice on intravenous or intramuscular injection at doses of up to 100 micrograms, but was found to form channels (ca. 2.3 pS) in a lipid bilayer membrane by a patch clamp technique. The role of domain B of the tetanus toxin molecule in the mechanism of action of the toxin is discussed.

  5. Freshwater Wetland Habitat Loss and Fragmentation: Implications for Aquatic Biodiversity Conservation

    Science.gov (United States)

    Wolaver, B. D.; Pierre, J. P.; Labay, B. J.; Ryberg, W. A.; Hibbits, T. J.; Prestridge, H. L.

    2015-12-01

    Anthropogenic land use changes have caused widespread wetland loss and fragmentation. This trend has important implications for aquatic biota conservation, including the semi-aquatic Western Chicken Turtle (Deirochelys reticularia miaria). This species inhabits seasonally inundated, ephemeral water bodies and adjacent uplands in the southeastern U.S. However, wetland conversion to agriculture and urbanization is thought to cause the species' decline, particularly in Texas, which includes the westernmost part of its range. Because the species moves only a few kilometers between wetlands, it particularly sensitive to habitat loss and fragmentation. Thus, as part of the only state-funded species research program, this study provides the U.S. Fish and Wildlife Service (FWS) with scientific data to determine if the species warrants protection under the Endangered Species Act (ESA). We use a species distribution model to map potentially suitable habitat for most of East Texas. We evaluate landscape-scale anthropogenic activities in this region which may be contributing to the species' decline. We identify areas of urbanization, agricultural expansion, forestry, and resulting wetland loss. We find that between 2001 and 2011 approximately 80 km2 of wetlands were lost in potentially suitable habitat, including the urbanizing Houston area. We use spatial geostatistics to quantify wetland habitat fragmentation. We also introduce the Habitat Alteration Index (HAI), which calculates total landscape alteration and mean probability of occurrence to identify high-quality habitat most at risk of recent anthropogenic alteration. Population surveys by biologists are targeting these areas and future management actions may focus on mitigating anthropogenic activities there. While this study focuses on D. r. miaria, this approach can evaluate wetland habitat of other aquatic organisms.

  6. Molecular identification of Giardia duodenalis in Ecuador by polymerase chain reaction-restriction fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Richard Atherton

    2013-06-01

    Full Text Available The aim of this study was to determine the genetic diversity of Giardia duodenalis present in a human population living in a northern Ecuadorian rain forest. All Giardia positive samples (based on an ELISA assay were analysed using a semi-nested polymerase chain reaction-restriction fragment length polymorphism assay that targets the glutamate dehydrogenase (gdh gene; those amplified were subsequently genotyped using NlaIV and RsaI enzymes. The gdh gene was successfully amplified in 74 of 154 ELISA positive samples; 69 of the 74 samples were subsequently genotyped. Of these 69 samples, 42 (61% were classified as assemblage B (26 as BIII and 16 as BIV, 22 (32% as assemblage A (3 as AI and 19 as AII and five (7% as mixed AII and BIII types. In this study site we observe similar diversity in genotypes to other regions in Latin America, though in contrast to some previous studies, we found similar levels of diarrheal symptoms in those individuals infected with assemblage B compared with those infected with assemblage A.

  7. Effects of protein engineering and rational mutagenesis on crystal lattice of single chain antibody fragments.

    Science.gov (United States)

    Kalyoncu, Sibel; Hyun, Jeongmin; Pai, Jennifer C; Johnson, Jennifer L; Entzminger, Kevin; Jain, Avni; Heaner, David P; Morales, Ivan A; Truskett, Thomas M; Maynard, Jennifer A; Lieberman, Raquel L

    2014-09-01

    Protein crystallization is dependent upon, and sensitive to, the intermolecular contacts that assist in ordering proteins into a three-dimensional lattice. Here we used protein engineering and mutagenesis to affect the crystallization of single chain antibody fragments (scFvs) that recognize the EE epitope (EYMPME) with high affinity. These hypercrystallizable scFvs are under development to assist difficult proteins, such as membrane proteins, in forming crystals, by acting as crystallization chaperones. Guided by analyses of intermolecular crystal lattice contacts, two second-generation anti-EE scFvs were produced, which bind to proteins with installed EE tags. Surprisingly, although noncomplementarity determining region (CDR) lattice residues from the parent scFv framework remained unchanged through the processes of protein engineering and rational design, crystal lattices of the derivative scFvs differ. Comparison of energy calculations and the experimentally-determined lattice interactions for this basis set provides insight into the complexity of the forces driving crystal lattice choice and demonstrates the availability of multiple well-ordered surface features in our scFvs capable of forming versatile crystal contacts. © 2014 Wiley Periodicals, Inc.

  8. Evolution of the magic bullet: Single chain antibody fragments for the targeted delivery of immunomodulatory proteins.

    Science.gov (United States)

    Fercher, Christian; Keshvari, Sahar; McGuckin, Michael A; Barnard, Ross T

    2018-01-01

    Immunocytokines are fusion proteins that combine the specific antigen binding capacities of an antibody or derivative thereof and the potent bioactivity of a cytokine partner. These novel biopharmaceuticals have been directed to various targets of oncological as well as non-oncological origin and a handful of promising constructs are currently advancing in the clinical trial pipeline. Several factors such as the choice of a disease specific antigen, the antibody format and the modulatory nature of the payload are crucial, not only for therapeutic efficacy and safety but also for the commercial success of such a product. In this review, we provide an overview of the basic principles and obstacles in immunocytokine design with a specific focus on single chain antibody fragment-based constructs that employ interleukins as the immunoactive component. Impact statement Selective activation of the immune system in a variety of malignancies represents an attractive approach when existing strategies have failed to provide adequate treatment options. Immunocytokines as a novel class of bifunctional protein therapeutics have emerged recently and generated promising results in preclinical and clinical studies. In order to harness their full potential, multiple different aspects have to be taken into consideration. Several key points of these fusion constructs are discussed here and should provide an outline for the development of novel products based on an overview of selected formats.

  9. Display of single-chain variable fragments on bacteriophage MS2 virus-like particles.

    Science.gov (United States)

    Lino, Christopher A; Caldeira, Jerri C; Peabody, David S

    2017-02-13

    Virus-like particles (VLPs) of the RNA bacteriophage MS2 have many potential applications in biotechnology. MS2 VLPs provide a platform for peptide display and affinity selection (i.e. biopanning). They are also under investigation as vehicles for targeted drug delivery, using display of receptor-specific peptides or nucleic acid aptamers to direct their binding to specific cell-surface receptors. However, there are few molecules more suited to the precise targeting and binding of a cellular receptor than antibodies. Here we describe a strategy for display of four different functional single-chain variable fragments (scFvs) on the surface of the MS2 VLP. Each scFv is validated both for its presence on the surface of the VLP and for its ability to bind its cognate antigen. This work demonstrates the suitability of the MS2 VLP platform to display genetically fused scFvs, allowing for many potential applications of these VLPs and paving the way for future work with libraries of scFvs displayed in a similar manner on the VLP surface. These libraries can then be biopanned and novel scFv binders to targets can be readily discovered.

  10. Comet Wild 2 dust coma: conservation relationships between nucleus emission and dust fragmentation processes

    Science.gov (United States)

    McDonnell, J.; Green, S.

    constituent grains (characterised by a cumulative mass index, beta) within a single (larger) particle which is capable of fragmentation; 4. The distances of fragmentation. Within the coma, and under the assumption that dust mass is generally conserved except for minor components of volatile matrix evaporation (which may be responsible for the fragmentation), relationships between flux, alpha and beta are presented and possibilities for constraints examined within the Stardust data. A significant factor in the cascade process is the maximum liftable mass emitted.

  11. Conserving a geographically isolated Charaxes butterfly in response to habitat fragmentation and invasive alien plants

    Directory of Open Access Journals (Sweden)

    Casparus J. Crous

    2015-03-01

    Full Text Available In South Africa, much of the forest biome is vulnerable to human-induced disturbance. The forest-dwelling butterfly Charaxes xiphares occidentalis is naturally confined to a small forest region in the south-western Cape, South Africa. Most of the remaining habitat of this species is within a fragmented agricultural matrix. Furthermore, this geographical area is also heavily invaded by alien plants, especially Acacia mearnsii. We investigated how C. x. occidentalis behaviourally responds to different habitat conditions in the landscape. We were particularly interested in touring, patrolling and settling behaviour as a conservation proxy for preference of a certain habitat configuration in this agricultural matrix. Remnant forest patches in the agricultural matrix showed fewer behavioural incidents than in a reference protected area. Moreover, dense stands of A. mearnsii negatively influenced the incidence and settling pattern of this butterfly across the landscape, with fewer tree settlings associated with more heavily invaded forest patches. This settling pattern was predominantly seen in female butterflies. We also identified specific trees that were settled upon for longer periods by C. x. occidentalis. Distance to a neighbouring patch and patch size influenced behavioural incidences, suggesting that further patch degradation and isolation could be detrimental to this butterfly. Conservation implications: We highlight the importance of clearing invasive tree species from vulnerable forest ecosystems and identify key tree species to consider in habitat conservation and rehabilitation programmes for this butterfly. We also suggest retaining as much intact natural forest as possible. This information should be integrated in local biodiversity management plans.

  12. Identification of fungemia agents using the polymerase chain reaction and restriction fragment length polymorphism analysis

    Directory of Open Access Journals (Sweden)

    M.S. Santos

    2010-08-01

    Full Text Available Prompt and specific identification of fungemia agents is important in order to define clinical treatment. However, in most cases conventional culture identification can be considered to be time-consuming and not without errors. The aim of the present study was to identify the following fungemia agents: Candida albicans, Candida parapsilosis, Candida tropicalis, Candida glabrata, Cryptococcus neoformans, Cryptococcus gattii, and Histoplasma capsulatum using the polymerase chain reaction and restriction fragment length polymorphism analysis (PCR/RFLP. More specifically: a to evaluate 3 different amplification regions, b to investigate 3 different restriction enzymes, and c to use the best PCR/RFLP procedure to indentify 60 fungemia agents from a culture collection. All 3 pairs of primers (ITS1/ITS4, NL4/ITS5 and Primer1/Primer2 were able to amplify DNA from the reference strains. However, the size of these PCR products did not permit the identification of all the species studied. Three restriction enzymes were used to digest the PCR products: HaeIII, Ddel and Bfal. Among the combinations of pairs of primers and restriction enzymes, only one (primer pair NL4/ITS5 and restriction enzyme Ddel produced a specific RFLP pattern for each microorganism studied. Sixty cultures of fungemia agents (selected from the culture collection of Fundação de Medicina Tropical do Amazonas - FMTAM were correctly identified by PCR/RFLP using the prime pair NL4/ITS5 and Ddel. We conclude that the method proved to be both simple and reproducible, and may offer potential advantages over phenotyping methods.

  13. Isolation and characterization of anti c-met single chain fragment variable (scFv) antibodies.

    Science.gov (United States)

    Qamsari, Elmira Safaie; Sharifzadeh, Zahra; Bagheri, Salman; Riazi-Rad, Farhad; Younesi, Vahid; Abolhassani, Mohsen; Ghaderi, Sepideh Safaei; Baradaran, Behzad; Somi, Mohammad Hossein; Yousefi, Mehdi

    2017-12-01

    The receptor tyrosine kinase (RTK) Met is the cell surface receptor for hepatocyte growth factor (HGF) involved in invasive growth programs during embryogenesis and tumorgenesis. There is compelling evidence suggesting important roles for c-Met in colorectal cancer proliferation, migration, invasion, angiogenesis, and survival. Hence, a molecular inhibitor of an extracellular domain of c-Met receptor that blocks c-Met-cell surface interactions could be of great thera-peutic importance. In an attempt to develop molecular inhibitors of c-Met, single chain variable fragment (scFv) phage display libraries Tomlinson I + J against a specific synthetic oligopeptide from the extracellular domain of c-Met receptor were screened; selected scFv were then characterized using various immune techniques. Three c-Met specific scFv (ES1, ES2, and ES3) were selected following five rounds of panning procedures. The scFv showed specific binding to c-Met receptor, and significantly inhibited proliferation responses of a human colorectal carcinoma cell line (HCT-116). Moreover, anti- apoptotic effects of selected scFv antibodies on the HCT-116 cell line were also evaluated using Annexin V/PI assays. The results demonstrated rates of apoptotic cell death of 46.0, 25.5, and 37.8% among these cells were induced by use of ES1, ES2, and ES3, respectively. The results demonstrated ability to successfully isolate/char-acterize specific c-Met scFv that could ultimately have a great therapeutic potential in immuno-therapies against (colorectal) cancers.

  14. Urine of patients with early prostate cancer contains lower levels of light chain fragments of inter-alpha-trypsin inhibitor and saposin B but increased expression of an inter-alpha-trypsin inhibitor heavy chain 4 fragment.

    Science.gov (United States)

    Jayapalan, Jaime J; Ng, Keng L; Shuib, Adawiyah S; Razack, Azad H A; Hashim, Onn H

    2013-06-01

    The present study was aimed at the identification of proteins that are differentially expressed in the urine of patients with prostate cancer (PCa), those with benign prostatic hyperplasia (BPH) and age-matched healthy male control subjects. Using a combination of 2DE and MS/MS, significantly lower expression of urinary saposin B and two different fragments of inter-alpha-trypsin inhibitor light chain (ITIL) was demonstrated in the PCa patients compared to the controls. However, only one of the ITIL fragments was significantly different between the PCa and BPH patients. When image analysis was performed on urinary proteins that were transferred onto NC membranes and detected using a lectin that binds to O-glycans, a truncated fragment of inter-alpha-trypsin inhibitor heavy chain 4 was the sole protein found to be significantly enhanced in the PCa patients compared to the controls. Together, these urinary peptide fragments might be useful complementary biomarkers to indicate PCa as well as to distinguish it from BPH, although further epidemiological evidence on the specificity and sensitivity of the protein candidates is required. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. The Fate of Priority Areas for Conservation in Protected Areas: A Fine-Scale Markov Chain Approach

    Science.gov (United States)

    Tattoni, Clara; Ciolli, Marco; Ferretti, Fabrizio

    2011-02-01

    Park managers in alpine areas must deal with the increase in forest coverage that has been observed in most European mountain areas, where traditional farming and agricultural practices have been abandoned. The aim of this study is to develop a fine-scale model of a broad area to support the managers of Paneveggio Nature Park (Italy) in conservation planning by focusing on the fate of priority areas for conservation in the next 50-100 years. GIS analyses were performed to assess the afforestation dynamic over time using two historical maps (from 1859 and 1936) and a series of aerial photographs and ortho-photos (taken from 1954 to 2006) covering a time span of 150 years. The results show an increase in the forest surface area of about 35%. Additionally, the forest became progressively more compact and less fragmented, with a consequent loss of ecotones and open habitats that are important for biodiversity. Markov chain-cellular automata models were used to project future changes, evaluating the effects on a habitat scale. Simulations show that some habitats defined as priority by the EU Habitat Directive will be compromised by the forest expansion by 2050 and suffer a consistent loss by 2100. This protocol, applied to other areas, can be used for designing long-term management measures with a focus on habitats where conservation status is at risk.

  16. Detailed balance, internal consistency, and energy conservation in fragment orbital-based surface hopping

    Science.gov (United States)

    Carof, Antoine; Giannini, Samuele; Blumberger, Jochen

    2017-12-01

    We have recently introduced an efficient semi-empirical non-adiabatic molecular dynamics method for the simulation of charge transfer/transport in molecules and molecular materials, denoted fragment orbital-based surface hopping (FOB-SH) [J. Spencer et al., J. Chem. Phys. 145, 064102 (2016)]. In this method, the charge carrier wavefunction is expanded in a set of charge localized, diabatic electronic states and propagated in the time-dependent potential due to classical nuclear motion. Here we derive and implement an exact expression for the non-adiabatic coupling vectors between the adiabatic electronic states in terms of nuclear gradients of the diabatic electronic states. With the non-adiabatic coupling vectors (NACVs) available, we investigate how different flavours of fewest switches surface hopping affect detailed balance, internal consistency, and total energy conservation for electron hole transfer in a molecular dimer with two electronic states. We find that FOB-SH satisfies detailed balance across a wide range of diabatic electronic coupling strengths provided that the velocities are adjusted along the direction of the NACV to satisfy total energy conservation upon a surface hop. This criterion produces the right fraction of energy-forbidden (frustrated) hops, which is essential for correct population of excited states, especially when diabatic couplings are on the order of the thermal energy or larger, as in organic semiconductors and DNA. Furthermore, we find that FOB-SH is internally consistent, that is, the electronic surface population matches the average quantum amplitudes, but only in the limit of small diabatic couplings. For large diabatic couplings, inconsistencies are observed as the decrease in excited state population due to frustrated hops is not matched by a corresponding decrease in quantum amplitudes. The derivation provided here for the NACV should be generally applicable to any electronic structure approach where the electronic

  17. Results Chains: a Tool for Conservation Action Design, Management, and Evaluation

    Directory of Open Access Journals (Sweden)

    Richard Margoluis

    2013-09-01

    Full Text Available Every day, the challenges to achieving conservation grow. Threats to species, habitats, and ecosystems multiply and intensify. The conservation community has invested decades of resources and hard work to reduce or eliminate these threats. However, it struggles to demonstrate that its efforts are having an impact. In recent years, conservation project managers, teams, and organizations have found themselves under increasing pressure to demonstrate measurable impacts that can be attributed to their actions. To do so, they need to answer three important questions: (1 Are we achieving our desired impact?; (2 Have we selected the best interventions to achieve our desired impact?; and (3 Are we executing our interventions in the best possible manner? We describe results chains, an important tool for helping teams clearly specify their theory of change behind the actions they are implementing. Results chains help teams make their assumptions behind an action explicit and positions the team to develop relevant objectives and indicators to monitor and evaluate whether their actions are having the intended impact. We describe this tool and how it is designed to tackle the three main questions above. We also discuss the purposes for which results chains have been used and the implications of their use. By using results chains, the conservation community can learn, adapt, and improve at a faster pace and, consequently, better address the ongoing threats to species, habitats, and ecosystems.

  18. SINGLE CHAIN VARIABLE FRAGMENTS OF ANTIBODIES AGAINST DIPHTHERIA TOXIN B-SUBUNIT ISOLATED FROM PHAGE DISPLAY HUMAN ANTIBODY LIBRARY

    Directory of Open Access Journals (Sweden)

    Oliinyk O. S.

    2014-02-01

    Full Text Available Diphtheria toxin is an exoantigen of Corynebacterium diphtheriae that inhibits protein synthesis and kills sensitive cells. The aim of this study was to obtain human recombinant single-chain variable fragment (scFv antibodies against receptor-binding B subunit of diphtheria toxin. 12 specific clones were selected after three rounds of a phage display naїve (unimmunized human antibody library against recombinant B-subunit. scFv DNA inserts from these 12 clones were digested with MvaI, and 6 unique restriction patterns were found. Single-chain antibodies were expressed in Escherichia coli XL1-blue. The recombinant proteins were characterized by immunoblotting of bacterial extracts and detection with an anti-E-tag antibody. The toxin B-subunit-binding function of the single-chain antibody was shown by ELISA. The affinity constants for different clones were found to be from 106 to 108 М–1. Due to the fact, that these antibody fragments recognized epitopes in the receptor-binding Bsubunit of diphtheria toxin, further studies are interesting to evaluate their toxin neutralization properties and potential for therapeutic applications. Obtained scFv-antibodies can also be used for detection and investigation of biological properties of diphtheria toxin.

  19. Habitat fragmentation and interspecific competition: Implications for lynx conservation [Chapter 4

    Science.gov (United States)

    Steven W. Buskirk

    2000-01-01

    Habitat fragmentation and interspecific competition are two important forces that potentially affect lynx populations. Fragmentation operates by various mechanisms, including direct habitat loss, vehicle collisions and behavioral disturbance from roads, and changes in landscape features such as edges. Competition takes two forms: Exploitation competition involves...

  20. Conservation among vertebrate immunoglobulin chains detected by antibodies to a synthetic joining segment peptide.

    Science.gov (United States)

    Schluter, S F; Rosenshein, I L; Hubbard, R A; Marchalonis, J J

    1987-06-15

    We used affinity purified antibodies produced against a synthetic peptide sequence corresponding to the entire J beta of a human T cell receptor gene to screen sera of man, mouse and other vertebrates to determine the presence of cross-reactive molecules. Little evidence for free alpha/beta heterodimers was found, but the antibody reacted with light chains of many vertebrate species, including characterized myeloma proteins of man and mouse. Some vertebrate orders, notably Aves, lacked polypeptide chains cross-reactive with J beta, but detectable determinants occurred in primitive vertebrates such as the galapagos shark (Carcharhinus galapagensis). In addition to the strong cross-reaction with purified light chains, human heavy chains reacted weakly with the antibody. The cross-reaction correlated with the sequence of the denatured immunoglobulins and was inhibitable with free peptide. These results establish the similarity of T cell receptor beta chains to immunoglobulin chains and support the conclusion that J region sequences were conserved, not only within mammalian immunoglobulins and T cell receptors, but in vertebrate evolution.

  1. A novel variable antibody fragment dimerized by leucine zippers with enhanced neutralizing potency against rabies virus G protein compared to its corresponding single-chain variable antibody fragment.

    Science.gov (United States)

    Li, Zhuang; Cheng, Yue; Xi, Hualong; Gu, Tiejun; Yuan, Ruosen; Chen, Xiaoxu; Jiang, Chunlai; Kong, Wei; Wu, Yongge

    2015-12-01

    Fatal rabies can be prevented effectively by post-exposure prophylactic (PEP) with rabies immunoglobulin (RIG). Single-chain variable fragments (scFv), which are composed of a variable heavy chain (VH) and a variable light chain (VL) connected by a peptide linker, can potentially be used to replace RIG. However, in our previous study, a scFv (scFV57S) specific for the rabies virus (RV) G protein showed a lower neutralizing potency than that of its parent IgG due to lower stability and altered peptide assembly pattern. In monoclonal antibodies, the VH and VL interact non-covalently, while in scFvs the VH is connected covalently with the VL by the artificial linker. In this study, we constructed and expressed two peptides 57VL-JUN-HIS and 57VH-FOS-HA in Escherichia coli. The well-known Fos and Jun leucine zippers were utilized to dimerize VH and VL similarly to the IgG counterpart. The two peptides assembled to form zipFv57S in vitro. Due to the greater similarity in structure with IgG, the zipFv57S protein showed a higher binding ability and affinity resulting in notable improvement of in vitro neutralizing activity over its corresponding scFv. The zipFv57S protein was also found to be more stable and showed similar protective rate as RIG in mice challenged with a lethal dose of RV. Our results not only indicated zipFv57S as an ideal alternative for RIG in PEP but also offered a novel and efficient hetero-dimerization pattern of VH and VL leading to enhanced neutralizing potency. Copyright © 2015. Published by Elsevier Ltd.

  2. Human Islet Amyloid Polypeptide N-Terminus Fragment Self-Assembly: Effect of Conserved Disulfide Bond on Aggregation Propensity

    Science.gov (United States)

    Ilitchev, Alexandre I.; Giammona, Maxwell J.; Do, Thanh D.; Wong, Amy G.; Buratto, Steven K.; Shea, Joan-Emma; Raleigh, Daniel P.; Bowers, Michael T.

    2016-06-01

    Amyloid formation by human islet amyloid polypeptide (hIAPP) has long been implicated in the pathogeny of type 2 diabetes mellitus (T2DM) and failure of islet transplants, but the mechanism of IAPP self-assembly is still unclear. Numerous fragments of hIAPP are capable of self-association into oligomeric aggregates, both amyloid and non-amyloid in structure. The N-terminal region of IAPP contains a conserved disulfide bond between cysteines at position 2 and 7, which is important to hIAPP's in vivo function and may play a role in in vitro aggregation. The importance of the disulfide bond in this region was probed using a combination of ion mobility-based mass spectrometry experiments, molecular dynamics simulations, and high-resolution atomic force microscopy imaging on the wildtype 1-8 hIAPP fragment, a reduced fragment with no disulfide bond, and a fragment with both cysteines at positions 2 and 7 mutated to serine. The results indicate the wildtype fragment aggregates by a different pathway than either comparison peptide and that the intact disulfide bond may be protective against aggregation due to a reduction of inter-peptide hydrogen bonding.

  3. Deforestation and fragmentation of natural forests in the upper Changhua watershed, Hainan, China: implications for biodiversity conservation.

    Science.gov (United States)

    Zhai, De-Li; Cannon, Charles H; Dai, Zhi-Cong; Zhang, Cui-Ping; Xu, Jian-Chu

    2015-01-01

    Hainan, the largest tropical island in China, belongs to the Indo-Burma biodiversity hotspot. The Changhua watershed is a center of endemism for plants and birds and the cradle of Hainan's main rivers. However, this area has experienced recent and ongoing deforestation and habitat fragmentation. To quantify habitat loss and fragmentation of natural forests, as well as the land-cover changes in the Changhua watershed, we analyzed Landsat images obtained in 1988, 1995, and 2005. Land-cover dynamics analysis showed that natural forests increased in area (97,909 to 104,023 ha) from 1988 to 1995 but decreased rapidly to 76,306 ha over the next decade. Rubber plantations increased steadily throughout the study period while pulp plantations rapidly expanded after 1995. Similar patterns of land cover change were observed in protected areas, indicating a lack of enforcement. Natural forests conversion to rubber and pulp plantations has a general negative effect on biodiversity, primarily through habitat fragmentation. The fragmentation analysis showed that natural forests area was reduced and patch number increased, while patch size and connectivity decreased. These land-cover changes threatened local biodiversity, especially island endemic species. Both natural forests losses and fragmentation should be stopped by strict enforcement to prevent further damage. Preserving the remaining natural forests and enforcing the status of protected areas should be a management priority to maximize the watershed's biodiversity conservation value.

  4. Photoluminescent silicon nanocrystal-polymer hybrid materials via surface initiated reversible addition-fragmentation chain transfer (RAFT) polymerization

    Science.gov (United States)

    Höhlein, Ignaz M. D.; Werz, Patrick D. L.; Veinot, Jonathan G. C.; Rieger, Bernhard

    2015-04-01

    Silicon-polymer core-shell hybrid materials are obtained via surface initiated reversible addition-fragmentation chain transfer (RAFT) polymerization from photoluminescent silicon nanocrystals (SiNCs). Polymer grafted SiNCs and free polymers in solution are separated using ultracentrifugation. The polymerization on the surface proceeds in a living manner which is confirmed via GPC, DLS and TGA measurements. This method was applied to various other monomers. The obtained materials all show bright red photoluminescence originating from the SiNC core.

  5. Carprofen-imprinted monolith prepared by reversible addition-fragmentation chain transfer polymerization in room temperature ionic liquids.

    Science.gov (United States)

    Ban, Lu; Han, Xu; Wang, Xian-Hua; Huang, Yan-Ping; Liu, Zhao-Sheng

    2013-10-01

    To obtain fast separation, ionic liquids were used as porogens first in combination with reversible addition-fragmentation chain transfer (RAFT) polymerization to prepare a new type of molecularly imprinted polymer (MIP) monolith. The imprinted monolithic column was synthesized using a mixture of carprofen (template), 4-vinylpyridine, ethylene glycol dimethacrylate, [BMIM]BF4, and chain transfer agent (CTA). Some polymerization factors, such as template-monomer molar ratio, the degree of crosslinking, the composition of the porogen, and the content of CTA, on the column efficiency and imprinting effect of the resulting MIP monolith were systematically investigated. Affinity screening of structurally similar compounds with the template can be achieved in 200 s on the MIP monolith due to high column efficiency (up to 12,070 plates/m) and good column permeability. Recognition mechanism of the imprinted monolith was also investigated.

  6. The effect of varying the peptide linker length in a single chain variable fragment antibody against wogonin glucuronide.

    Science.gov (United States)

    Paudel, Madan Kumar; Sakamoto, Seiichi; Van Huy, Le; Tanaka, Hiroyuki; Miyamoto, Tomofumi; Morimoto, Satoshi

    2017-06-10

    Peptide linkers of three different lengths were constructed to join the variable regions of the heavy chain (VH) and the light chain (VL) in a single-chain variable fragment antibody (scFv) specific for wogonin glucuronide (Wgn) that has the structure VH-(GGGGS) n -VL (n=3, 5, or 7). The scFv antibodies, which were expressed in Escherichia coli, were derived from an anti-Wgn monoclonal antibody (315A). An indirect competitive enzyme-linked immunosorbent assay (icELISA) was used to evaluate their reactivity and sensitivity, which is also used for quantitative analysis of Wgn. Our results, showed that the reactivity and specificity of the three different scFvs were, in fact, similar. Subsequently, the scFv having a VH-(GGGGS) 3 -VL linker which was slightly better that other two scFvs against Wgn, was applied to indirect competitive ELISA (icELISA) to analyze Scutellariae Radix (S. Radix). The utility of the icELISA was demonstrated for quality control and analysis of S. Radix in this report. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Population genetics data help to guide the conservation of palm species with small population sizes and fragmented habitats in Madagascar.

    Science.gov (United States)

    Gardiner, Lauren M; Rakotoarinivo, Mijoro; Rajaovelona, Landy R; Clubbe, Colin

    2017-01-01

    The need to incorporate genetic data into conservation management decisions is increasingly recognised. However, many published studies represent a 'gold standard' of sampling, techniques, and analyses. Such rigour is often not possible with limited funding and resourcing available for developing plans for the increasing number of threatened species requiring conservation management. Two endemic palm species of the Itremo Massif in central Madagascar, Dypsis ambositrae and D. decipiens, are known to be threatened with extinction and conservation management for these species is a priority for the newly created protected area in the region. The genetic diversity of these two species was studied using the relatively low-cost and rapid AFLP technique. DNA fragments generated using three primer combinations were analysed for 20 and 50 individuals of the two species, respectively, from across their ranges. Genetic diversity was relatively low for both species. The two sites where the highly restricted D. ambositrae grows were found to be genetically distinct (although overall heterozygosity was low). Despite having a much wider distribution and relatively large population, D. decipiens did not show clear geographical nor genetic groupings and had similarly low genetic heterozygosity to D. ambositrae. With so few individuals remaining in the wild and two genetically distinct subpopulations, it is recommended that both sites of D. ambositrae are conserved and that seed are collected from both for ex situ conservation and potential future reintroduction. It may be less important to focus resources on conserving or collecting ex situ material from all sites where D. decipiens is found, as the genetic diversity represented by each subpopulation is limited and increasing sampling may not protect significantly higher levels of genetic diversity. This study provides data that inform and support conservation decisions taken for both species within this region, and in the

  8. Climate change meets habitat fragmentation: linking landscape and biogeographical scale levels in research and conservation

    NARCIS (Netherlands)

    Opdam, P.F.M.; Wascher, D.M.

    2004-01-01

    Climate change and habitat fragmentation are considered key pressures on biodiversity. In this paper we explore the potential synergetic effects between these factors. We argue that processes at two levels of spatial scale interact: the metapopulation level and the species range level. Current

  9. Expression and Functional Properties of an Anti-Triazophos High-Affinity Single-Chain Variable Fragment Antibody with Specific Lambda Light Chain

    Directory of Open Access Journals (Sweden)

    Rui Liu

    2016-06-01

    Full Text Available Triazophos is a widely used organophosphorous insecticide that has potentially adverse effects to organisms. In the present study, a high-affinity single-chain variable fragment (scFv antibody with specific lambda light chain was developed for residue monitoring. First, the specific variable regions were correctly amplified from a hybridoma cell line 8C10 that secreted monoclonal antibody (mAb against triazophos. The regions were then assembled as scFv via splicing by overlap extension polymerase chain reaction. Subsequently, the recombinant anti-triazophos scFv-8C10 was successfully expressed in Escherichia coli strain HB2151 in soluble form, purified through immobilized metal ion affinity chromatography, and verified via Western blot and peptide mass fingerprinting analyses. Afterward, an indirect competitive enzyme-linked immunosorbent assay was established based on the purified anti-triazophos scFv-8C10 antibody. The assay exhibited properties similar to those based on the parent mAb, with a high sensitivity (IC50 of 1.73 ng/mL to triazophos and no cross reaction for other organophosphorus pesticides; it was reliable in detecting triazophos residues in spiked water samples. Moreover, kinetic measurement using a surface plasmon resonance biosensor indicated that the purified scFv-8C10 antibody had a high affinity of 1.8 × 10−10 M and exhibited good binding stability. Results indicated that the recombinant high-affinity scFv-8C10 antibody was an effective detection material that would be promising for monitoring triazophos residues in environment samples.

  10. Thermo-Responsive and Biocompatible Diblock Copolymers Prepared via Reversible Addition-Fragmentation Chain Transfer (RAFT Radical Polymerization

    Directory of Open Access Journals (Sweden)

    Kenichi Fukuda

    2014-03-01

    Full Text Available Poly(2-(methacryloyloxyethyl phosphorylcholine-b-poly(N,N-diethyl acrylamide (PMPCm-PDEAn was synthesized via reversible addition-fragmentation chain transfer (RAFT controlled radical polymerization. Below, the critical aggregation temperature (CAT the diblock copolymer dissolved in water as a unimer with a hydrodynamic radius (Rh of ca. 5 nm. Above the CAT the diblock copolymers formed polymer micelles composed of a PDEA core and biocompatible PMPC shells, due to hydrophobic self-aggregation of the thermo-responsive PDEA block. A fluorescence probe study showed that small hydrophobic small guest molecules could be incorporated into the core of the polymer micelle above the CAT. The incorporated guest molecules were released from the core into the bulk aqueous phase when the temperature decreased to values below the CAT because of micelle dissociation.

  11. Development of anti-CD47 single-chain variable fragment targeted magnetic nanoparticles for treatment of human bladder cancer.

    Science.gov (United States)

    Rezaei, Gashin; Habibi-Anbouhi, Mahdi; Mahmoudi, Morteza; Azadmanesh, Kayhan; Moradi-Kalbolandi, Shima; Behdani, Mahdi; Ghazizadeh, Leila; Abolhassani, Mohsen; Shokrgozar, Mohammad Ali

    2017-03-01

    To develop a novel anti-CD47 single-chain variable fragment (scFv) functionalized magnetic nanoparticles (MNPs) for targeting bladder cell lines and its applicability in thermotherapy. An immunized murine antibody phage display library was constructed and screened to isolate anti-CD47 binders. A scFv was selected and conjugated to MNPs which was then utilized to discriminate CD47+ bladder cells along with assessing its efficacy in thermotherapy. An scFv with high affinity to bladder cells was efficiently conjugated to MNPs. Following a hyperthermia treatment, the function of scFv-MNP conjugates led to a considerable reduction in cell viability. The anti-CD47 scFv-MNP conjugate was an effective cancer cell thermotherapy tool that might pave the way for development of bionano-based targeting techniques in both early detection and treatment of cancer.

  12. Construction of Recombinant Single Chain Variable Fragment (ScFv) Antibody Against Superantigen for Immunodetection Using Antibody Phage Display Technology.

    Science.gov (United States)

    Singh, Pawan Kumar; Agrawal, Ranu; Kamboj, D V; Singh, Lokendra

    2016-01-01

    Superantigens are a class of antigens that bind to the major histocompatibility complex class (MHC) II and T-cell receptor (TCR) and cause the nonspecific activation of T cells, resulting in a massive release of pro-inflammatory mediators. They are produced by the gram-positive organisms Staphylococcus aureus and Streptococcus pyogenes, and by a variety of other microbes such as viruses and mycoplasma, and cause toxic shock syndrome (TSS) and even death in some cases. The immunodetection of superantigens is difficult due to the polyclonal activation of T-cells leading to nonspecific antibody production. The production of recombinant monoclonal antibodies against superantigens can solve this problem and are far better than polyclonal antibodies in terms of detection. Here, we describe the construction of recombinant single chain variable fragments (ScFv) antibodies against superantigens with specific reference to SEB (staphylococcal enterotoxin B) using antibody phage display technology.

  13. Simplification of the synthesis of the reversible addition–fragmentation chain transfer agent 2-(2-cyanopropyl-dithiobenzoate

    Directory of Open Access Journals (Sweden)

    MILOŠ B. MILOVANOVIĆ

    2010-12-01

    Full Text Available The general literature procedure for the preparation of the reversible addition–fragmentation chain transfer (RAFT agent 2-(2-cyanopropyl-dithiobenzoate (CPDB was modified by omitting the recrystallisation of the intermediate di(thiobenzoyldisulphide. The yield of the CPDB in the simplified synthesis was increased four times compared to the standard one. The behaviour of the CPDB obtained by the modified procedure and by the standard one in the polymerisation of methyl methacrylate was investigated. The CPDB synthesized by the simplified procedure showed itself to be a good RAFT agent, giving excellent control over the polymerisation of methyl methacrylate and it behaved in the same manner as the CPDB prepared by the literature method. The obtained poly(methyl methacrylate had a narrow molecular weight distibution (PD = 1.1.

  14. A single-chain variable fragment intrabody prevents intracellular polymerization of Z α1-antitrypsin while allowing its antiproteinase activity

    Science.gov (United States)

    Ordóñez, Adriana; Pérez, Juan; Tan, Lu; Dickens, Jennifer A.; Motamedi-Shad, Neda; Irving, James A.; Haq, Imran; Ekeowa, Ugo; Marciniak, Stefan J.; Miranda, Elena; Lomas, David A.

    2015-01-01

    Mutant Z α1-antitrypsin (E342K) accumulates as polymers within the endoplasmic reticulum (ER) of hepatocytes predisposing to liver disease, whereas low levels of circulating Z α1-antitrypsin lead to emphysema by loss of inhibition of neutrophil elastase. The ideal therapy should prevent polymer formation while preserving inhibitory activity. Here we used mAb technology to identify interactors with Z α1-antitrypsin that comply with both requirements. We report the generation of an mAb (4B12) that blocked α1-antitrypsin polymerization in vitro at a 1:1 molar ratio, causing a small increase of the stoichiometry of inhibition for neutrophil elastase. A single-chain variable fragment (scFv) intrabody was generated based on the sequence of mAb4B12. The expression of scFv4B12 within the ER (scFv4B12KDEL) and along the secretory pathway (scFv4B12) reduced the intracellular polymerization of Z α1-antitrypsin by 60%. The scFv4B12 intrabody also increased the secretion of Z α1-antitrypsin that retained inhibitory activity against neutrophil elastase. MAb4B12 recognized a discontinuous epitope probably located in the region of helices A/C/G/H/I and seems to act by altering protein dynamics rather than binding preferentially to the native state. This novel approach could reveal new target sites for small-molecule intervention that may block the transition to aberrant polymers without compromising the inhibitory activity of Z α1-antitrypsin.—Ordóñez, A., Pérez, J., Tan, L., Dickens, J. A., Motamedi-Shad, N., Irving, J. A., Haq, I., Ekeowa, U., Marciniak, S. J., Miranda, E., Lomas, D. A. A single-chain variable fragment intrabody prevents intracellular polymerization of Z α1-antitrypsin while allowing its antiproteinase activity. PMID:25757566

  15. Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis.

    Science.gov (United States)

    Samah, S; Valadez-Moctezuma, E; Peláez-Luna, K S; Morales-Manzano, S; Meza-Carrera, P; Cid-Contreras, R C

    2016-06-03

    Molecular methods are powerful tools in characterizing and determining relationships between plants. The aim of this study was to study genetic divergence between 103 accessions of Mexican Opuntia. To accomplish this, polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of three chloroplast intergenic spacers (atpB-rbcL, trnL-trnF, and psbA-trnH), one chloroplast gene (ycf1), two nuclear genes (ppc and PhyC), and one mitochondrial gene (cox3) was conducted. The amplified products from all the samples had very similar molecular sizes, and there were only very small differences between the undigested PCR amplicons for all regions, with the exception of ppc. We obtained 5850 bp from the seven regions, and 136 fragments were detected with eight enzymes, 37 of which (27.2%) were polymorphic. We found that 40% of the fragments from the chloroplast regions were polymorphic, 9.8% of the bands detected in the nuclear genes were polymorphic, and 20% of the bands in the mitochondrial locus were polymorphic. trnL-trnF and psbA-trnH were the most variable regions. The Nei and Li/Dice distance was very short, and ranged from 0 to 0.12; indeed, 77 of the 103 genotypes had the same genetic profile. All the xoconostle accessions (acidic fruits) were grouped together without being separated from three genotypes of prickly pear (sweet fruits). We assume that the genetic divergence between prickly pears and xoconostles is very low, and question the number of Opuntia species currently considered in Mexico.

  16. Molecular differentiation of Angiostrongylus costaricensis, A. cantonensis, and A. vasorum by polymerase chain reaction- restriction fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Caldeira Roberta L

    2003-01-01

    Full Text Available Angiostrongylus cantonensis, A. costaricensis, and A. vasorum are etiologic agents of human parasitic diseases. Their identification, at present, is only possible by examining the adult worm after a 40-day period following infection of vertebrate hosts with the third-stage larvae. In order to obtain a diagnostic tool to differentiate larvae and adult worm from the three referred species, polymerase chain reaction-restriction fragment length polymorphism was carried out. The rDNA second internal transcribed spacer (ITS2 and mtDNA cytochrome oxidase I regions were amplified, followed by digestion of fragments with the restriction enzymes RsaI, HapII, AluI, HaeIII, DdeI and ClaI. The enzymes RsaI and ClaI exhibited the most discriminating profiles for the differentiation of the regions COI of mtDNA and ITS2 of rDNA respectively. The methodology using such regions proved to be efficient for the specific differentiation of the three species of Angiostrongylus under study.

  17. Morphological and polymerase chain reaction-restriction fragment lenght polymorphism characterization of Biomphalaria kuhniana and Biomphalaria amazonica from Colombia

    Directory of Open Access Journals (Sweden)

    Luz E Velásquez

    2002-10-01

    Full Text Available In Colombia, five Biomphalaria planorbid species are known: B. kuhniana, B. straminea, B. peregrina, B. canonica and B. oligoza(var. B. philippiana. Among them, B. straminea is intermediate host of Schistosoma mansoni and B. peregrina has been found to be experimentally susceptible to this parasite. B. straminea is commonly confused with B. kuhniana and they have been clustered together with B. intermedia in the complex named B. straminea. The difficulties involved in the specific identification, based on morphological data, have motivated the use of new techniques as auxiliary tools in cases of inconclusive morphological identification of such planorbid. In the present study, five Biomphalaria populations from the Colombian Amazon region and from Interandian Valleys were morphologically identified and characterized by polymerase chain reaction-restriction fragment lenght polymorphism directed at the internal transcribed spacer region of the rRNA gene, followed by digestion of the generated fragment with restriction enzymes (DdeI, AluI, RsaI, MvaI and HaeIII. Known profiles of the Brazilian species B. straminea, B. peregrina, B. kuhniana, B. intermedia and B. amazonica, besides B. kuhniana from Colombia, were used for comparison. The five populations under study were morphologically and molecularly identified as B. kuhniana and B. amazonica.

  18. Selection of single chain antibody fragments binding to the extracellular domain of 4-1BB receptor by phage display technology.

    Science.gov (United States)

    Bagheri, Salman; Yousefi, Mehdi; Safaie Qamsari, Elmira; Riazi-Rad, Farhad; Abolhassani, Mohsen; Younesi, Vahid; Dorostkar, Ruhollah; Movassaghpour, Ali Akbar; Sharifzadeh, Zahra

    2017-03-01

    The 4-1BB is a surface glycoprotein that pertains to the tumor necrosis factor-receptor family. There is compelling evidence suggesting important roles for 4-1BB in the immune response, including cell activation and proliferation and also cytokine induction. Because of encouraging results of different agonistic monoclonal antibodies against 4-1BB in the treatment of cancer, infectious, and autoimmune diseases, 4-1BB has been suggested as an attractive target for immunotherapy. In this study, single chain variable fragment phage display libraries, Tomlinson I+J, were screened against specific synthetic oligopeptides (peptides I and II) designed from 4-1BB extracellular domain. Five rounds of panning led to selection of four 4-1BB specific single chain variable fragments (PI.12, PI.42, PII.16, and PII.29) which showed specific reaction to relevant peptides in phage enzyme-linked immunosorbent assay. The selected clones were successfully expressed in Escherichia coli Rosetta-gami 2, and their expression was confirmed by western blot analysis. Enzyme-linked immunosorbent assay experiments indicated that these antibodies were able to specifically recognize 4-1BB without any cross-reactivity with other antigens. Flow cytometry analysis demonstrated an acceptable specific binding of the single chain variable fragments to 4-1BB expressed on CCRF-CEM cells, while no binding was observed with an irrelevant antibody. Anti-4-1BB single chain variable fragments enhanced surface CD69 expression and interleukin-2 production in stimulated CCRF-CEM cells which confirmed the agonistic effect of the selected single chain variable fragments. The data from this study have provided a rationale for further experiments involving the biological functions of anti-4-1BB single chain variable fragments in future studies.

  19. Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin

    Energy Technology Data Exchange (ETDEWEB)

    Ecale Zhou, C L; Zemla, A T; Roe, D; Young, M; Lam, M; Schoeniger, J; Balhorn, R

    2005-01-29

    Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers, or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting. We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set of ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context, and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A we identified a conserved/unique pocket in close proximity (but not overlapping) the active site that is suitable for bi-dentate ligand development. These methods are generally applicable to identification of surface epitopes and binding pockets for development of diagnostic reagents, therapeutics, and vaccines.

  20. Self-assembly of block copolymer micelles: synthesis via reversible addition-fragmentation chain transfer polymerization and aqueous solution properties.

    Science.gov (United States)

    Mya, Khine Y; Lin, Esther M J; Gudipati, Chakravarthy S; Gose, Halima B A S; He, Chaobin

    2010-07-22

    Poly(hexafluorobutyl methacrylate) (PHFBMA) homopolymer was synthesized by reversible addition-fragmentation chain transfer (RAFT)-mediated living radical polymerization in the presence of cyano-2-propyl dithiobenzoate (CPDB) RAFT agent. A block copolymer of PHFBMA-poly(propylene glycol acrylate) (PHFBMA-b-PPGA) with dangling poly(propylene glycol) (PPG) side chains was then synthesized by using CPDB-terminated PHFBMA as a macro-RAFT agent. The amphiphilic properties and self-assembly of PHFBMA-b-PPGA block copolymer in aqueous solution were investigated by dynamic and static light scattering (DLS and SLS) studies, in combination with fluorescence spectroscopy and transmission electron microscopy (TEM). Although PPG shows moderately hydrophilic character, the formation of nanosize polymeric micelles was confirmed by fluorescence and TEM studies. The low value of the critical aggregation concentration exhibited that the tendency for the formation of copolymer aggregates in aqueous solution was very high due to the strong hydrophobicity of the PHFBMA(145)-b-PPGA(33) block copolymer. The combination of DLS and SLS measurements revealed the existence of micellar aggregates in aqueous solution with an association number of approximately 40 +/- 7 for block copolymer micelles. It was also found in TEM observation that there are 40-50 micelles accumulated into one aggregate and these micelles are loosely packed inside the aggregate.

  1. Early career: Templating of liquid crystal microstructures by reversible addition-fragmentation chain transfer polymerization

    Energy Technology Data Exchange (ETDEWEB)

    Heinen, Jennifer M. (O' Donnell) [Iowa State Univ., Ames, IA (United States)

    2014-12-31

    This research has shown that the microstructure of self-assembled copolymers can be decoupled from the polymer chemistry. The simplest polymer architecture, linear block copolymers, is valuable for a broad range of applications, including adhesives and coatings, medical devices, electronics and energy storage, because these block copolymers reproducibly self-assemble into microphase separated nanoscale domains. Unfortunately, the self-assembled microstructure is tuned by polymer composition, thus limiting the potential to simultaneously optimize chemical, mechanical, and transport properties for desired applications. To this end, much work was been put into manipulating block copolymer self-assembly independently of polymer composition. These efforts have included the use of additives or solvents to alter polymer chain conformation, the addition of a third monomer to produce ABC triblock terpolymers, architectures with mixed blocks, such as tapered/gradient polymers, and the synthesis of other nonlinear molecular architectures. This work has shown that the microstructures formed by linear ABC terpolymers can be altered by controlling the architecture of the polymer molecules at a constant monomer composition, so that the microstructure is tuned independently from the chemical properties.

  2. [Construction and application of a lentiviral vector of single-chain variable fragment antibody against human hepatocyte growth factor receptor].

    Science.gov (United States)

    Chen, Yonghua; Guo, Jia; Yin, Yanxin; Jiang, Ming; Zhu, Hongsheng; Zhang, Guodong; Li, Bingyu

    2014-09-01

    To construct a lentiviral expression vector carrying the single-chain variable fragment (scFv) antibody against human hepatocyte growth factor receptor (HGFR), express it in transfected HEK293 cells, and observe its biological function of specific binding to antigen. The variable regions of the heavy chain (VH) and light chain (VL) genes were amplified directly from the cDNA of hybridoma cell line 8E8 secreting mouse anti-human HGFR antibody and assembled using the splice overlap extension-PCR (SOE-PCR). The constructed HGFR-scFv gene with the signal peptide SP-VH-linker-VL was ligated into the cloning vector pCR-Blunt. After cut off from pCR-Blunt using enzyme digestion, HGFR-scFv gene was subcloned into the lentiviral transfer vector pRRL-CMV, which was identified by the restriction enzyme digestion and sequencing. The lentiviral expression vector pRRL HGFR-scFv was then tansfected together with the packaging plasmids into HEK293T cells to obtain virus particles, and green fluorescent protein (GFP) expression was detected under a fluorescent microscope. Then the virus particles were used to infect HEK293 cells. The scFv expression was detected by RT-PCR and its biological affinity as antibody was measured by ELISA. The lentiviral expression vector pRRL HGFR-scFv was constructed correctly. After HEK293T cells were transfected with the pRRL HGFR-scFv plasmid, the GFP was visible. After HEK293 cells were infected with virus particles, the scFv antibody expressed could bind to HGFR specifically. The lentiviral expression vector of HGFR-scFv was constructed successfully, which would help to study the important role of HGFR in following experiments.

  3. Restriction fragment length polymorphism analysis shows that the hippuricase gene of Campylobacter jejuni is highly conserved.

    Science.gov (United States)

    Slater, E R; Owen, R J

    1997-10-01

    A 1151-bp amplicon containing the hippuricase (hipO) gene was obtained from 118 strains of Campylobacter jejuni and double-digested with AluI and DdeI to give five different PCR-RFLP patterns. Most strains had the six-banded profile predicted from sequence data. Lack of polymorphisms within the hipO gene indicated it was highly conserved amongst strains of Camp.jejuni, and the RFLP analysis provided only low discrimination as an epidemiological typing method. Detection of hipO by PCR provided a useful test for confirmatory identification of Camp. jejuni.

  4. Generation and characterization of a human single-chain fragment variable (scFv antibody against cytosine deaminase from Yeast

    Directory of Open Access Journals (Sweden)

    Tombesi Marina

    2008-09-01

    Full Text Available Abstract Background The ability of cytosine deaminase (CD to convert the antifungal agent 5-fluorocytosine (5-FC into one of the most potent and largely used anticancer compound such as 5-fluorouracil (5-FU raised considerable interest in this enzyme to model gene or antibody – directed enzyme-prodrug therapy (GDEPT/ADEPT aiming to improve the therapeutic ratio (benefit versus toxic side-effects of cancer chemotherapy. The selection and characterization of a human monoclonal antibody in single chain fragment (scFv format represents a powerful reagent to allow in in vitro and in vivo detection of CD expression in GDEPT/ADEPT studies. Results An enzymatic active recombinant CD from yeast (yCD was expressed in E. coli system and used as antigen for biopanning approach of the large semi-synthetic ETH-2 antibody phage library. Several scFvs were isolated and specificity towards yCD was confirmed by Western blot and ELISA. Further, biochemical and functional investigations demonstrated that the binding of specific scFv with yCD did not interfere with the activity of the enzyme in converting 5-FC into 5-FU. Conclusion The construction of libraries of recombinant antibody fragments that are displayed on the surface of filamentous phage, and the selection of phage antibodies against target antigens, have become an important biotechnological tool in generating new monoclonal antibodies for research and clinical applications. The scFvH5 generated by this method is the first human antibody which is able to detect yCD in routinary laboratory techniques without interfering with its enzymatic function.

  5. Preparation of a monolithic cation-exchange material with hydrophilic external layers by two-step reversible addition-fragmentation chain transfer polymerization.

    Science.gov (United States)

    Lin, Shen; Zhang, Yingying; Huang, Wei; Dong, Xiangchao

    2017-04-01

    In recent years, the efficient analysis of biological samples has become more important due to the advances of life science and pharmaceutical research and practice. Because biological sample pretreatment is the bottleneck for fast process, material development for efficient sample process in the high-performance liquid chromatography analysis is highly desirable. In this research, a cation-exchange restricted access monolithic column was synthesized by a reversible addition-fragmentation chain transfer polymerization method. Utilizing the controlled/living property of the reversible addition-fragmentation chain transfer method, a monolithic column of cross-linked poly(sulfopropyl methacrylate) was prepared first and then linear poly(glycerol mono-methacrylate) was immobilized covalently on the surface of the polymer. The monolithic material has both functionalities of cation-exchange and protein exclusion. Protein recovery of 94.6% was obtained after grafting of poly(glycerol mono-methacrylate) while the cation-exchange property of the column is still retained. In the study, the relation between the synthetic conditions and properties of the materials was studied. The synthesis conditions including the porogen, monomer concentration, and ratio of monomers/initiator/reversible addition-fragmentation chain transfer agent were optimized. The study provided a method for the preparation of restricted access monolithic columns: a bifunctional material by reversible addition-fragmentation chain transfer polymerization method. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Characterisation of Toxoplasma gondii isolates using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) of the non-coding Toxoplasma gondii (TGR)-gene sequences

    DEFF Research Database (Denmark)

    Høgdall, Estrid; Vuust, Jens; Lind, Peter

    2000-01-01

    of using TGR gene variants as markers to distinguish among T. gondii isolates from different animals and different geographical sources. Based on the band patterns obtained by restriction fragment length polymorphism (RFLP) analysis of the polymerase chain reaction (PCR) amplified TGR sequences, the T...

  7. Production of bifunctional proteins by Aspergillus awamori: Llama variable heavy chain antibody fragment (VHH) R9 coupled to Arthromyces ramosus peroxidase (ARP)

    NARCIS (Netherlands)

    Joosten, V.; Roelofs, M.S.; Dries, N. van den; Goosen, T.; Verrips, C.T.; Hondel, C.A.M.J.J. van den; Lokman, B.C.

    2005-01-01

    The Arthromyces ramosus peroxidase gene (arp) was genetically fused to either the 5′- or 3′-terminal ends of the gene encoding llama variable heavy chain antibody fragment VHH R9, resulting in the fusion expression cassettes ARP-R9 or R9-ARP. Aspergillus awamori transformants were obtained which

  8. Development of single chain variable fragment (scFv) antibodies against Xylella fastidiosa subsp. pauca by phage display.

    Science.gov (United States)

    Yuan, Qing; Jordan, Ramon; Brlansky, Ronald H; Istomina, Olga; Hartung, John

    2015-10-01

    Xylella fastidiosa is a member of the gamma proteobacteria. It is fastidious, insect-vectored and xylem-limited and causes a variety of diseases, some severe, on a wide range of economically important perennial crops, including grape and citrus. Antibody based detection assays are commercially available for X. fastidiosa, and are effective at the species, but not at the subspecies level. We have made a library of scFv antibody fragments directed against X. fastidiosa subsp. pauca strain 9a5c (citrus) by using phage display technology. Antibody gene repertoires were PCR-amplified using 23 primers for the heavy chain variable region (V(H)) and 21 primers for the light chain variable region (V(L)). The V(H) and V(L) were joined by overlap extension PCR, and then the genes of the scFv library were ligated into the phage vector pKM19. The library contained 1.2×10(7) independent clones with full-length scFv inserts. In each of 3cycles of affinity-selection with 9a5c, about 1.0×10(12) phage were used for panning with 4.1×10(6), 7.1×10(6), 2.1×10(7) phage recovered after the first, second and third cycles, respectively. Sixty-six percent of clones from the final library bound X. fastidiosa 9a5c in an ELISA. Some of these scFv antibodies recognized strain 9a5c and did not recognize X. fastidiosa strains that cause Pierce's disease of grapevine. Published by Elsevier B.V.

  9. Reversible addition-fragmentation chain transfer polymerization of N-isopropylacrylamide: a comparison between a conventional and a fast initiator.

    Science.gov (United States)

    Bouchékif, Hassen; Narain, Ravin

    2007-09-27

    The reversible addition-fragmentation chain transfer (RAFT) polymerization of N-isopropylacrylamide (NIPAM) was studied to determine the reasons for deviation of experimental molecular weights to lower molecular weight at high monomer conversion when S-1-dodecyl-S-(alpha,alpha'-dimethyl-alpha' '-acetic acid)trithiocarbonate (CTAm) and S,S-bis(alpha,alpha'-dimethyl-alpha' '-acetic acid)trithiocarbonate (CTAd) were used as RAFT agents at 65 degrees C. For this purpose, experiments were performed in N,N'-dimethylformamide (DMF) at the NIPAM/CTA ratio of 200 with initiators capable of yielding fast and slow initiation, respectively by photochemical and thermal process, either at ambient temperature or at 65 degrees C. When the polymerization of NIPAM was conducted under these conditions with Irgacure-2959 (IRGC) as photoinitiator, a continuing supply of primary radicals by incremental initiator addition was required to achieve reasonably high conversion. This effect was also apparent by the loss of linearity of the first-order kinetic plot with a conventional initiator (4,4-azobis(4-cyanovaleric acid) (ACVA) as azo-initiator, 10h (t1/2) decomposition at 65 degrees C) indicating that steady-state concentration of the macroradical decreases significantly with the initiator consumption. Nevertheless, polymers with predictable number-average molecular weight Mn (i.e., based on [monomer]/([CTA] + [initiator]) ratio) and narrow polydispersities were obtained (PDIs polymerization of NIPAM with the controlled process in the presence of CTA at 65 degrees C. Similar drift from the linear dependence Mn vs conversion was also observed at 65 degrees C when a significant number of low molecular weight polymer chains were generated intentionally by photodecomposition of IRGC.

  10. Functional Characterization of AAV-Expressed Recombinant Anti-VEGF Single-Chain Variable Fragments In Vitro.

    Science.gov (United States)

    Wimmer, Tobias; Lorenz, Birgit; Stieger, Knut

    2015-06-01

    Most retinal neovascular disorders are caused by upregulation of vascular endothelial growth factor (VEGF) expression. These disorders are treated with repeated injections of anti-VEGF molecules, which may have severe side effects. The expression of anti-VEGF molecules by the retina itself in a controlled manner following adeno-associated viral (AAV) gene transfer could be a replacement of this therapy. The open reading frames (orf) of the light and the heavy chain of ranibizumab were cloned into an expression plasmid separated by an internal ribosomal entry site (IRES). The construct was mutated to generate ranibizumab single-chain variable fragments (scFv). Expression was verified by western blotting and the concentrations were measured with a custom-made ranibizumab ELISA. Biological activity, VEGF-binding properties, and the doxycycline-dependent induction of anti-VEGF expression were tested. An AAV2/5 vector was generated containing the optimal variant Ra02. Ra01-Ra05 molecules were detected in the cell culture medium. While the VEGF-binding affinity was significantly lower for Ra01 and Ra02 compared to Lucentis(®), the inhibition of cell migration was comparable and the maximum inhibition of Ra01 and Ra02 was reached at lower doses. The expression of Ra01 and Ra02 was shown to be regulable with the TetOn-system(®) as plasmid (Ra01, Ra02) and AAV vector construct (Ra02). Ra01 and Ra02 can be produced in eukaryotic cells after AAV-mediated gene transfer in a regulable manner in vitro and display comparable biological activity as Lucentis. These results are the basis for in vivo studies in human VEGF-overexpressing mice, a model for human neovascular disorders.

  11. Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation.

    Science.gov (United States)

    Barelli, Claudia; Albanese, Davide; Donati, Claudio; Pindo, Massimo; Dallago, Chiara; Rovero, Francesco; Cavalieri, Duccio; Tuohy, Kieran Michael; Hauffe, Heidi Christine; De Filippo, Carlotta

    2015-10-07

    The expansion of agriculture is shrinking pristine forest areas worldwide, jeopardizing the persistence of their wild inhabitants. The Udzungwa red colobus monkey (Procolobus gordonorum) is among the most threatened primate species in Africa. Primarily arboreal and highly sensitive to hunting and habitat destruction, they provide a critical model to understanding whether anthropogenic disturbance impacts gut microbiota diversity. We sampled seven social groups inhabiting two forests (disturbed vs. undisturbed) in the Udzungwa Mountains of Tanzania. While Ruminococcaceae and Lachnospiraceae dominated in all individuals, reflecting their role in extracting energy from folivorous diets, analysis of genus composition showed a marked diversification across habitats, with gut microbiota α-diversity significantly higher in the undisturbed forest. Functional analysis suggests that such variation may be associated with food plant diversity in natural versus human-modified habitats, requiring metabolic pathways to digest xenobiotics. Thus, the effects of changes in gut microbiota should not be ignored to conserve endangered populations.

  12. Limits of a rapid identification of common Mediterranean sandflies using polymerase chain reaction-restriction fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Azzedine Bounamous

    2014-07-01

    Full Text Available A total of 131 phlebotomine Algerian sandflies have been processed in the present study. They belong to the species Phlebotomus bergeroti, Phlebotomus alexandri, Phlebotomus sergenti, Phlebotomus chabaudi, Phlebotomus riouxi, Phlebotomus perniciosus, Phlebotomus longicuspis, Phlebotomus perfiliewi, Phlebotomus ariasi, Phlebotomus chadlii, Sergentomyia fallax, Sergentomyia minuta, Sergentomyia antennata, Sergentomyia schwetzi, Sergentomyia clydei, Sergentomyia christophersi and Grassomyia dreyfussi. They have been characterised by sequencing of a part of the cytochrome b (cyt b, t RNA serine and NADH1 on the one hand and of the cytochrome C oxidase I of the mitochondrial DNA (mtDNA on the other hand. Our study highlights two sympatric populations within P. sergenti in the area of its type-locality and new haplotypes of P. perniciosus and P. longicuspis without recording the specimens called lcx previously found in North Africa. We tried to use a polymerase chain reaction-restriction fragment length polymorphism method based on a combined double digestion of each marker. These method is not interesting to identify sandflies all over the Mediterranean Basin.

  13. Modulation of plumbagin production in Plumbago zeylanica using a single-chain variable fragment antibody against plumbagin.

    Science.gov (United States)

    Sakamoto, Seiichi; Putalun, Waraporn; Pongkitwitoon, Benyakan; Juengwatanatrakul, Thaweesak; Shoyama, Yukihiro; Tanaka, Hiroyuki; Morimoto, Satoshi

    2012-01-01

    A single-chain variable fragment antibody (scFv) against plumbagin (PL) accumulated the PL production in the hairy roots of Plumbago zeylanica. Recombinant Agrobacterium rhizogenes (ATCC 15834) containing an scFv gene against PL (PL-scFv) were obtained through triparental mating and transformed into P. zeylanica to induce PL-scFv protein in the hairy roots. Up to 40 μg recombinant PL-scFv were expressed per milligram of soluble protein in transgenic P. zeylanica hairy root cultures. The mean PL content obtained from transgenic hairy roots (12.24 μg/100 mg dry weight) exhibited 2.2 times higher than those obtained from wild-type (5.48 μg/100 mg dry weight). The high correlation between the PL-scFv expression level and PL content of the recombinant plants suggested that the PL biosynthesis pathway had been modulated by the expression of PL-scFv protein in the hairy roots of P. zeylanica.

  14. Scale-up of the Reversible Addition-Fragmentation Chain Transfer (RAFT Polymerization Using Continuous Flow Processing

    Directory of Open Access Journals (Sweden)

    Nenad Micic

    2014-01-01

    Full Text Available A controlled radical polymerization process using the Reversible Addition-Fragmentation Chain Transfer (RAFT approach was scaled up by a factor of 100 from a small laboratory scale of 5 mL to a preparative scale of 500 mL, using batch and continuous flow processing. The batch polymerizations were carried out in a series of different glass vessels, using either magnetic or overhead stirring, and different modes of heating: Microwave irradiation or conductive heating in an oil bath. The continuous process was conducted in a prototype tubular flow reactor, consisting of 6 mm ID stainless steel tubing, fitted with static mixers. Both reactor types were tested for polymerizations of the acid functional monomers acrylic acid and 2-acrylamido-2-methylpropane-1-sulfonic acid in water at 80 °C with reaction times of 30 to 40 min. By monitoring the temperature during the exothermic polymerization process, it was observed that the type and size of reactor had a significant influence on the temperature profile of the reaction.

  15. Transgenic expression in citrus of single-chain antibody fragments specific to Citrus tristeza virus confers virus resistance.

    Science.gov (United States)

    Cervera, Magdalena; Esteban, Olga; Gil, Maite; Gorris, M Teresa; Martínez, M Carmen; Peña, Leandro; Cambra, Mariano

    2010-12-01

    Citrus tristeza virus (CTV) causes one of the most destructive viral diseases of citrus worldwide. Generation of resistant citrus genotypes through genetic engineering could be a good alternative to control CTV. To study whether production of single-chain variable fragment (scFv) antibodies in citrus could interfere and immunomodulate CTV infection, transgenic Mexican lime plants expressing two different scFv constructs, separately and simultaneously, were generated. These constructs derived from the well-referenced monoclonal antibodies 3DF1 and 3CA5, specific against CTV p25 major coat protein, whose mixture is able to detect all CTV isolates characterized so far. ScFv accumulation levels were low and could be readily detected just in four transgenic lines. Twelve homogeneous and vigorous lines were propagated and CTV-challenged by graft inoculation with an aggressive CTV strain. A clear protective effect was observed in most transgenic lines, which showed resistance in up to 40-60% of propagations. Besides, both a delay in symptom appearance and attenuation of symptom intensity were observed in infected transgenic plants compared with control plants. This effect was more evident in lines carrying the 3DF1scFv transgene, being probably related to the biological functions of the epitope recognized by this antibody. This is the first report describing successful protection against a pathogen in woody transgenic plants by ectopic expression of scFv recombinant antibodies.

  16. Single chain variable fragment antibodies block aggregation and toxicity induced by familial ALS-linked mutant forms of SOD1.

    Science.gov (United States)

    Ghadge, Ghanashyam D; Pavlovic, John D; Koduvayur, Sujatha P; Kay, Brian K; Roos, Raymond P

    2013-08-01

    Approximately 10% of amyotrophic lateral sclerosis (ALS) cases are familial (known as FALS) with an autosomal dominant inheritance pattern, and ~25% of FALS cases are caused by mutations in Cu/Zn superoxide dismutase (SOD1). There is convincing evidence that mutant SOD1 (mtSOD1) kills motor neurons (MNs) because of a gain-of-function toxicity, most likely related to aggregation of mtSOD1. A number of recent reports have suggested that antibodies can be used to treat mtSOD1-induced FALS. To follow up on the use of antibodies as potential therapeutics, we generated single chain fragments of variable region antibodies (scFvs) against SOD1, and then expressed them as 'intrabodies' within a motor neuron cell line. In the present study, we describe isolation of human scFvs that interfere with mtSOD1 in vitro aggregation and toxicity. These scFvs may have therapeutic potential in sporadic ALS, as well as FALS, given that sporadic ALS may also involve abnormalities in the SOD1 protein or activity. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. A guide to the synthesis of block copolymers using reversible-addition fragmentation chain transfer (RAFT) polymerization.

    Science.gov (United States)

    Keddie, Daniel J

    2014-01-21

    The discovery of reversible-deactivation radical polymerization (RDRP) has provided an avenue for the synthesis of a vast array of polymers with a rich variety of functionality and architecture. The preparation of block copolymers has received significant focus in this burgeoning research field, due to their diverse properties and potential in a wide range of research environments. This tutorial review will address the important concepts behind the design and synthesis of block copolymers using reversible addition-fragmentation chain transfer (RAFT) polymerization. RAFT polymerization is arguably the most versatile of the RDRP methods due to its compatibility with a wide range of functional monomers and reaction media along with its relative ease of use. With an ever increasing array of researchers that possess a variety of backgrounds now turning to RDRP, and RAFT in particular, to prepare their required polymeric materials, it is pertinent to discuss the important points which enable the preparation of high purity functional block copolymers with targeted molar mass and narrow molar mass distribution using RAFT polymerization. The key principles of appropriate RAFT agent selection, the order of monomer addition in block synthesis and potential issues with maintaining high end-group fidelity are addressed. Additionally, techniques which allow block copolymers to be accessed using a combination of RAFT polymerization and complementary techniques are touched upon.

  18. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP for rapid diagnosis of neonatal sepsis

    Directory of Open Access Journals (Sweden)

    Anusha Rohit

    2016-01-01

    Full Text Available Background & objectives: The difficulties in diagnosis of neonatal sepsis are due to varied clinical presentation, low sensitivity of blood culture which is considered the gold standard and empirical antibiotic usage affecting the outcome of results. Though polymerase chain reaction (PCR based detection of bacterial 16S rRNA gene has been reported earlier, this does not provide identification of the causative agent. In this study, we used restriction fragment length polymorphism (RFLP of amplified 16S rRNA gene to identify the organisms involved in neonatal sepsis and compared the findings with blood culture. Methods: Blood samples from 97 neonates were evaluated for diagnosis of neonatal sepsis using BacT/Alert (automated blood culture and PCR-RFLP. Results: Bacterial DNA was detected by 16S rRNA gene PCR in 55 cases, while BacT/Alert culture was positive in 34 cases. Staphylococcus aureus was the most common organism detected with both methods. Klebsiella spp. was isolated from four samples by culture but was detected by PCR-RFLP in five cases while Acinetobacter spp. was isolated from one case but detected in eight cases by PCR-RFLP. The sensitivity of PCR was found to be 82.3 per cent with a negative predictive value of 85.7 per cent. Eighty of the 97 neonates had prior exposure to antibiotics. Interpretation & conclusions:The results of our study demonstrate that PCR-RFLP having a rapid turnaround time may be useful for the early diagnosis of culture negative neonatal sepsis.

  19. A conjugate of an anti-midkine single-chain variable fragment to doxorubicin inhibits tumor growth

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Shuli [Immunology and Reproductive Biology Laboratory, Medical School & State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing (China); Nanjing Affiliated First Hospital, Nanjing Medical University, Nanjing (China); Zhao, Guangfeng; Xie, Hao; Huang, Yahong [Immunology and Reproductive Biology Laboratory, Medical School & State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing (China); Hou, Yayi [Immunology and Reproductive Biology Laboratory, Medical School & State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing (China); Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing (China)

    2012-01-27

    Doxorubicin (DOX) was conjugated to a single-chain variable fragment (scFv) against human midkine (MK), and the conjugate (scFv-DOX) was used to target the chemotherapeutic agent to a mouse solid tumor model in which the tumor cells expressed high levels of human MK. The His-tagged recombinant scFv was expressed in bacteria, purified by metal affinity chromatography, and then conjugated to DOX using oxidative dextran (Dex) as a linker. The molecular formula of this immunoconjugate was scFv(Dex){sub 1.3}(DOX){sub 20}. In vitro apoptosis assays showed that the scFv-DOX conjugate was more cytotoxic against MK-transfected human adenocarcinoma cells (BGC823-MK) than untransfected cells (55.3 ± 2.4 vs 22.4 ± 3.8%) for three independent experiments. Nude mice bearing BGC823-MK solid tumors received scFv-DOX or equivalent doses of scFv + DOX for 2 weeks and tumor growth was more effectively inhibited by the scFv-DOX conjugate than by scFv + DOX (51.83% inhibition vs 40.81%). Histological analysis of the tumor tissues revealed that the highest levels of DOX accumulated in tumors from mice treated with scFv-DOX and this resulted in more extensive tumor cell death than in animals treated with the equivalent dose of scFv + DOX. These results show that the scFv-DOX conjugate effectively inhibited tumor growth in vivo and suggest that antigen-specific scFv may be competent drug-carriers.

  20. Optimized extraction of a single-chain variable fragment of antibody by using aqueous micellar two-phase systems.

    Science.gov (United States)

    Malpiedi, Luciana P; Nerli, Bibiana B; Taqueda, Maria E S; Abdalla, Dulcineia S P; Pessoa, Adalberto

    2015-07-01

    In this work, the purification of a single-chain variable fragment (scFv) of an antibody by using liquid-liquid extraction in aqueous micellar two-phase systems was optimized by means of central composite design. Protein partitioning assays were performed by using the selected system composition in previous works: Triton X-114 at 4% wt/wt, yeast fermentation supernatant at 60% wt/wt, McIlvaine buffer pH 7.00. The other system component concentrations, Cibacron Blue F3GA (CB), Fabsorbent™ F1P HF (HF) and NaCl, were selected as independent variables. ScFv recovery percentage (%R) and purification factor (PF) were selected as the responses. According to the optimization process both, scFv recovery percentage and purification factor were favored with the addition of HF and NaCl in a range of concentrations around the central point of the second central composite design (HF 0.0120% w/w, CB 0.0200% w/w, NaCl 0.200% w/w). These experimental conditions allowed the concentration and pre-purification of scFv in the micelle-rich bottom phase of the systems with a recovery percentage superior to 88% and a purification factor of approximately 3.5. These results improved the previously presented works and demonstrated the convenience of using aqueous micellar two-phase systems as a first step in the purification of scFv molecules. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Covalent adaptable networks as dental restorative resins: stress relaxation by addition-fragmentation chain transfer in allyl sulfide-containing resins.

    Science.gov (United States)

    Park, Hee Young; Kloxin, Christopher J; Scott, Timothy F; Bowman, Christopher N

    2010-10-01

    The aim is to demonstrate significant polymerization shrinkage stress reduction in model resins through incorporation of addition-fragmentation chain transfer moieties that promote network stress accommodation by molecular rearrangement. Monomers containing allyl sulfide linkages are incorporated to affect the shrinkage stress that arises during photopolymerization of model resins that contain an initiator and dimethacrylates. Radical-mediated allyl sulfide addition-fragmentation is enabled during polymerization. We hypothesize that allyl sulfide incorporation into methacrylate polymerizations promotes stress relaxation by enabling network adaptation. A 1:2 mixture of tetrathiol and allyl sulfide-containing divinyl ethers is formulated with glass-forming dimethacrylates and compared to controls where the allyl sulfide is replaced with a propyl sulfide that is incapable of undergoing addition-fragmentation. Simultaneous shrinkage stress and functional group conversion measurements are performed. The T(g) is determined by DMA. Increasing allyl sulfide concentration reduces the relative stress by up to 75% in the resins containing the maximum amount of allyl sulfide. In glassy systems, at much lower allyl sulfide concentrations, the stress is reduced by up to 20% as compared to propyl sulfide-containing systems incapable of undergoing addition-fragmentation chain transfer. Shrinkage stress reduction, typically accompanying free-radical polymerization, is a primary focus in dental materials research and new product development. Allyl sulfide addition-fragmentation chain transfer is utilized as a novel approach to reduce stress in ternary thiol-ene-methacrylate polymerizations. The stress reduction effect depends directly on the allyl sulfide concentration in the given ternary systems, with stress reduction observed even in systems possessing super-ambient T(g)s and low allyl sulfide concentrations. Published by Elsevier Ltd.

  2. Efficient heterologous expression and secretion in Aspergillus oryzae of a llama variable heavy-chain antibody fragment V(HH) against EGFR.

    Science.gov (United States)

    Okazaki, Fumiyoshi; Aoki, Jun-ichi; Tabuchi, Soichiro; Tanaka, Tsutomu; Ogino, Chiaki; Kondo, Akihiko

    2012-10-01

    We have constructed a filamentous fungus Aspergillus oryzae that secretes a llama variable heavy-chain antibody fragment (V(HH)) that binds specifically to epidermal growth factor receptor (EGFR) in a culture medium. A major improvement in yield was achieved by fusing the V(HH) with a Taka-amylase A signal sequence (sTAA) and a segment of 28 amino acids from the N-terminal region of Rhizopus oryzae lipase (N28). The yields of secreted, immunologically active anti-EGFR V(HH) reached 73.8 mg/1 in a Sakaguchi flask. The V(HH) fragments were released from the sTAA or N28 proteins by an indigenous A. oryzae protease during cultivation. The purified recombinant V(HH) fragment was specifically recognized and could bind to the EGFR with a high affinity.

  3. Development of a multiplexed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay to identify common members of the Subgenera Culex (Culex) and Culex (Phenacomyia) in Guatemala.

    Science.gov (United States)

    Kent, Rebekah J; Deus, Stephen; Williams, Martin; Savage, Harry M

    2010-08-01

    Morphological differentiation of mosquitoes in the subgenera Culex (Culex) and Culex (Phenacomyia) in Guatemala is difficult, with reliable identification ensured only through examination of larval skins from individually reared specimens and associated male genitalia. We developed a multiplexed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay to identify common Cx. (Cux.) and Cx. (Phc.). Culex (Cux.) chidesteri, Cx. (Cux.) coronator, Cx. (Cux.) interrogator, Cx. (Cux.) quinquefasciatus, Cx. (Cux.) nigripalpus/Cx. (Cux.) thriambus, and Cx. (Phc.) lactator were identified directly with a multiplexed primer cocktail comprising a conserved forward primer and specific reverse primers targeting ribosomal DNA (rDNA). Culex nigripalpus and Cx. thriambus were differentiated by restriction digest of homologous amplicons. The assay was developed and optimized using well-characterized specimens from Guatemala and the United States and field tested with unknown material from Guatemala. This assay will be a valuable tool for mosquito identification in entomological and arbovirus ecology studies in Guatemala.

  4. Use of PCR-RFLP (Polymerase Chain Reaction - Restricted Fragment Length Polymorphism in the gene of the enzyme Stearoyl-CoA-Desaturase in Bubalus bubalis

    Directory of Open Access Journals (Sweden)

    H. Tonhati

    2010-02-01

    Full Text Available The milk is an important food because it contents Conjugated Linoleic Acids (CLA. These fatty acids are synthesized in mammary gland under action of the enzyme Stearoyl CoA-Desaturase (SCD and have showed some positive effects in human disease prevention and treatments. A variation of CLA in milk fat exists and can be partially explained by the different levels of expression of SCD. The aim was to study part of the encoding regions of SCD´s gene using PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism. Genomic DNA was extracted from lactating Murrah females. After this, PCR reactions were made by using primers Z43D1 that encloses exon I, II and intron I. The fragments amplified are composed by 938 pb. Then, RFLP techniques were applied in the fragments using the restriction enzymes Pst I and Sma I. The enzyme Pst I has generated fragments of 788pb and 150bp and the Sma I has generated fragments of 693pb and 245pb. All the animals showed the same migration standard for both enzymes, characterizing a genetic monomorphism for this region of SCD gene. The analysis determined that there aren’t genetic differences between these animals in the studied regions by using Pst I and Sma I enzymes.

  5. Study of behavior incentive mechanism of energy conservation and emission reduction for China freshwater live fish supply chain

    Directory of Open Access Journals (Sweden)

    Liming Chen

    2016-02-01

    Full Text Available Purpose: The purpose of this paper investigates the subject behavior of Energy conservation and emission reduction (ECER based on structured classification of the organization types of FLF supply chain, and explores reasonable behavior incentive mechanism for ECER of FLF supply chain in China. Design/methodology/approach: This paper classifies the organization subjects of FLF supply chain, and different characteristics of organization subjects are compared in detail. ECER behavior incentive mechanism modeling of FLF supply chain is explored by taking advantage of principal-agent model in view of asymmetry information. Incentives issue of different operating subjects is discussed as enlightenment of the model. Findings: Three types of the organization subjects of FLF supply chain in China have been identified as: loose organization, semi-compact organization and compact organization.Subjects of different types have different abilities to conduct ECER work. Government needs to propose differentiation polices of incentive compensation for different operating subjects, widen the gap of differentiated subsidies/rewards for different investment levels on ECER conducted by different operating subjects of FLF supply chain. Research limitations/implications: It will take long-term unremitting efforts to achieve the target of ECER work for FLF supply chain in China, the dynamic issues and simulation modeling on behavior incentive mechanism of ECER should be developed in future research. Practical implications: Clear understanding of structured classification of the organization subject types of FLF supply chain and the behavior incentive mechanism for ECER, will help government to improve the ECER work in an efficient and effective way. Originality/value: Research to behavior incentive mechanism of ECER has important theoretical value and practical significance. This paper contributes to distinguish three types of operating subjects of FLF supply chain in

  6. Study of behavior incentive mechanism of energy conservation and emission reduction for China freshwater live fish supply chain

    Energy Technology Data Exchange (ETDEWEB)

    Liming, C.; Fengjun, L.; Xiaohong, L.

    2016-07-01

    The purpose of this paper investigates the subject behavior of Energy conservation and emission reduction (ECER) based on structured classification of the organization types of FLF supply chain, and explores reasonable behavior incentive mechanism for ECER of FLF supply chain in China. Design/methodology/approach: This paper classifies the organization subjects of FLF supply chain, and different characteristics of organization subjects are compared in detail. ECER behavior incentive mechanism modeling of FLF supply chain is explored by taking advantage of principal-agent model in view of asymmetry information. Incentives issue of different operating subjects is discussed as enlightenment of the model. Findings: Three types of the organization subjects of FLF supply chain in China have been identified as: loose organization, semi-compact organization and compact organization.Subjects of different types have different abilities to conduct ECER work. Government needs to propose differentiation polices of incentive compensation for different operating subjects, widen the gap of differentiated subsidies/rewards for different investment levels on ECER conducted by different operating subjects of FLF supply chain. Research limitations/implications: It will take long-term unremitting efforts to achieve the target of ECER work for FLF supply chain in China, the dynamic issues and simulation modeling on behavior incentive mechanism of ECER should be developed in future research. Practical implications: Clear understanding of structured classification of the organization subject types of FLF supply chain and the behavior incentive mechanism for ECER, will help government to improve the ECER work in an efficient and effective way... (Author)

  7. Implications of Fine-Grained Habitat Fragmentation and Road Mortality for Jaguar Conservation in the Atlantic Forest, Brazil.

    Directory of Open Access Journals (Sweden)

    Laury Cullen

    Full Text Available Jaguar (Panthera onca populations in the Upper Paraná River, in the Brazilian Atlantic Forest region, live in a landscape that includes highly fragmented areas as well as relatively intact ones. We developed a model of jaguar habitat suitability in this region, and based on this habitat model, we developed a spatially structured metapopulation model of the jaguar populations in this area to analyze their viability, the potential impact of road mortality on the populations' persistence, and the interaction between road mortality and habitat fragmentation. In more highly fragmented populations, density of jaguars per unit area is lower and density of roads per jaguar is higher. The populations with the most fragmented habitat were predicted to have much lower persistence in the next 100 years when the model included no dispersal, indicating that the persistence of these populations are dependent to a large extent on dispersal from other populations. This, in turn, indicates that the interaction between road mortality and habitat fragmentation may lead to source-sink dynamics, whereby populations with highly fragmented habitat are maintained only by dispersal from populations with less fragmented habitat. This study demonstrates the utility of linking habitat and demographic models in assessing impacts on species living in fragmented landscapes.

  8. Implications of Fine-Grained Habitat Fragmentation and Road Mortality for Jaguar Conservation in the Atlantic Forest, Brazil.

    Science.gov (United States)

    Cullen, Laury; Stanton, Jessica C; Lima, Fernando; Uezu, Alexandre; Perilli, Miriam L L; Akçakaya, H Reşit

    2016-01-01

    Jaguar (Panthera onca) populations in the Upper Paraná River, in the Brazilian Atlantic Forest region, live in a landscape that includes highly fragmented areas as well as relatively intact ones. We developed a model of jaguar habitat suitability in this region, and based on this habitat model, we developed a spatially structured metapopulation model of the jaguar populations in this area to analyze their viability, the potential impact of road mortality on the populations' persistence, and the interaction between road mortality and habitat fragmentation. In more highly fragmented populations, density of jaguars per unit area is lower and density of roads per jaguar is higher. The populations with the most fragmented habitat were predicted to have much lower persistence in the next 100 years when the model included no dispersal, indicating that the persistence of these populations are dependent to a large extent on dispersal from other populations. This, in turn, indicates that the interaction between road mortality and habitat fragmentation may lead to source-sink dynamics, whereby populations with highly fragmented habitat are maintained only by dispersal from populations with less fragmented habitat. This study demonstrates the utility of linking habitat and demographic models in assessing impacts on species living in fragmented landscapes.

  9. Identification of blood meal sources of Lutzomyia longipalpis using polymerase chain reaction-restriction fragment length polymorphism analysis of the cytochrome B gene.

    Science.gov (United States)

    Soares, Vítor Yamashiro Rocha; Silva, Jailthon Carlos da; Silva, Kleverton Ribeiro da; Pires e Cruz, Maria do Socorro; Santos, Marcos Pérsio Dantas; Ribolla, Paulo Eduardo Martins; Alonso, Diego Peres; Coelho, Luiz Felipe Leomil; Costa, Dorcas Lamounier; Costa, Carlos Henrique Nery

    2014-06-01

    An analysis of the dietary content of haematophagous insects can provide important information about the transmission networks of certain zoonoses. The present study evaluated the potential of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mitochondrial cytochrome B (cytb) gene to differentiate between vertebrate species that were identified as possible sources of sandfly meals. The complete cytb gene sequences of 11 vertebrate species available in the National Center for Biotechnology Information database were digested with Aci I, Alu I, Hae III and Rsa I restriction enzymes in silico using Restriction Mapper software. The cytb gene fragment (358 bp) was amplified from tissue samples of vertebrate species and the dietary contents of sandflies and digested with restriction enzymes. Vertebrate species presented a restriction fragment profile that differed from that of other species, with the exception of Canis familiaris and Cerdocyon thous. The 358 bp fragment was identified in 76 sandflies. Of these, 10 were evaluated using the restriction enzymes and the food sources were predicted for four: Homo sapiens (1), Bos taurus (1) and Equus caballus (2). Thus, the PCR-RFLP technique could be a potential method for identifying the food sources of arthropods. However, some points must be clarified regarding the applicability of the method, such as the extent of DNA degradation through intestinal digestion, the potential for multiple sources of blood meals and the need for greater knowledge regarding intraspecific variations in mtDNA.

  10. Identification of blood meal sources of Lutzomyia longipalpis using polymerase chain reaction-restriction fragment length polymorphism analysis of the cytochrome B gene

    Directory of Open Access Journals (Sweden)

    Vítor Yamashiro Rocha Soares

    2014-06-01

    Full Text Available An analysis of the dietary content of haematophagous insects can provide important information about the transmission networks of certain zoonoses. The present study evaluated the potential of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP analysis of the mitochondrial cytochrome B (cytb gene to differentiate between vertebrate species that were identified as possible sources of sandfly meals. The complete cytb gene sequences of 11 vertebrate species available in the National Center for Biotechnology Information database were digested with Aci I, Alu I, Hae III and Rsa I restriction enzymes in silico using Restriction Mapper software. The cytb gene fragment (358 bp was amplified from tissue samples of vertebrate species and the dietary contents of sandflies and digested with restriction enzymes. Vertebrate species presented a restriction fragment profile that differed from that of other species, with the exception of Canis familiaris and Cerdocyon thous. The 358 bp fragment was identified in 76 sandflies. Of these, 10 were evaluated using the restriction enzymes and the food sources were predicted for four: Homo sapiens (1, Bos taurus (1 and Equus caballus (2. Thus, the PCR-RFLP technique could be a potential method for identifying the food sources of arthropods. However, some points must be clarified regarding the applicability of the method, such as the extent of DNA degradation through intestinal digestion, the potential for multiple sources of blood meals and the need for greater knowledge regarding intraspecific variations in mtDNA.

  11. Identification of planorbids from Venezuela by polymerase chain reaction amplification and restriction fragment length polymorphism of internal transcriber spacer of the RNA ribosomal gene

    Directory of Open Access Journals (Sweden)

    Caldeira Roberta L

    2000-01-01

    Full Text Available Snails of the genus Biomphalaria from Venezuela were subjected to morphological assessment as well as polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP analysis. Morphological identification was carried out by comparison of characters of the shell and the male and female reproductive apparatus. The PCR-RFLP involved amplification of the internal spacer region ITS1 and ITS2 of the RNA ribosomal gene and subsequent digestion of this fragment by the restriction enzymes DdeI, MnlI, HaeIII and MspI. The planorbids were compared with snails of the same species and others reported from Venezuela and present in Brazil, Cuba and Mexico. All the enzymes showed a specific profile for each species, that of DdeI being the clearest. The snails were identified as B. glabrata, B. prona and B. kuhniana.

  12. The influence of the boat-to-chair conversion on the demetallation of the nickel(II) complex of an open-chain tetramine containing a piperazine fragment.

    Science.gov (United States)

    Boiocchi, Massimo; Bonizzoni, Marco; Fabbrizzi, Luigi; Foti, Francesco; Licchelli, Maurizio; Taglietti, Angelo; Zema, Michele

    2004-02-21

    The nickel(II) complex with an open chain tetramine containing a piperazine fragment (1) displays an unusual resistance to demetallation in acidic solution and exhibits a lifetime of about five minutes in a solution 0.1 M in HClO4 and 7.0 M in NaClO4. Sluggishness with respect to the demetallation is ascribed to the occurrence of the boat-to-chair conformational conversion of the piperazine fragment, which implies the passage through the highly energetic half-boat transition state. The use of a high concentration of the inert electrolyte induces a 'salting out' effect on both thermodynamics (stability of metal complexes is enhanced) and kinetics (resistance to demetallation is increased).

  13. HLA-DPB1 typing with polymerase chain reaction and restriction fragment length polymorphism technique in Danes

    DEFF Research Database (Denmark)

    Hviid, T V; Madsen, H O; Morling, N

    1992-01-01

    endonucleases: RsaI, FokI, ApaI, SacI, BstUI, EcoNI, and DdeI, and the DNA fragments were separated by electrophoresis in agarose gels. Altogether, 71 individuals were investigated and 16 different HLA-DPB1 types were observed in 26 different heterozygotic combinations, as well as five possible homozygotes...

  14. Ten-Year Follow-Up of a Fragment Reattachment to an Anterior Tooth: A Conservative Approach

    Science.gov (United States)

    Mendes, Luiz; Laxe, Laisa

    2017-01-01

    This report describes the 10-year follow-up data of a patient who underwent fragment reattachment to the maxillary central incisor after coronal fracture with pulp exposure as well as the procedures followed for functional and esthetic adjustments. A 9-year-old female patient presented at the clinic of dentistry at the State University of Rio de Janeiro with a coronal fracture and pulp exposure of the right maxillary central incisor that had occurred immediately after an accident. The intact tooth fragment was recovered at the accident site and stored in milk. The treatment plan followed was to perform direct pulp capping and tooth fragment reattachment. When the patient was 14 years old, adhesion between fragment and remaining tooth was lost, and fragment reattachment was performed. Five years later, the same tooth presented clinical discoloration and absence of sensitivity during pulp vitality tests. Subsequently, a new treatment plan was formulated, which included endodontic treatment, followed by nonvital tooth bleaching and light-cured composite resin restoration. An esthetic and natural-looking restoration was achieved. Tooth fragment reattachment is not a temporary restorative technique and requires functional and esthetic adjustments over time to maintain the biomimetic characteristics of traumatized anterior teeth and predictable outcomes. PMID:28740741

  15. Ten-Year Follow-Up of a Fragment Reattachment to an Anterior Tooth: A Conservative Approach

    Directory of Open Access Journals (Sweden)

    Luiz Mendes

    2017-01-01

    Full Text Available This report describes the 10-year follow-up data of a patient who underwent fragment reattachment to the maxillary central incisor after coronal fracture with pulp exposure as well as the procedures followed for functional and esthetic adjustments. A 9-year-old female patient presented at the clinic of dentistry at the State University of Rio de Janeiro with a coronal fracture and pulp exposure of the right maxillary central incisor that had occurred immediately after an accident. The intact tooth fragment was recovered at the accident site and stored in milk. The treatment plan followed was to perform direct pulp capping and tooth fragment reattachment. When the patient was 14 years old, adhesion between fragment and remaining tooth was lost, and fragment reattachment was performed. Five years later, the same tooth presented clinical discoloration and absence of sensitivity during pulp vitality tests. Subsequently, a new treatment plan was formulated, which included endodontic treatment, followed by nonvital tooth bleaching and light-cured composite resin restoration. An esthetic and natural-looking restoration was achieved. Tooth fragment reattachment is not a temporary restorative technique and requires functional and esthetic adjustments over time to maintain the biomimetic characteristics of traumatized anterior teeth and predictable outcomes.

  16. Identification of Nile perch (Lates niloticus), grouper (Epinephelus guaza), and wreck fish (Polyprion americanus) by polymerase chain reaction-restriction fragment length polymorphism of a 12S rRNA gene fragment.

    Science.gov (United States)

    Asensio, L; González, I; Fernández, A; Céspedes, A; Hernández, P E; García, T; Martín, R

    2000-09-01

    Restriction site analysis of polymerase chain reaction (PCR) products from a conserved region of the 12S rRNA gene has been used for the specific identification of Nile perch (Lates niloticus), grouper (Epinephelus guaza), and wreck fish (Polyprion americanus). Amplification of DNA isolated from muscle samples was carried out using a set of primers flanking a region of 436 bp from the mitochondrial 12S rRNA gene. Digestions of the PCR products with RsaI and Sau96I endonucleases, followed by agarose gel electrophoresis of the digested PCR products, yielded specific profiles that enabled direct identification of each species analyzed.

  17. Who controls the logistics emissions? Challenges in making fragmented supply chains environmentally sustainable from logistics service providers’ perspective

    DEFF Research Database (Denmark)

    Abbasi, Maisam; Sternberg, Henrik; Nilsson, Fredrik

    2014-01-01

    of logistics activities in the supply chain? Design/methodology/approach The methodology of this paper is a literature review, a qualitative interview survey, and three case studies. A framework on sustainability challenges in supply chains derived from the literature is used to structure and analyze...... that impact the cost and time requirements from customers of logistics services are not yet a reality. Research limitations/implications (if applicable) This paper implies that LSP sustainability cannot be investigated in isolation if a company does not manage proprietary resources. Practical implications (if...

  18. A specific polymerase chain reaction based on the gyrB gene sequence and subsequent restriction fragment length polymorphism analysis of Pasteurella pneumotropica isolates from laboratory mice.

    Science.gov (United States)

    Hayashimoto, Nobuhito; Ueno, Masami; Takakura, Akira; Itoh, Toshio

    2007-03-01

    For a molecular identification and typing tool, we developed a specific polymerase chain reaction (PCR) based on the gyrB gene sequence and a subsequent restriction fragment length polymorphism (RFLP) analysis using the products amplified from the specific PCR to facilitate discrimination of biotypes of Pasteurella pneumotropica from laboratory mice. Appropriate PCR products, a 1039-basepair fragment for biotype Jawetz and a 1033-basepair fragment for biotype Heyl, were amplified by use of the primers CZO-1 and NJO-2 from all 105 P. pneumotropica isolates tested and the 2 reference strains but not from other bacterial species tested. MspI digestion of PCR-generated products showed 3 RFLP patterns among the 105 isolates, and these patterns correlated with the biotype of the isolate (RFLP pattern 1, biotype Jawetz; RFLP pattern 2, biotype Heyl; and RFLP pattern 3, biotype Jawetz with Beta-hemolytic activity). Our procedure identifies and biotypes isolates of P. pneumotropica from laboratory mice, using simple PCR and enzymatic restriction techniques. Therefore, this procedure is useful as a rapid identification and biotyping tool for isolates of P. pneumotropica from laboratory mice.

  19. Simultaneous and rapid differential diagnosis of Mycoplasma genitalium and Ureaplasma urealyticum based on a polymerase chain reaction-restriction fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    R Mirnejad

    2011-01-01

    Full Text Available Objectives: The aim of this investigation was to simultaneously detect and differentiate Mycoplasma genitalium and Ureaplasma urealyticum in female patients suffering from genital complications by polymerase chain reaction (PCR-restriction fragment length polymorphism (RFLP. Materials and Methods : Genital swabs were taken from 210 patients. They were transported to the laboratory in phosphate-buffered saline. For PCR, samples were analysed with genus-specific MyUu-R and MyUu-F primers. This primer set, which was originally designed in our laboratory, amplified a 465 bp fragment (M. genitalium and a 559 bp fragment (U. urealyticum. Samples containing a band of the expected sizes for the Mycoplasma strains were subjected to digestion with a restriction endonuclease enzyme of TaqI and Cac8I. Results: Of the 210 samples, a total of 100 (47.6% samples were found to be positive for Mycoplasmas (seven M. genitalium isolates, 3.3%; and 89 U. urealyticum isolates, 42.4%, and coinfections with both species were detected in four samples (1.9%. The PCR-RFLP results showed that M. genitalium and U. urealyticum are different by enzyme patterns. Conclusion: PCR-RFLP offers a rapid and easily applicable protocol to simultaneous detection and differentiation of M. genitalium and U. urealyticum from clinical samples when specific primers and restriction enzymes are used.

  20. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies

    KAUST Repository

    Wang, Yong

    2009-10-09

    Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519-539, E969- 983, E1063-1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies. © 2009 Wang, Qian.

  1. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies.

    Directory of Open Access Journals (Sweden)

    Yong Wang

    Full Text Available Bacterial 16S ribosomal DNA (rDNA amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90% were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519-539, E969-983, E1063-1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies.

  2. Lack of a 5.9 kDa peptide C-terminal fragment of fibrinogen α chain precedes fibrosis progression in patients with liver disease.

    Science.gov (United States)

    Marfà, Santiago; Crespo, Gonzalo; Reichenbach, Vedrana; Forns, Xavier; Casals, Gregori; Morales-Ruiz, Manuel; Navasa, Miquel; Jiménez, Wladimiro

    2014-01-01

    Early detection of fibrosis progression is of major relevance for the diagnosis and management of patients with liver disease. This study was designed to find non-invasive biomarkers for fibrosis in a clinical context where this process occurs rapidly, HCV-positive patients who underwent liver transplantation (LT). We analyzed 93 LT patients with HCV recurrence, 41 non-LT patients with liver disease showing a fibrosis stage F≥1 and 9 patients without HCV recurrence who received antiviral treatment before LT, as control group. Blood obtained from 16 healthy subjects was also analyzed. Serum samples were fractionated by ion exchange chromatography and their proteomic profile was analyzed by SELDI-TOF-MS. Characterization of the peptide of interest was performed by ion chromatography and electrophoresis, followed by tandem mass spectrometry identification. Marked differences were observed between the serum proteome profile of LT patients with early fibrosis recurrence and non-recurrent LT patients. A robust peak intensity located at 5905 m/z was the distinguishing feature of non-recurrent LT patients. However, the same peak was barely detected in recurrent LT patients. Similar results were found when comparing samples of healthy subjects with those of non-LT fibrotic patients, indicating that our findings were not related to either LT or HCV infection. Using tandem mass-spectrometry, we identified the protein peak as a C-terminal fragment of the fibrinogen α chain. Cell culture experiments demonstrated that TGF-β reduces α-fibrinogen mRNA expression and 5905 m/z peak intensity in HepG2 cells, suggesting that TGF-β activity regulates the circulating levels of this protein fragment. In conclusion, we identified a 5.9 kDa C-terminal fragment of the fibrinogen α chain as an early serum biomarker of fibrogenic processes in patients with liver disease.

  3. Lack of a 5.9 kDa peptide C-terminal fragment of fibrinogen α chain precedes fibrosis progression in patients with liver disease.

    Directory of Open Access Journals (Sweden)

    Santiago Marfà

    Full Text Available Early detection of fibrosis progression is of major relevance for the diagnosis and management of patients with liver disease. This study was designed to find non-invasive biomarkers for fibrosis in a clinical context where this process occurs rapidly, HCV-positive patients who underwent liver transplantation (LT. We analyzed 93 LT patients with HCV recurrence, 41 non-LT patients with liver disease showing a fibrosis stage F≥1 and 9 patients without HCV recurrence who received antiviral treatment before LT, as control group. Blood obtained from 16 healthy subjects was also analyzed. Serum samples were fractionated by ion exchange chromatography and their proteomic profile was analyzed by SELDI-TOF-MS. Characterization of the peptide of interest was performed by ion chromatography and electrophoresis, followed by tandem mass spectrometry identification. Marked differences were observed between the serum proteome profile of LT patients with early fibrosis recurrence and non-recurrent LT patients. A robust peak intensity located at 5905 m/z was the distinguishing feature of non-recurrent LT patients. However, the same peak was barely detected in recurrent LT patients. Similar results were found when comparing samples of healthy subjects with those of non-LT fibrotic patients, indicating that our findings were not related to either LT or HCV infection. Using tandem mass-spectrometry, we identified the protein peak as a C-terminal fragment of the fibrinogen α chain. Cell culture experiments demonstrated that TGF-β reduces α-fibrinogen mRNA expression and 5905 m/z peak intensity in HepG2 cells, suggesting that TGF-β activity regulates the circulating levels of this protein fragment. In conclusion, we identified a 5.9 kDa C-terminal fragment of the fibrinogen α chain as an early serum biomarker of fibrogenic processes in patients with liver disease.

  4. IG and TR single chain fragment variable (scFv) sequence analysis: a new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST.

    Science.gov (United States)

    Giudicelli, Véronique; Duroux, Patrice; Kossida, Sofia; Lefranc, Marie-Paule

    2017-06-26

    IMGT®, the international ImMunoGeneTics information system® ( http://www.imgt.org ), was created in 1989 in Montpellier, France (CNRS and Montpellier University) to manage the huge and complex diversity of the antigen receptors, and is at the origin of immunoinformatics, a science at the interface between immunogenetics and bioinformatics. Immunoglobulins (IG) or antibodies and T cell receptors (TR) are managed and described in the IMGT® databases and tools at the level of receptor, chain and domain. The analysis of the IG and TR variable (V) domain rearranged nucleotide sequences is performed by IMGT/V-QUEST (online since 1997, 50 sequences per batch) and, for next generation sequencing (NGS), by IMGT/HighV-QUEST, the high throughput version of IMGT/V-QUEST (portal begun in 2010, 500,000 sequences per batch). In vitro combinatorial libraries of engineered antibody single chain Fragment variable (scFv) which mimic the in vivo natural diversity of the immune adaptive responses are extensively screened for the discovery of novel antigen binding specificities. However the analysis of NGS full length scFv (~850 bp) represents a challenge as they contain two V domains connected by a linker and there is no tool for the analysis of two V domains in a single chain. The functionality "Analyis of single chain Fragment variable (scFv)" has been implemented in IMGT/V-QUEST and, for NGS, in IMGT/HighV-QUEST for the analysis of the two V domains of IG and TR scFv. It proceeds in five steps: search for a first closest V-REGION, full characterization of the first V-(D)-J-REGION, then search for a second V-REGION and full characterization of the second V-(D)-J-REGION, and finally linker delimitation. For each sequence or NGS read, positions of the 5'V-DOMAIN, linker and 3'V-DOMAIN in the scFv are provided in the 'V-orientated' sense. Each V-DOMAIN is fully characterized (gene identification, sequence description, junction analysis, characterization of mutations and amino

  5. Taenia saginata: differential diagnosis of human taeniasis by polymerase chain reaction-restriction fragment length polymorphism assay.

    Science.gov (United States)

    Nunes, Cáris Maroni; Dias, Ana Karina Kerche; Dias, Francisca Elda Ferreira; Aoki, Sérgio Moraes; de Paula, Henrique Borges; Lima, Luis Gustavo Ferraz; Garcia, José Fernando

    2005-08-01

    Speciation of Taenia in human stool is important because of their different clinical and epidemiological features. DNA analysis has recently become possible which overcomes the problems of differentiating human taeniid cestodes morphologically. In the present study, we evaluated PCR coupled to restriction fragment length polymorphism to differentiate Taenia solium from Taenia saginata eggs present in fecal samples from naturally infected patients. A different DraI-RFLP pattern: a two-band pattern (421 and 100 bp) for T. saginata and a three-band pattern (234, 188, and 99 bp) for T. solium was observed allowing the two species to be separated. The lower detection limit of the PCR-RFLP using a non-infected fecal sample prepared with a given number of T. saginata eggs was 34 eggs in 2 g stool sediment. The 521 bp mtDNA fragment was detected in 8 out of 12 Taenia sp. carriers (66.6%). Of these, three showed a T. solium pattern and five a T. saginata pattern.

  6. Characterization of the native and denatured herceptin by enzyme linked immunosorbent assay and quartz crystal microbalance using a high-affinity single chain fragment variable recombinant antibody.

    Science.gov (United States)

    Shang, Yuqin; Mernaugh, Ray; Zeng, Xiangqun

    2012-10-02

    Herceptin/Trastuzumab is a humanized IgG1κ light chain antibody used to treat some forms of breast cancer. A phage-displayed recombinant antibody library was used to obtain a single chain fragment variable (scFv, designated 2B4) to a linear synthetic peptide representing Herceptin's heavy chain CDR3. Enzyme linked immunosorbent assays (ELISAs) and piezoimmunosensor/quartz crystal microbalance (QCM) assays were used to characterize 2B4-binding activity to both native and heat denatured Herceptin. The 2B4 scFv specifically bound to heat denatured Herceptin in a concentration dependent manner over a wide (35-220.5 nM) dynamic range. Herceptin denatures and forms significant amounts of aggregates when heated. UV-vis characterization confirms that Herceptin forms aggregates as the temperature used to heat Herceptin increases. QCM affinity assay shows that binding stoichiometry between 2B4 scFv and Herceptin follows a 1:2 relationship proving that 2B4 scFv binds strongly to the dimers of heat denatured Herceptin aggregates and exhibits an affinity constant of 7.17 × 10(13) M(-2). The 2B4-based QCM assay was more sensitive than the corresponding ELISA. Combining QCM with ELISA can be used to more fully characterize nonspecific binding events in assays. The potential theoretical and clinical implications of these results and the advantages of the use of QCM to characterize human therapeutic antibodies in samples are also discussed.

  7. Activatable bispecific liposomes bearing fibroblast activation protein directed single chain fragment/Trastuzumab deliver encapsulated cargo into the nuclei of tumor cells and the tumor microenvironment simultaneously.

    Science.gov (United States)

    Tansi, Felista L; Rüger, Ronny; Böhm, Claudia; Steiniger, Frank; Kontermann, Roland E; Teichgraeber, Ulf K; Fahr, Alfred; Hilger, Ingrid

    2017-05-01

    Molecular targeting plays a significant role in cancer diagnosis and therapy. However, the heterogeneity of tumors is a limiting obstacle for molecular targeting. Consequently, clinically approved drug delivery systems such as liposomes still rely on passive targeting to tumors, which does not address tumor heterogeneity. In this work, we therefore designed and elucidated the potentials of activatable bispecific targeted liposomes for simultaneous detection of fibroblast activation protein (FAP) and the human epidermal growth factor receptor 2 (HER2). The bispecific liposomes were encapsulated with fluorescence-quenched concentrations of the near-infrared fluorescent dye, DY-676-COOH, making them detectable solely post processing within target cells. The liposomes were endowed with a combination of single chain antibody fragments specific for FAP and HER2 respectively, or with the FAP single chain antibody fragment in combination with Trastuzumab, which is specific for HER2. The Trastuzumab based bispecific formulation, termed Bi-FAP/Tras-IL revealed delivery of the encapsulated dye into the nuclei of HER2 expressing cancer cells and caused cell death at significantly higher rates than the free Trastuzumab. Furthermore, fluorescence imaging and live microscopy of tumor models in mice substantiated the delivery of the encapsulated cargo into the nuclei of target tumor cells and tumor stromal fibroblasts. Hence, they convey potentials to address tumor plasticity, to improve targeted cancer therapy and reduce Trastuzumab resistance in the future. This work demonstrates the design of activatable bispecific liposomes aimed to target HER2, a poor prognosis tumor marker in many tumor types, and fibroblast activation protein (FAP), a universal tumor marker overexpressed on tumor fibroblasts and pericytes of almost all solid tumors. Encapsulating liposomes with a quenched concentration of a NIRF dye which only fluoresced after cellular degradation and activation enabled

  8. Single-chain variable fragment antibody against ginsenoside Re as an effective tool for the determination of ginsenosides in various ginsengs.

    Science.gov (United States)

    Pongkitwitoon, Benyakan; Sakamoto, Seiichi; Morinaga, Osamu; Juengwatanatrakul, Thaweesak; Shoyama, Yukihiro; Tanaka, Hiroyuki; Morimoto, Satoshi

    2011-01-01

    A single-chain variable fragment antibody (scFv) against ginsenoside Re (G-Re) was constructed and applied to an enzyme-linked immunosorbent assay (ELISA) for determining the total concentration of ginsenosides in various ginsengs. The variable heavy and light chain genes were cloned directly from the cDNA of the 4G10 hybridoma cell line and assembled by means of splicing by overlapping extension PCR (SOE-PCR) using specific primers designed to have flexible peptide (Gly(4)Ser)(3) between the variable heavy chain and light chain domains. The constructed scFv gene was ligated into the pET28a expression vector and transformed into E. coli BL21 (DE3). The recombinant scFv against G-Re (GRe-scFv) was expressed as a chimera protein containing the His6-tag at its N-termini, purified by immobilized metal ion affinity chromatography (IMAC), and refolded by a stepwise dialysis method. The yield of GRe-scFv after purification was 1.7 mg per liter of culture medium. Characterization of GRe-scFv revealed that it retained the characteristics of the parental monoclonal antibody (MAb) against G-Re (MAb-4G10) which has wide cross-reactivity with 20(S)-protopanaxadiol- and 20(S)-protopanaxatriol-type ginsenosides. The detectable range for G-Re in ELISA using scFv antibody was 0.02-10 µg/ml. Based on validation analysis, the use of GRe-scFv in ELISA is a precise, accurate, and sensitive method. In light of the time-consuming and labor-intensive procedures for the preparation of MAb, speedy bacterial expression of GRe-scFv is a powerful alternative tool for producing MAb to use in ELISA for quantitative analysis of total ginsenoside concentrations.

  9. Mycobacterium avium restriction fragment lenght polymorphism-IS IS1245 and the simple double repetitive element polymerase chain reaction typing method to screen genetic diversity in Brazilian strains

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    Patrícia Carvalho de Sequeira

    2005-11-01

    Full Text Available Simple double repetitive element polymerase chain reaction (MaDRE-PCR and Pvu II-IS1245 restriction fragment length polymorphism (RFLP typing methods were used to type 41 Mycobacterium avium isolates obtained from 14 Aids inpatients and 10 environment and animals specimens identified among 53 mycobacteria isolated from 237 food, chicken, and pig. All environmental and animals strains showed orphan patterns by both methods. By MaDRE-PCR four patients, with multiple isolates, showed different patterns, suggesting polyclonal infection that was confirmed by RFLP in two of them. This first evaluation of MaDRE-PCR on Brazilian M. avium strains demonstrated that the method seems to be useful as simple and less expensive typing method for screening genetic diversity in M. avium strains on selected epidemiological studies, although with limitation on analysis identical patterns except for one band.

  10. Labeling of Anti-MUC-1 Binding Single Chain Fv Fragments to Surface Modified Upconversion Nanoparticles for an Initial in Vivo Molecular Imaging Proof of Principle Approach

    Science.gov (United States)

    Hischemöller, Anja; Walter, Claudia; Weiler, Volker; Hummel, Helga; Thepen, Theo; Huhn, Michael; Barth, Stephan; Hoheisel, Werner; Köhler, Karen; Dimova-Landen, Diana; Bremer, Christoph; Haase, Markus; Waldeck, Jens

    2012-01-01

    In vivo optical Imaging is an inexpensive and highly sensitive modality to investigate and follow up diseases like breast cancer. However, fluorescence labels and specific tracers are still works in progress to bring this promising modality into the clinical day-to-day use. In this study an anti-MUC-1 binding single-chain antibody fragment was screened, produced and afterwards labeled with newly designed and surface modified NaYF4:Yb,Er upconversion nanoparticles as fluorescence reporter constructs. The MUC-1 binding of the conjugate was examined in vitro and in vivo using modified state-of-the-art small animal Imaging equipment. Binding of the newly generated upconversion nanoparticle based probe to MUC-1 positive cells was clearly shown via laser scanning microscopy and in an initial proof of principal small animal optical imaging approach. PMID:22605971

  11. Labeling of Anti-MUC-1 Binding Single Chain Fv Fragments to Surface Modified Upconversion Nanoparticles for an Initial in Vivo Molecular Imaging Proof of Principle Approach

    Directory of Open Access Journals (Sweden)

    Markus Haase

    2012-03-01

    Full Text Available In vivo optical Imaging is an inexpensive and highly sensitive modality to investigate and follow up diseases like breast cancer. However, fluorescence labels and specific tracers are still works in progress to bring this promising modality into the clinical day-to-day use. In this study an anti-MUC-1 binding single-chain antibody fragment was screened, produced and afterwards labeled with newly designed and surface modified NaYF4:Yb,Er upconversion nanoparticles as fluorescence reporter constructs. The MUC-1 binding of the conjugate was examined in vitro and in vivo using modified state-of-the-art small animal Imaging equipment. Binding of the newly generated upconversion nanoparticle based probe to MUC-1 positive cells was clearly shown via laser scanning microscopy and in an initial proof of principal small animal optical imaging approach.

  12. Magnetite magnetosome and fragmental chain formation of Magnetospirillum magneticum AMB-1: transmission electron microscopy and magnetic observations

    Science.gov (United States)

    Li, Jinhua; Pan, Yongxin; Chen, Guanjun; Liu, Qingsong; Tian, Lanxiang; Lin, Wei

    2009-04-01

    Stable single-domain (SD) magnetite formed intracellularly by magnetotactic bacteria is of fundamental interest in sedimentary and environmental magnetism. In this study, we studied the time course of magnetosome growth and magnetosome chain formation (0-96 hr) in Magnetospirillum magneticum AMB-1 by transmission electron microscopy (TEM) observation and rock magnetism. The initial non-magnetic cells were microaerobically batch cultured at 26 °C in a modified magnetic spirillum growth medium. TEM observations indicated that between 20 and 24 hr magnetosome crystals began to mineralize simultaneously at multiple sites within the cell body, followed by a phase of rapid growth lasting up to 48 hr cultivation. The synthesized magnetosomes were found to be assembled into 3-5 subchains, which were linearly aligned along the long axis of the cell, supporting the idea that magnetosome vesicles were linearly anchored to the inner membrane of cell. By 96 hr cultivation, 14 cubo-octahedral magnetosome crystals in average with a mean grain size of ~44.5 nm were formed in a cell. Low-temperature (10-300 K) thermal demagnetization, room-temperature hysteresis loops and first-order reversal curves (FORCs) were conducted on whole cell samples. Both coercivity (4.7-18.1 mT) and Verwey transition temperature (100-106 K) increase with increasing cultivation time length, which can be explained by increasing grain size and decreasing non-stoichiometry of magnetite, respectively. Shapes of hysteresis loops and FORCs indicated each subchain behaving as an `ideal' uniaxial SD particle and extremely weak magnetostatic interaction fields between subchains. Low-temperature thermal demagnetization of remanence demonstrated that the Moskowitz test is valid for such linear subchain configurations (e.g. δFC/δZFC > 2.0), implying that the test is applicable to ancient sediments where magnetosome chains might have been broken up into short chains due to disintegration of the organic scaffold

  13. Selection and Characterization of Single Chain Antibody Fragments Specific for Hsp90 as a Potential Cancer Targeting Molecule

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    Edyta Petters

    2015-08-01

    Full Text Available Heat shock proteins play an essential role in facilitating malignant transformation and they have been recognized as important factors in human cancers. One of the key elements of the molecular chaperones machinery is Hsp90 and it has recently become a target for anticancer therapeutic approaches. The potential and importance of Hsp90-directed agents becomes apparent when one realizes that disruption of Hsp90 function may influence over 200 oncogenic client proteins. Here, we described the selection and characterization of Hsp90-specific antibody fragments from commercially available Tomlinson I and J phage display libraries. The affinities of Hsp90-binding scFv variants were measured using SPR method. Then, based on the best clone selected, we performed the affinity maturation procedure and obtained valuable Hsp90-specific clones. The selected binders were expressed and applied for immunostaining, ELISA and SPR analysis using model cancer cell lines. All performed experiments confirmed the ability of selected antibodies to interact with the Hsp90. Therefore, the presented Hsp90-specific scFv, might be a starting point for the development of a novel antibody-based strategy targeting cancer.

  14. [Expression of single chain fragment variable P1D3 antibody against shrimp white spot syndrome virus in Pichia pastoris].

    Science.gov (United States)

    Yang, Yi; Zhang, Min; Yuan, Li; Zhang, Xiao-Hua; Dai, He-Ping

    2006-11-01

    White spot syndrome virus (WSSV) is a major pathogen in aquaculture penaeid shrimp, which caused catastrophic economic losses in the worldwide. No adequate treatments against WSSV are available. In order to study infection mechanism of WSSV, a phage display scFv cDNA library against WSSV was constructed and a neutralizing antibody of scFv P1D3 was selected in our lab previously. In this study, scFv P1D3 was expressed successfully in yeast. Firstly, the original expression vector of P1D3, M13 phagmid, was used as a template to design primers with restriction sites of SnaB I and EcoR I . Then the gene of P1D3 was amplified by PCR. After digested by SnaB I and EcoR I , the fragment of scFv P1D3 with E-tag was inserted into yeast and E. coli shuttle plasmid pPIC9k. The recombinant plasmid pPIC9k-scFv P1D3-Etag was linearized with Bgl II and then transformed into Pichia pastoris GS115 by electroporation. Positive clones were selected and verified by PCR and DNA sequencing. The scFv PID3 was induced to express in yeast by methanol. The results of ELISA demonstrate that scFv P1D3 expressed in yeast still has high specificity to bind on WSSV and the binding activity is higher than that expressed in E. coli TG1. After several optimizing experiments, the results show that the expression amount of scFv P1D3 can reach to 302 mg/L in yeast culture supernatant. This experiment has offered a new source of antibody for the researches on passive immunology for shrimp.

  15. Preparation of novel magnetic molecular imprinted polymers nanospheres via reversible addition - fragmentation chain transfer polymerization for selective and efficient determination of tetrabromobisphenol A.

    Science.gov (United States)

    Shao, Yanming; Zhou, Lincheng; Wu, Qiong; Bao, Chao; Liu, Mingzhu

    2017-10-05

    A well-defined molecularly imprinted polymer nanospheres with excellent specific recognition ability was prepared on Fe3O4 nanoparticles via the combination of click chemistry and surface-initiated reversible addition-fragmentation chain transfer (RAFT) polymerization and using Tetrabromobisphenol A as template. Concretely, Fe3O4 nanoparticles were prepared by solvothermal method and then modified by 4-vinylbenylchloride through distillation-precipitation, which makes azide groups easily introduced on the surface of magnetic nanoparticles to form the relatively large amount of benzyl chloride groups. With high efficiency, alkyne terminated RAFT chain transfer agent were then immobilized onto the surface of Fe3O4 by means of click chemistry, which is Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The highly uniform imprinted thin film was finally fabricated on the surface of RAFT agent modified Fe3O4 nanoparticles. The binding results demonstrated that as-prepared imprinted beads exhibited remarkable molecular imprinting effects to the template molecule, fast rebinding kinetics and an excellent selectivity to compounds with similar configuration. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Evidence for non-conservative current-induced forces in the breaking of Au and Pt atomic chains

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    Carlos Sabater

    2015-12-01

    Full Text Available This experimental work aims at probing current-induced forces at the atomic scale. Specifically it addresses predictions in recent work regarding the appearance of run-away modes as a result of a combined effect of the non-conservative wind force and a ‘Berry force’. The systems we consider here are atomic chains of Au and Pt atoms, for which we investigate the distribution of break down voltage values. We observe two distinct modes of breaking for Au atomic chains. The breaking at high voltage appears to behave as expected for regular break down by thermal excitation due to Joule heating. However, there is a low-voltage breaking mode that has characteristics expected for the mechanism of current-induced forces. Although a full comparison would require more detailed information on the individual atomic configurations, the systems we consider are very similar to those considered in recent model calculations and the comparison between experiment and theory is very encouraging for the interpretation we propose.

  17. Genetic polymorphism of toll-like receptors 4 gene by polymerase chain reaction-restriction fragment length polymorphisms, polymerase chain reaction-single-strand conformational polymorphism to correlate with mastitic cows

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    Pooja H. Gupta

    2015-05-01

    Full Text Available Aim: An attempt has been made to study the toll-like receptors 4 (TLR4 gene polymorphism from cattle DNA to correlate with mastitis cows. Materials and Methods: In present investigation, two fragments of TLR4 gene named T4CRBR1 and T4CRBR2 of a 316 bp and 382 bp were amplified by polymerase chain reaction (PCR, respectively from Kankrej (22 and Triple cross (24 cattle. The genetic polymorphisms in the two populations were detected by a single-strand conformational polymorphism in the first locus and by digesting the fragments with restriction endonuclease Alu I in the second one. Results: Results showed that both alleles (A and B of two loci were found in all the two populations and the value of polymorphism information content indicated that these were highly polymorphic. Statistical results of χ2 test indicated that two polymorphism sites in the two populations fit with Hardy–Weinberg equilibrium (p˂0.05. Meanwhile, the effect of polymorphism of TLR4 gene on the somatic cell score (SCS indicated the cattle with allele a in T4CRBR1 showed lower SCS than that of allele B (p<0.05. Thus, the allele A might play an important role in mastitis resistance in cows. Conclusion: The relationship between the bovine mastitis trait and the polymorphism of TLR4 gene indicated that the bovine TLR4 gene may play an important role in mastitis resistance.

  18. Non-surface activity and micellization behavior of cationic amphiphilic block copolymer synthesized by reversible addition-fragmentation chain transfer process.

    Science.gov (United States)

    Ghosh, Arjun; Yusa, Shin-ichi; Matsuoka, Hideki; Saruwatari, Yoshiyuki

    2011-08-02

    Cationic amphiphilic diblock copolymers of poly(n-butylacrylate)-b-poly(3-(methacryloylamino)propyl)trimethylammonium chloride) (PBA-b-PMAPTAC) with various hydrophobic and hydrophilic chain lengths were synthesized by a reversible addition-fragmentation chain transfer (RAFT) process. Their molecular characteristics such as surface activity/nonactivity were investigated by surface tension measurements and foam formation observation. Their micelle formation behavior and micelle structure were investigated by fluorescence probe technique, static and dynamic light scattering (SLS and DLS), etc., as a function of hydrophilic and hydrophobic chain lengths. The block copolymers were found to be non-surface active because the surface tension of the aqueous solutions did not change with increasing polymer concentration. Critical micelle concentration (cmc) of the polymers could be determined by fluorescence and SLS measurements, which means that these polymers form micelles in bulk solution, although they were non-surface active. Above the cmc, the large blue shift of the emission maximum of N-phenyl-1-naphthylamine (NPN) probe and the low micropolarity value of the pyrene probe in polymer solution indicate the core of the micelle is nonpolar in nature. Also, the high value of the relative intensity of the NPN probe and the fluorescence anisotropy of the 1,6-diphenyl-1,3,5-hexatriene (DPH) probe indicated that the core of the micelle is highly viscous in nature. DLS was used to measure the average hydrodynamic radii and size distribution of the copolymer micelles. The copolymer with the longest PBA block had the poorest water solubility and consequently formed micelles with larger size while having a lower cmc. The "non-surface activity" was confirmed for cationic amphiphilic diblock copolymers in addition to anionic ones studied previously, indicating the universality of non-surface activity nature.

  19. Population Genetic Patterns of Threatened European Mudminnow (Umbra krameri Walbaum, 1792 in a Fragmented Landscape: Implications for Conservation Management.

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    Péter Takács

    Full Text Available The European mudminnow (Umbra krameri is a Middle Danubian endemic fish species, which is characterised by isolated populations living mainly in artificial habitats in the centre of its range, in the Carpathian Basin. For their long term preservation, reliable information is needed about the structure of stocks and the level of isolation. The recent distribution pattern, and the population genetic structure within and among regions were investigated to designate the Evolutionary Significant, Conservation and Management Units (ESUs, CUs, MUs and to explore the conservation biological value of the shrinking populations. In total, eight microsatellite loci were studied in 404 specimens originating from eight regions. The results revealed a pronounced population structure, where strictly limited gene flow was detected among regions, as well as various strengths of connections within regions. Following the results of hierarchical structure analyses, two ESUs were supposed in the Carpathian Basin, corresponding to the Danube and Tisza catchments. Our results recommend designating the borders of CUs in an 80-90km range and 16 clusters should be set up as MUs for the 33 investigated populations. How these genetic findings can be used to better allocate conservation resources for the long term maintenance of the metapopulation structure of this threathened endemic fish is discussed.

  20. Space use and movements of moose in Massachusetts: implications for conservation of large mammals in a fragmented environment

    Science.gov (United States)

    Wattles, David W.; DeStefano, Stephen

    2013-01-01

    Moose (Alces alces) have recently re-occupied a portion of their range in the temperate deciduous forest of the northeastern United States after a >200 year absence. In southern New England, moose encounter different forest types, more human development, and higher temperatures than in other parts of their geographic range in North America. We analyzed seasonal minimum convex polygon home ranges, utilization distributions, movement rates, and home range composition of GPS-collared moose in Massachusetts. Seasonal home range sizes were not different for males and females and were within the range reported for low latitudes elsewhere in North America. Seasonal movement patterns reflected the seasonal changes in metabolic rate and the influence of the species’ reproductive cycle and weather. Home ranges consisted almost entirely of forested habitat, included large amounts of conservation land, and had lower road densities as compared to the landscape as a whole, indicating that human development may be a limiting factor for moose in the region. The size and configuration of home ranges, seasonal movement patterns, and use relative to human development have implications for conservation of moose and other wide-ranging species in more highly developed portions of their ranges.

  1. Synthesis of PNVP-Based Copolymers with Tunable Thermosensitivity by Sequential Reversible Addition–Fragmentation Chain Transfer Copolymerization and Ring-Opening Polymerization

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    Yi-Shen Huang

    2017-06-01

    Full Text Available Through the reversible addition–fragmentation chain transfer (RAFT copolymerization of 3-ethyl-1-vinyl-2-pyrrolidone (C2NVP and N-vinylpyrrolidone (NVP, a series of well-defined P(C2NVP-co-NVP copolymers were synthesized (Mn = ca. 8000 to 16,000 and Mw/Mn <1.5 by using a difunctional chain transfer agent, S-(1-methyl-4-hydroxyethyl acetate O-ethyl xanthate (MHEX. Copolymerizing kinetics and different monomer ratio in feeds were conducted to study the apparent monomer reaction rate and reactivity ratios of NVP and C2NVP, which indicated similar reaction rates and predominantly ideal random copolymers for the two monomers. The Tgs of the obtaining P(C2NVP-co-NVP copolymers significantly corresponded to not only molecular weights MWs but also copolymer compositions. These copolymers presented characteristic lower critical solution temperatures (LCST behavior. We then studied the cloud points (CPs of the copolymers with varying MWs and compositions. With different MWs, the CPs were linearly decreased from ca. 51 to 45 °C. With different compositions, the CPs of the copolymers decreased from ca. 48 to 29 °C with C2NVP content (i.e., from 60.8 to 89.9 mol %. Fitting the CPs by the theoretical equation, the result illustrated that the introduction of more hydrophobic units of C2NVP suppressed the hydrophilic interaction between the polymer chain and water. We then successfully proceeded the chain extension through the ring-opening polymerization (ROP of ε-caprolactone (CL to the synthesis of a novel P(C2NVP-co-NVP-b-PCL amphiphilic block copolymer (Mn,NMR = 14,730 and Mw/Mn = 1.59. The critical micelle concentration (CMC of the block copolymer had a value of ca. 1.46 × 10−4 g/L. The block copolymer micelle was traced by dynamic light scattering (DLS, obtaining thermosensitive behaviors with a particle size of ca. 240 nm at 25 °C and ca. 140 nm at 55 °C, respectively.

  2. Microhabitat use of the western black-crested gibbon inhabiting an isolated forest fragment in southern Yunnan, China: implications for conservation of an endangered species.

    Science.gov (United States)

    Ni, Qingyong; Liang, Zongli; Xie, Meng; Xu, Huailiang; Yao, Yongfang; Zhang, Mingwang; Li, Yan; Li, Ying; Jiang, Xuelong

    2018-01-01

    Due to the synergistic effects of hunting and habitat loss, populations of the western black-crested gibbon are currently restricted to isolated forest fragments. The home range use of this species in fragmented forests is presumptively related to spatial, food and vegetation attributes, as in other primates. We examined the distributions of different food resources, the structure of the vegetation (tree density, DBH, and height), and the microhabitat use of one gibbon group in an isolated and disturbed forest at Bajiaohe in southern Yunnan, China. The results indicated that the gibbons used the edge habitat frequently, which was subject to more anthropogenic disturbance than the interior forest, and they appeared to adapt to discontinuous canopy cover by using bamboo and tsaoko plants for travel. The group also modified its diet in response to fluctuations in food availability and the local flora. However, the gibbons intensively used areas with high tree fruit availability across the two study periods. It is suggested that the microhabitat use by the group was mostly affected by the distribution of particular food resources and canopy gaps caused by selective logging. Protecting the current distribution area and planting native important food species to boost habitat quality and connectivity should be considered as part of conservation plans of the western black crested gibbon living in limited areas.

  3. PEGylation of a High-Affinity Anti-(+)Methamphetamine Single Chain Antibody Fragment Extends Functional Half-Life by Reducing Clearance.

    Science.gov (United States)

    Reichard, Emily E; Nanaware-Kharade, Nisha; Gonzalez, Guillermo A; Thakkar, Shraddha; Owens, S Michael; Peterson, Eric C

    2016-12-01

    Methamphetamine (METH) abuse is a worldwide drug problem, yet no FDA-approved pharmacological treatments are available for METH abuse. Therefore, we produced an anti-METH single chain antibody fragment (scFv7F9Cys) as a pharmacological treatment for METH abuse. ScFv's have a short half-life due to their small size, limiting their clinical use. Thus, we examined the pharmacokinetic effects of conjugating poly(ethylene) glycol (-PEG) to scFv7F9Cys to extend its functional half-life. The affinity of scFv7F9Cys and PEG conjugates to METH was determined in vitro via equilibrium dialysis saturation binding. Pharmacokinetic and parameters of scFv7F9Cys and scFv7F9Cys-PEG20K (30 mg/kg i.v. each) and their ability to bind METH in vivo were determined in male Sprague-Dawley rats receiving a subcutaneous infusion of METH (3.2 mg/kg/day). Of three PEGylated conjugates, scFv7F9Cys-PEG20K was determined the most viable therapeutic candidate. PEGylation of scFv7F9Cys did not alter METH binding functionality in vitro, and produced a 27-fold increase in the in vivo half-life of the antibody fragment. Furthermore, total METH serum concentrations increased following scFv7F9Cys or scFv7F9Cys-PEG20K administration, with scFv7F9Cys-PEG20K producing significantly longer changes in METH distribution than scFv7F9Cys. PEGylation of scFv7F9Cys significantly increase the functional half-life of scFv7F9Cys, suggesting it may be a long-lasting pharmacological treatment option for METH abuse.

  4. Generation and expression in plants of a single-chain variable fragment antibody against the immunodominant membrane protein of Candidatus phytoplasma aurantifolia.

    Science.gov (United States)

    Shahryari, F; Safarnejad, M R; Shams-Bakhsh, M; Schillberg, S; Nölke, G

    2013-08-01

    Witches' broom of lime is a disease caused by Candidatus Phytoplasma aurantifolia, which represents the most significant global threat to the production of lime trees (Citrus aurantifolia). Conventional disease management strategies have shown little success, and new approaches based on genetic engineering need to be considered. The expression of recombinant antibodies and fragments thereof in plant cells is a powerful approach that can be used to suppress plant pathogens. We have developed a single-chain variable fragment antibody (scFvIMP6) against the immunodominant membrane protein (IMP) of witches' broom phytoplasma and expressed it in different plant cell compartments. We isolated scFvIMP6 from a naïve scFv phage display library and expressed it in bacteria to demonstrate its binding activity against both recombinant IMP and intact phytoplasma cells. The expression of scFvIMP6 in plants was evaluated by transferring the scFvIMP6 cDNA to plant expression vectors featuring constitutive or phloem specific promoters in cassettes with or without secretion signals, therefore causing the protein to accumulate either in the cytosol or apoplast. All constructs were transiently expressed in Nicotiana benthamiana by agroinfiltration, and antibodies of the anticipated size were detected by immunoblotting. Plant-derived scFvIMP6 was purified by affinity chromatography, and specific binding to recombinant IMP was demonstrated by enzyme-linked immunosorbent assay. Our results indicate that scFvIMP6 binds with high activity and can be used for the detection of Ca. Phytoplasma aurantifolia and is also a suitable candidate for stable expression in lime trees to suppress witches' broom of lime.

  5. Development of recombinant single-chain variable fragment against hepatitis A virus and its use in quantification of hepatitis A antigen.

    Science.gov (United States)

    Nimmagadda, Sridevi V; Aavula, Shukra M; Biradhar, Neelakantam; Sula, Samuel; Lingala, Rajendra; Chandran, Dev; Villuppanoor, Srinivasan Alwar

    2012-07-01

    Phage display technology has been utilized for identification of specific binding molecules to an antigenic target thereby enabling the rapid generation and selection of high affinity, fully human antibodies directed towards disease target appropriate for antibody therapy. In the present study, single chain Fv antibody fragment (scFv) to hepatitis A virus (HAV) was selected from phage displayed antibody library constructed from peripheral blood lymphocytes (PBLs) of a vaccinated donor. The variable heavy (V(H)) and light chains (V(L)) were amplified using cDNA as template, assembled into scFv using splicing by overlap extension PCR (SOE PCR) and cloned into phagemid vector as a fusion for display of scFv on bacteriophage. The phage displaying antibody fragments were subjected to three rounds of panning with HAV antigen on solid phase. High affinity antibodies reactive to hepatitis A virus were identified by phage ELISA and cloned into a bacterial expression vector pET20b. The scFv was purified by immobilized metal affinity chromatography (IMAC) on a nickel-nitrilotriacetic acid (NTA) agarose column and characterized. The binding activity and specificity of the scFv was established by its non-reactivity towards other human viral antigens as determined by ELISA and immunoblot analysis. The scFv was further used in the development of an in-house IC-ELISA format in combination with a commercially available mouse monoclonal antibody for the quantification of hepatitis A virus antigen in human vaccine preparations. The adjusted r² values obtained by subjecting the values obtained by quantification of the NIBSC standards using the commercial and the in-house ELISA kits by regression analysis were 0.99 and 0.95. 39 vaccine samples were subjected to quantification using both the kits. Regressional statistical analysis through the origin of the samples indicated International Unit (IU) values of 0.0416x and 0.0419x, respectively for the commercial and in-house kit

  6. The preparation of high-capacity boronate affinity adsorbents by surface initiated reversible addition fragmentation chain transfer polymerization for the enrichment of ribonucleosides in serum.

    Science.gov (United States)

    Wang, Chaozhan; Xu, Huanhuan; Wei, Yinmao

    2016-01-01

    Boronate affinity adsorption is uniquely selective for cis-diol-containing molecules. The preparation and application of boronate affinity materials has attracted much attention in recent years. In this work, a high-capacity boronate affinity adsorbent was prepared by surface-initiated reversible addition-fragmentation chain transfer polymerization (SI-RAFT). Commercial aminated poly(glycidyl methacrylate) (PGMA) microspheres were modified with the chain transfer agent (CTA) S-1-dodecyl-S-(α,α-dimethyl-α-acetic acid)trithiocarbonate (DDATC). Boronate-affinity adsorbents were then prepared via SI-RAFT polymerization employing 3-acrylamidophenylboronic acid (AAPBA) as the monomer. The Fourier transform infrared spectroscopy (FT-IR), nitrogen adsorption and desorption measurements have proven the successful grafting of AAPBA on PGMA microspheres surface. The boronate affinity adsorbents thus prepared possess much higher adsorption capacity (99.2 µmol/g of adenosine) and both faster adsorption and desorption speed towards ribonucleosides, the adsorption and desorption could be completed in 2 min. The high selectivity of the adsorbents to ribonucleosides was verified in the presence of a large excess of deoxynucleosides. The boronate affinity adsorbents were then employed for sample pretreatment before HPLC analysis of ribonucleosides in serum. The ribonucleosides were effectively enriched by boronate affinity dispersive solid-phase extraction (BA-DSPE), with high mass recoveries and good precision. The simultaneous determination of uridine and guanosine in calf serum was achieved by utilizing the standard addition method, their contents were determined to be 170 ± 11.6 ng/mL and 39.6 ± 4.4 ng/mL respectively. The results proved that the prepared boronate affinity materials could be applied for sample pretreatment of cis-diol containing molecules in biological samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Molecular identification of Candida species isolated from cases of neonatal candidemia using polymerase chain reaction-restriction fragment length polymorphism in a tertiary care hospital.

    Science.gov (United States)

    Fatima, Akeela; Bashir, Gulnaz; Wani, Tehmeena; Jan, Abiroo; Kohli, Amrish; Khan, Mosin S

    2017-01-01

    Candida spp. is an emerging cause of bloodstream infections worldwide. Delay in speciation of Candida isolates by conventional methods and resistance to antifungal drugs in various Candida species are responsible for the increase in morbidity and mortality due to candidemia. Hence, the rapid identification of Candida isolates is very important for the proper management of patients with candidemia. The aim was to re-evaluate the identification of various Candida spp. by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) and to evaluate the accuracy, speed, and cost of phenotypic methodology versus PCR-RFLP. Hospital-based cross-sectional study. Ninety consecutive clinical isolates of seven Candida species, isolated from blood of neonates and identified by routine phenotypic methods, were re-evaluated using universal primers internal transcribed spacer 1 (ITS1) and ITS4 for PCR amplification and Msp I restriction enzyme for RFLP. Kappa test for agreement. The results of PCR-RFLP were 100% in agreement with those obtained using conventional phenotypic methods. Identification could be achieved within 3 work days by both the methods. Our routine methods proved to be cost effective than PCR-RFLP. We can continue with our routine phenotypic methods and PCR-RFLP can be used for periodic quality control or when conventional methods fail to identify a species.

  8. Comparative study of the molecularly imprinted polymers prepared by reversible addition-fragmentation chain transfer "bulk" polymerization and traditional radical "bulk" polymerization.

    Science.gov (United States)

    Ma, Yue; Pan, Guoqing; Zhang, Ying; Guo, Xianzhi; Zhang, Huiqi

    2013-05-01

    Bisphenol A (BPA) and propranolol-imprinted polymers have been prepared via both reversible addition-fragmentation chain transfer "bulk" polymerization (RAFTBP) and traditional radical "bulk" polymerization (TRBP) under similar reaction conditions, and their equilibrium binding properties were compared in detail for the first time. The chemical compositions, specific surface areas, equilibrium bindings, and selectivity of the obtained molecularly imprinted polymers (MIPs) were systematically characterized. The experimental results showed that the MIPs with molecular imprinting effects and quite fast binding kinetics could be readily prepared via RAFTBP, but they did not show improved template binding properties in comparison with those prepared via TRBP, which is in sharp contrast to many previous reports. This could be attributed to the heavily interrupted equilibrium between the dormant species and active radicals in the RAFT mechanism because of the occurrence of fast gelation during RAFTBP. The findings presented here strongly demonstrates that the application of controlled radical polymerizations (CRPs) in molecular imprinting does not always benefit the binding properties of the resultant MIPs, which is of significant importance for the rational use of CRPs in generating MIPs with improved properties. Copyright © 2013 John Wiley & Sons, Ltd.

  9. Magnetic molecularly imprinted polymers synthesized by surface-initiated reversible addition-fragmentation chain transfer polymerization for the enrichment and determination of synthetic estrogens in aqueous solution.

    Science.gov (United States)

    Chen, Fangfang; Zhang, Jingjing; Wang, Minjun; Kong, Jie

    2015-08-01

    Magnetic molecularly imprinted polymers have attracted significant interest because of their multifunctionality of selective recognition of target molecules and rapid magnetic response. In this contribution, magnetic molecularly imprinted polymers were synthesized via surface-initiated reversible addition addition-fragmentation chain transfer polymerization using diethylstilbestrol as the template for the enrichment of synthetic estrogens. The uniform imprinted surface layer and the magnetic property of the magnetic molecularly imprinted polymers favored a fast binding kinetics and rapid analysis of target molecules. The static and selective binding experiments demonstrated a desirable adsorption capacity and good selectivity of the magnetic molecularly imprinted polymers in comparison to magnetic non-molecularly imprinted polymers. Accordingly, a corresponding analytical method was developed in which magnetic molecularly imprinted polymers were employed as magnetic solid-phase extraction materials for the concentration and determination of four synthetic estrogens (diethylstilbestrol, hexestrol, dienestrol, and bisphenol A) in fish pond water. The recoveries of these synthetic estrogens in spiked fish pond water samples ranged from 61.2 to 99.1% with a relative standard deviation of lower than 6.3%. This study provides a versatile approach to prepare well-defined magnetic molecularly imprinted polymers sorbents for the analysis of synthetic estrogens in water solution. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Characterization of a single-chain variable fragment recognizing a linear epitope of aβ: a biotechnical tool for studies on Alzheimer's disease?

    Directory of Open Access Journals (Sweden)

    Silke Dornieden

    Full Text Available Alzheimer's disease (AD is a progressive neurodegenerative disorder with devastating effects. Currently, therapeutic options are limited to symptomatic treatment. For more than a decade, research focused on immunotherapy for the causal treatment of AD. However, clinical trials with active immunization using Aβ encountered severe complications, for example meningoencephalitis. Consequently, attention focused on passive immunization using antibodies. As an alternative to large immunoglobulins (IgGs, Aβ binding single-chain variable fragments (scFvs were used for diagnostic and therapeutic research approaches. scFvs can be expressed in E. coli and may provide improved pharmacokinetic properties like increased blood-brain barrier permeability or reduced side-effects in vivo. In this study, we constructed an scFv from an Aβ binding IgG, designated IC16, which binds the N-terminal region of Aβ (Aβ(1-8. scFv-IC16 was expressed in E. coli, purified and characterized with respect to its interaction with different Aβ species and its influence on Aβ fibril formation. We were able to show that scFv-IC16 strongly influenced the aggregation behavior of Aβ and could be applied as an Aβ detection probe for plaque staining in the brains of transgenic AD model mice. The results indicate potential for therapy and diagnosis of AD.

  11. Expression of anti-tumor necrosis factor alpha (TNFα) single-chain variable fragment (scFv) in Spirodela punctata plants transformed with Agrobacterium tumefaciens.

    Science.gov (United States)

    Balaji, Parthasarathy; Satheeshkumar, P K; Venkataraman, Krishnan; Vijayalakshmi, M A

    2016-05-01

    Therapeutic antibodies against tumor necrosis factor alpha (TNFα) have been considered effective for some of the autoimmune diseases such as rheumatoid arthritis, Crohn's diseases, and so on. But associated limitations of the current therapeutics in terms of cost, availability, and immunogenicity have necessitated the need for alternative candidates. Single-chain variable fragment (scFv) can negate the limitations tagged with the anti-TNFα therapeutics to a greater extent. In the present study, Spirodela punctata plants were transformed with anti-TNFα through in planta transformation using Agrobacterium tumefaciens strain, EHA105. Instead of cefotaxime, garlic extract (1 mg/mL) was used to remove the agrobacterial cells after cocultivation. To the best of our knowledge, this report shows for the first time the application of plant extracts in transgenic plant development. 95% of the plants survived screening under hygromycin. ScFv cDNA integration in the plant genomic DNA was confirmed at the molecular level by PCR. The transgenic protein expression was followed up to 10 months. Expression of scFv was confirmed by immunodot blot. Protein expression levels of up to 6.3% of total soluble protein were observed. β-Glucuronidase and green fluorescent protein expressions were also detected in the antibiotic resistant plants. The paper shows the generation of transgenic Spirodela punctuata plants through in planta transformation. © 2015 International Union of Biochemistry and Molecular Biology, Inc.

  12. Mapping the carriage of flaA-restriction fragment length polymorphism Campylobacter genotypes on poultry carcasses through the processing chain and comparison to clinical isolates.

    Science.gov (United States)

    Duffy, Lesley L; Blackall, Patrick J; Cobbold, Rowland N; Fegan, Narelle

    2015-06-01

    Poultry are considered a major source for campylobacteriosis in humans. A total of 1866 Campylobacter spp. isolates collected through the poultry processing chain were typed using flaA-restriction fragment length polymorphism to measure the impact of processing on the genotypes present. Temporally related human clinical isolates (n = 497) were also typed. Isolates were obtained from whole chicken carcass rinses of chickens collected before scalding, after scalding, before immersion chilling, after immersion chilling and after packaging as well as from individual caecal samples. A total of 32 genotypes comprising at least four isolates each were recognised. Simpson's Index of Diversity (D) was calculated for each sampling site within each flock, for each flock as a whole and for the clinical isolates. From caecal collection to after packaging samples the D value did not change in two flocks, decreased in one flock and increased in the fourth flock. Dominant genotypes occurred in each flock but their constitutive percentages changed through processing. There were 23 overlapping genotypes between clinical and chicken isolates. The diversity of Campylobacter is flock dependant and may alter through processing. This study confirms that poultry are a source of campylobacteriosis in the Australian population although other sources may contribute. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

  13. Polymerase chain reaction-restriction fragment length polymorphism analysis of the genes involved in the biosynthesis of the lipopolysaccharide of Pasteurella multocida.

    Science.gov (United States)

    Tsai, Yu-Chen; Shien, Jui-Hung; Wu, Jin-Ru; Shieh, Happy K; Chang, Poa-Chun

    2011-05-01

    The lipopolysaccharide, also known as the somatic antigen or O-antigen, is an important virulence factor of Pasteurella multocida. In the current study, the genes involved in the biosynthesis of the outer core region of the lipopolysaccharide, which were obtained from somatic type reference strains and field strains of P. multocida, were subjected to polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. The PCR-RFLP analysis classified 11 out of the 16 serotypes into 5 PCR-RFLP types (I-V). Types I and V contain strains belong to serotypes 1 and 13, respectively. The rest of the PCR-RFLP types contain strains belong to certain groups of serotypes. Typing of 38 field strains from poultry using PCR-RFLP analysis and the gel diffusion precipitation test showed consistent results. These results indicate that the PCR-RFLP analysis can be a useful tool for rapid somatic typing of some strains of P. multocida. © 2011 The Author(s)

  14. Synthesis of Thermally Switchable Chromatographic Materials with Immobilized Ti4+ for Enrichment of Phosphopeptides by Reversible Addition Fragmentation Chain Transfer Polymerization

    Science.gov (United States)

    Wang, Di; Cao, Zhihan; Pang, Xinzhu; Deng, Yulin; Li, Bo; Dai, Rongji

    2018-01-01

    Reversible phosphorylation of proteins is one of the most crucial types of post-translational modifications (PTMs). And it shows significant work in diversified biological processes. However, the separation technology of phosphorylated peptides is still an analytical challenge in phosphoproteomics, because phosphopeptides are alway in low stoichiometry. Thus, enrichment of phosphopeptides before detection is indispensable. In this study, a novel temperature regulated separation protocol was developed. Silica@p (NIPAAm-co-IPPA)-Ti4+, a new Ti(IV)-IMAC (Immobilized Metal Affinity chromatography) materials was synthesized by reversible addition fragmentation chain transfer polymerization (RAFT). By the unique thermally responsive properties of poly(N-isopropylacrylamide) (PNIPAAm), the captured phosphorylated peptides could be released by changing temperature only without applying any other eluant which could damage the phosphopeptides. We employed isopropanol phosphonic acid (IPPA) as an IMAC ligand for the immobilization of Ti(IV) which could increase the specific adsorption of phosphopeptides. The enrichment and release properties were examined by treatment with pyridoxal 5’-phosphate (PLP) and casein phosphopeptides (CPP). Two phosphorylated compounds above have temperature-stimulated binding to Ti4+. Finally, silica@p (NIPAAm-co-IPPA)-Ti4+ was successfully employed in pretreatment of phosphopeptides in a tryptic digest of a-casein and human serum albumin (HSA). The results indicated a great potential of this new temperature-responsive material in phosphoproteomics study.

  15. Molecular identification of Candida species isolated from cases of neonatal candidemia using polymerase chain reaction-restriction fragment length polymorphism in a tertiary care hospital

    Directory of Open Access Journals (Sweden)

    Akeela Fatima

    2017-01-01

    Full Text Available Context: Candida spp. is an emerging cause of bloodstream infections worldwide. Delay in speciation of Candida isolates by conventional methods and resistance to antifungal drugs in various Candida species are responsible for the increase in morbidity and mortality due to candidemia. Hence, the rapid identification of Candida isolates is very important for the proper management of patients with candidemia. Aims: The aim was to re-evaluate the identification of various Candida spp. by polymerase chain reaction (PCR-restriction fragment length polymorphism (RFLP and to evaluate the accuracy, speed, and cost of phenotypic methodology versus PCR-RFLP. Settings and Design: Hospital-based cross-sectional study. Materials and Methods: Ninety consecutive clinical isolates of seven Candida species, isolated from blood of neonates and identified by routine phenotypic methods, were re-evaluated using universal primers internal transcribed spacer 1 (ITS1 and ITS4 for PCR amplification and Msp I restriction enzyme for RFLP. Statistical Analysis Used: Kappa test for agreement. Results: The results of PCR-RFLP were 100% in agreement with those obtained using conventional phenotypic methods. Identification could be achieved within 3 work days by both the methods. Our routine methods proved to be cost effective than PCR-RFLP. Conclusions: We can continue with our routine phenotypic methods and PCR-RFLP can be used for periodic quality control or when conventional methods fail to identify a species.

  16. Development of a single-chain variable fragment-alkaline phosphatase fusion protein and a sensitive direct competitive chemiluminescent enzyme immunoassay for detection of ractopamine in pork

    Energy Technology Data Exchange (ETDEWEB)

    Dong Jiexian; Li Zhenfeng; Lei Hongtao; Sun Yuanming [Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642 (China); Ducancel, Frederic [CEA, iBiTec-S, Service de Pharmacologie et d' Immnoanalyse (SPI), CEA Saclay, F-91191 Gif sur Yvette (France); Xu Zhenlin [Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642 (China); Boulain, Jean-Claude [CEA, iBiTec-S, Service de Pharmacologie et d' Immnoanalyse (SPI), CEA Saclay, F-91191 Gif sur Yvette (France); Yang Jinyi; Shen Yudong [Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642 (China); Wang Hong, E-mail: gzwhongd@63.com [Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642 (China)

    2012-07-29

    Graphical abstract: Detection model of dc-CLEIA based on anti-RAC scFv-AP fusion protein. Highlights: Black-Right-Pointing-Pointer The scFv-AP fusion protein against ractopamine (RAC) was produced. Black-Right-Pointing-Pointer A dc-CLEIA for RAC was developed based on the purified scFv-AP fusion protein. Black-Right-Pointing-Pointer The sensitivity of dc-CLEIA was 10 times as sensitive as dc-ELISA for RAC. Black-Right-Pointing-Pointer Recovery tests from pork samples were studied. Black-Right-Pointing-Pointer Good accuracy was obtained. - Abstract: A rapid, sensitive chemiluminescent enzyme immunoassay (CLEIA) for ractopamine (RAC) based on a single-chain variable fragment (scFv)-alkaline phosphatase (AP) fusion protein was developed. The scFv gene was prepared by cloning the heavy- and light-chain variable region genes (V{sub H} and V{sub L}) from hybridoma cell line AC2, which secretes antibodies against RAC, and assembling V{sub H} and V{sub L} genes with a linker by means of splicing overlap extension polymerase chain reaction. The resulting scFv gene was inserted into the expression vector pLIP6/GN containing AP to produce the fusion protein in Escherichia coli strain BL21. The purified scFv-AP fusion protein was used to develop a direct competitive CLEIA (dcCLEIA) protocol for detection of RAC. The average concentration required for 50% inhibition of binding and the limit of detection of the assay were 0.25 {+-} 0.03 and 0.02 {+-} 0.004 ng mL{sup -1}, respectively, and the linear response range extended from 0.05 to 1.45 ng mL{sup -1}. The assay was 10 times as sensitive as the corresponding enzyme-linked immunosorbent assay based on the same fusion protein. Cross-reactivity studies showed that the fusion protein did not cross react with RAC analogs. DcCLEIA was used to analyze RAC spiked pork samples, and the validation was confirmed by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS). The results showed a good correlation between

  17. Partial characterization of immunoglobulin light chains of carcharhine sharks: evidence for phylogenetic conservation of variable region and divergence of constant region structure.

    Science.gov (United States)

    Marchalonis, J J; Schluter, S F; Rosenshein, I L; Wang, A C

    1988-01-01

    Isolated light chains of IgM-type immunoglobulins of carcharhine sharks were analyzed by serological and biochemical means. When analyzed by isoelectric focusing analysis, light chains of the tiger shark (Galecerdo cuvieri), the galapagos shark (Carcharhinus galapagensis) and the sandbar shark (Carcharhinus plumbeus) showed a broad, but patterned, spectrum of bands ranging from pI 5.0 to 7.7 in which discrete families were observed. Serologically, light chains of the galapagos shark cross-reacted with rabbit antibodies against mouse immunoglobulin and a synthetic peptide corresponding to the J segment of T cell receptor beta chain. The latter cross-reaction is shared among light chains and T cell receptors. Although there was considerable heterogeneity in isoelectric focusing analysis, the light chains were homogeneous on the basis of apparent mass (23 kDa) and those of tiger shark and galapagos shark had relatively homogeneous dominant N-terminal sequences representing the first framework. The N-terminal sequences of these two shark light chains, were strongly homologous to one another and showed 75% identity to certain V kappa sequences of man and dog. Homology was also shown to V lambda sequences, but the degree of identity was approximately 50%. Following cleavage of the tiger shark light chain with o-iodosobenzoic acid which cleaves at tryptophanyl residues, a constant region peptide was isolated by gel filtration. It was possible to identify the homolog of this peptide within the constant regions of mammalian kappa and lambda chain, but the relationship to C kappa chain was stronger. The degree of identity among the corresponding C region peptides of mammalian, avian and elasmobranch species was much less than that observed for the framework 1 sequence of the light chain variable region. These data support the concept that variable and J region sequence have been conserved in the evolution of placoderm-derived vertebrates, but that constant regions show much

  18. A rare disease-associated mutation in the medium-chain acyl-CoA dehydrogenase (MCAD) gene changes a conserved arginine, previously shown to be functionally essential in short-chain acyl-CoA dehydrogenase (SCAD)

    DEFF Research Database (Denmark)

    Andresen, B S; Bross, P; Jensen, T G

    1993-01-01

    157 mutation was verified in genomic DNA from the patient and her mother by a PCR-based assay. The mutation changes conserved arginine at position 28 (R28C) of the mature MCAD protein. The effect of the T157 mutation on MCAD protein was investigated by expression of mutant MCAD cDNA in COS-7 cells....... On the basis of knowledge about the three-dimensional structure of the MCAD protein, we suggest that the mutation destroys a salt bridge between arginine28 and glutamate86, thereby affecting the formation of enzymatically active protein. Twenty-two additional families with compound heterozygous patients were......-chain acyl-CoA dehydrogenase (SCAD) gene of a patient with SCAD deficiency, suggesting that the conserved arginine is crucial for formation of active enzyme in the straight-chain acyl-CoA dehydrogenases....

  19. A conserved hydrophobic patch on Vβ domains revealed by TCRβ chain crystal structures: implications for pre-TCR dimerization

    Directory of Open Access Journals (Sweden)

    Bo eZhou

    2011-03-01

    Full Text Available The αβ T cell receptor (TCR is a multimeric complex whose β chain plays a crucial role in thymocyte development as well as antigen recognition by mature T lymphocytes. We report here crystal structures of individual β subunits, termed N15β (Vβ5.2Dβ2Jβ2.6Cβ2 and N30β (Vβ13Dβ1Jβ1.1Cβ2, derived from two αβ TCRs specific for the immunodominant Vesicular Stomatitis Virus octapeptide (VSV-8 bound to the murine H-2Kb MHC classⅠmolecule. The crystal packing of the N15β structure reveals a homodimer formed through two Vβ domains. The Vβ/Vβ module is topologically very similar to the Vα/Vβ module in the N15αβ heterodimer. By contrast, in the N30β structure, the Vβ domain’s external hydrophobic CFG face is covered by the neighboring molecule’s Cβ domain. In conjunction with systematic investigation of previously published TCR single subunit structures, we identified several conserved residues forming a concave hydrophobic patch at the center of the CFG outer face of the Vβ and other V-type Ig-like domains. This hydrophobic patch is shielded from solvent exposure in the crystal packing, implying that it is unlikely to be thermodynamically stable if exposed on the thymocyte surface. Accordingly, we propose a dimeric pre-TCR model distinct from those suggested previously by others and discuss its functional and structural implications.

  20. Therapeutic anti-IgE monoclonal antibody single chain variable fragment (scFv) safety and immunomodulatory effects after one time injection in four dogs.

    Science.gov (United States)

    Hammerberg, Bruce; Eguiluz-Hernandez, Sitka

    2017-02-01

    The therapeutic monoclonal antibody omalizumab that is specific for IgE has proven to be an effective addition to the treatment of allergic disease in humans. The aims of this study were to demonstrate the safety and immunomodulating effects of a single injection of a monoclonal antibody single chain variable fragments (scFv) specific for canine IgE in normal dogs. Three normal dogs were bled for EDTA whole blood samples for 112 days post-injection (dpi). A fourth dog was monitored for 28 days. Anti-IgE scFv was pegylated to minimize scFv dimerization. Four normal dogs were injected once subcutaneously with anti-IgE scFv at 1 mg/kg. Flow cytometry was performed on whole blood. Plasma levels of IgE were measured by ELISA. None of the four dogs showed signs of anaphylaxis. All dogs demonstrated decreases in IgE(+) cells in lymphocyte-gated events by 14 dpi. Dogs C and D returned to pre-injection levels by 21 days, whereas dogs A and B remained below pre-injection levels until Day 112. Similar differences were seen in IgE-bearing granulocyte-gated cells. Free plasma IgE decreased below pre-injection levels by 47% in Dog A and by 52% in Dog B at 112 days. Dogs C and D did not change by more than 32% from preinjection levels. A single injection of monomeric, pegylated scFv with high affinity for dog IgE was demonstrated to be safe. Marked reduction in IgE-bearing lymphocytes and granulocytes accompanied by reduced "free" plasma IgE level in two of four dogs is analogous to omalizumab in humans. © 2016 ESVD and ACVD.

  1. Generation of a Highly Reactive Chicken-Derived Single-Chain Variable Fragment against Fusarium verticillioides by Phage Display

    Directory of Open Access Journals (Sweden)

    Zu-Quan Hu

    2012-06-01

    Full Text Available Fusarium verticillioides is the primary causal agent of Fusarium ear and kernel rot in maize, producing fumonisin mycotoxins that are toxic to humans and domestic animals. Rapid detection and monitoring of fumonisin-producing fungi are pivotally important for the prevention of mycotoxins from entering into food/feed products. Chicken-derived single-chain variable fragments (scFvs against cell wall-bound proteins from F. verticillioides were isolated from an immunocompetent phage display library. Comparative phage enzyme-linked immunosorbant assays (ELISAs and sequencing analyses identified four different scFv antibodies with high sensitivity. Soluble antibody ELISAs identified two highly sensitive scFv antibodies, FvCA3 and FvCA4, with the latter being slightly more sensitive. Three-dimensional modeling revealed that the FvCA4 may hold a better overall structure with CDRH3, CDRL1 and CDRL3 centered in the core region of antibody surface compared with that of other scFvs. Immunofluorescence labeling revealed that the binding of FvCA4 antibody was localized to the cell walls of conidiospores and hyphae of F. verticillioides, confirming the specificity of this antibody for a surface target. This scFv antibody was able to detect the fungal mycelium as low as 10−2 μg/mL and contaminating mycelium at a quantity of 10−2 mg/g maize. This is the first report that scFv antibodies derived from phage display have a wide application for rapid and accurate detection and monitoring of fumonisin-producing pathogens in agricultural samples.

  2. A Novel Fully Human Agonistic Single Chain Fragment Variable Antibody Targeting Death Receptor 5 with Potent Antitumor Activity In Vitro and In Vivo

    Directory of Open Access Journals (Sweden)

    Gaoxin Lei

    2017-09-01

    Full Text Available Agonistic antibodies, which bind specifically to death receptor 5 (DR5, can trigger apoptosis in tumor cells through the extrinsic pathway. In this present study, we describe the use of a phage display to isolate a novel fully human agonistic single chain fragment variable (scFv antibody, which targets DR5. After five rounds of panning a large (1.2 × 108 clones phage display library on DR5, a total of over 4000 scFv clones were screened by the phage ELISA. After screening for agonism in a cell-viability assay in vitro, a novel DR5-specific scFv antibody TR2-3 was isolated, which inhibited COLO205 and MDA-MB-231 tumor cell growth without any cross-linking agents. The activity of TR2-3 in inducing apoptosis in cancer cells was evaluated by using an Annexin V-PE apoptosis detection kit in combination with flow cytometry and the Hoechst 33342 and propidium iodide double staining analysis. In addition, the activation of caspase-dependent apoptosis was evaluated by Western blot assays. The results indicated that TR2-3 induced robust apoptosis of the COLO205 and MDA-MB-231 cells in a dose-dependent and time-dependent manner, while it remarkably upregulated the cleavage of caspase-3 and caspase-8. Furthermore, TR2-3 suppressed the tumor growth significantly in the xenograft model. Taken together, these data suggest that TR2-3 exhibited potent antitumor activity both in vitro and in vivo. This work provides a novel human antibody, which might be a promising candidate for cancer therapy by targeting DR5.

  3. Expression and Characterization of a Single-Chain Variable Fragment against Human LOX-1 inEscherichia coliandBrevibacillus choshinensis.

    Science.gov (United States)

    Hu, Wei; Xiang, Jun-Yan; Kong, Ping; Liu, Ling; Xie, Qiuhong; Xiang, Hongyu

    2017-05-28

    The single-chain variable fragment (scFv) against lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a promising molecule for its potential use in the diagnosis and immunotherapy of atherosclerosis. Producing this scFv in several milligram amounts could be the starting point for further engineering and application of the scFv. In this study, the abundant expression of the anti-LOX-1 scFv was attempted using Escherichia coli ( E. coli ) and Brevibacillus choshinensis (B. choshinensis) . The scFv had limited soluble yield in E. coli , but it was efficiently secreted by B. choshinensis . The optimized fermentation was determined using the Plackett-Burman screening design and response surface methodology, under which the yield reached up to 1.5 g/l in a 5-L fermentor. Moreover, the properties of the scFvs obtained from the two expression systems were different. The antigen affinity, transition temperature, and particle diameter size were 1.01E-07 M, 55.2 ± 0.3°C, and 9.388 nm for the scFv expressed by B. choshinensis , and 4.53E-07 M, 52.5 ± 0.3°C, and 13.54 nm for the scFv expressed by E. coli . This study established an efficient scale-up production methodology for the anti-LOX-1 scFv, which will boost its use in LOX-1-based therapy.

  4. Anti-CD20 single chain variable antibody fragment-apolipoprotein A-I chimera containing nanodisks promote targeted bioactive agent delivery to CD20-positive lymphomas.

    Science.gov (United States)

    Crosby, Natasha M; Ghosh, Mistuni; Su, Betty; Beckstead, Jennifer A; Kamei, Ayako; Simonsen, Jens B; Luo, Bing; Gordon, Leo I; Forte, Trudy M; Ryan, Robert O

    2015-08-01

    A fusion protein comprising an α-CD20 single chain variable fragment (scFv) antibody, a spacer peptide, and human apolipoprotein (apo) A-I was constructed and expressed in Escherichia coli. The lipid interaction properties intrinsic to apoA-I as well as the antigen recognition properties of the scFv were retained by the chimera. scFv•apoA-I was formulated into nanoscale reconstituted high-density lipoprotein particles (termed nanodisks; ND) and incubated with cultured cells. α-CD20 scFv•apoA-I ND bound to CD20-positive non-Hodgkins lymphoma (NHL) cells (Ramos and Granta) but not to CD20-negative T lymphocytes (i.e., Jurkat). Binding to NHL cells was partially inhibited by pre-incubation with rituximab, a monoclonal antibody directed against CD20. Confocal fluorescence microscopy analysis of Granta cells following incubation with α-CD20 scFv•apoA-I ND formulated with the intrinsically fluorescent hydrophobic polyphenol, curcumin, revealed α-CD20 scFv•apoA-I localizes to the cell surface, while curcumin off-loads and gains entry to the cell. Compared to control incubations, viability of cultured NHL cells was decreased upon incubation with α-CD20 scFv•apoA-I ND harboring curcumin. Thus, formulation of curcumin ND with α-CD20 scFv•apoA-I as the scaffold component confers cell targeting and enhanced bioactive agent delivery, providing a strategy to minimize toxicity associated with chemotherapeutic agents.

  5. Anti-CHMP5 single chain variable fragment antibody retrovirus infection induces programmed cell death of AML leukemic cells in vitro.

    Science.gov (United States)

    Wang, Hai-rong; Xiao, Zhen-yu; Chen, Miao; Wang, Fei-long; Liu, Jia; Zhong, Hua; Zhong, Ji-hua; Ou-Yang, Ren-rong; Shen, Yan-lin; Pan, Shu-ming

    2012-06-01

    Over-expressed CHMP5 was found to act as oncogene that probably participated in leukemogenesis. In this study, we constructed the CHMP5 single chain variable fragment antibody (CHMP5-scFv) retrovirus and studied the changes of programmed cell death (PCD) of AML leukemic cells after infection by the retrovirus. The anti-CHMP5 KC14 hybridoma cell line was constructed to generate monoclonal antibody of CHMP5. The protein expression of CHMP5 was studied using immunofluorescence analysis. pMIG-CHMP5 scFv antibody expressible retroviral vector was constructed to prepare CHMP5-scFv retrovirus. AML leukemic U937 cells were infected with the retrovirus, and programmed cell death was studied using confocal microscope, FCM and Western blot. We obtained a monoclonal antibody of CHMP5, and found the expression of CHMP5 was up-regulated in the leukemic cells. After U937 cells were infected with CHMP5-scFv retrovirus, CHMP5 protein was neutralized. Moreover, the infection resulted in a significant increase in apoptosis and necrosis of U937 cells. In U937 cells infected with CHMP5-scFv retrovirus, apoptosis-inducing factor (AIF)-mediated caspase-independent necrotic PCD was activated, but autophagic programmed cell death was not observed. Neither the intrinsic nor extrinsic apoptotic PCD pathway was activated. The granzyme B/perforin-mediated caspase-dependent apoptotic PCD pathway was not activated. CHMP5-scFv retrovirus can neutralize the abnormally high levels of the CHMP5 protein in the cytosol of AML leukemic U937 cells, thereby inducing the programmed cell death of the leukemic cells via AIF-mediated caspase-independent necrosis and apoptosis.

  6. Expression of a single-chain variable-fragment antibody against a Fusarium virguliforme toxin peptide enhances tolerance to sudden death syndrome in transgenic soybean plants.

    Science.gov (United States)

    Brar, Hargeet K; Bhattacharyya, Madan K

    2012-06-01

    Plants do not produce antibodies. However, plants can correctly assemble functional antibody molecules encoded by mammalian antibody genes. Many plant diseases are caused by pathogen toxins. One such disease is the soybean sudden death syndrome (SDS). SDS is a serious disease caused by the fungal pathogen Fusarium virguliforme. The pathogen, however, has never been isolated from diseased foliar tissues. Thus, one or more toxins produced by the pathogen have been considered to cause foliar SDS. One of these possible toxins, FvTox1, was recently identified. We investigated whether expression of anti-FvTox1 single-chain variable-fragment (scFv) antibody in transgenic soybean can confer resistance to foliar SDS. We have created two scFv antibody genes, Anti-FvTox1-1 and Anti-FvTox1-2, encoding anti-FvTox1 scFv antibodies from RNAs of a hybridoma cell line that expresses mouse monoclonal anti-FvTox1 7E8 antibody. Both anti-FvTox1 scFv antibodies interacted with an antigenic site of FvTox1 that binds to mouse monoclonal anti-FvTox1 7E8 antibody. Binding of FvTox1 by the anti-FvTox1 scFv antibodies, expressed in either Escherichia coli or transgenic soybean roots, was initially verified on nitrocellulose membranes. Expression of anti-FvTox1-1 in stable transgenic soybean plants resulted in enhanced foliar SDS resistance compared with that in nontransgenic control plants. Our results suggest that i) FvTox1 is an important pathogenicity factor for foliar SDS development and ii) expression of scFv antibodies against pathogen toxins could be a suitable biotechnology approach for protecting crop plants from toxin-induced diseases.

  7. Substitution of a conserved cysteine-996 in a cysteine-rich motif of the laminin {alpha}2-chain in congenital muscular dystrophy with partial deficiency of the protein

    Energy Technology Data Exchange (ETDEWEB)

    Nissinen, M.; Xu Zhang; Tryggvason, K. [Univ. of Oulu (Finland)

    1996-06-01

    Congenital muscular dystrophies (CMDs) are autosomal recessive muscle disorders of early onset. Approximately half of CMD patients present laminin {alpha}2-chain (merosin) deficiency in muscle biopsies, and the disease locus has been mapped to the region of the LAMA2 gene (6q22-23) in several families. Recently, two nonsense mutations in the laminin {alpha}2-chain gene were identified in CMD patients exhibiting complete deficiency of the laminin {alpha}2-chain in muscle biopsies. However, a subset of CMD patients with linkage to LAMA2 show only partial absence of the laminin {alpha}2-chain around muscle fibers, by immunocytochemical analysis. In the present study we have identified a homozygous missense mutation in the {alpha}2-chain gene of a consanguineous Turkish family with partial laminin {alpha}2-chain deficiency. The T{r_arrow}C transition at position 3035 in the cDNA sequence results in a Cys996{r_arrow}Arg substitution. The mutation that affects one of the conserved cysteine-rich repeats in the short arm of the laminin {alpha}2-chain should result in normal synthesis of the chain and in formation and secretion of a heterotrimeric laminin molecule. Muscular dysfunction is possibly caused either by abnormal disulfide cross-links and folding of the laminin repeat, leading to the disturbance of an as yet unknown binding function of the laminin {alpha}2-chain and to shorter half-life of the muscle-specific laminin-2 and laminin-4 isoforms, or by increased proteolytic sensitivity, leading to truncation of the short arm. 42 refs., 7 figs.

  8. Development of a Multiplexed Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Assay to Identify Common Members of the Subgenera Culex (Culex) and Culex (Phenacomyia) in Guatemala

    OpenAIRE

    Kent, Rebekah J.; Deus, Stephen; Williams, Martin; Savage, Harry M.

    2010-01-01

    Morphological differentiation of mosquitoes in the subgenera Culex (Culex) and Culex (Phenacomyia) in Guatemala is difficult, with reliable identification ensured only through examination of larval skins from individually reared specimens and associated male genitalia. We developed a multiplexed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay to identify common Cx. (Cux.) and Cx. (Phc.). Culex (Cux.) chidesteri, Cx. (Cux.) coronator, Cx. (Cux.) interrogator...

  9. A set of primers conserved in genus Parnassius (Lepidoptera, Papilionidae) for amplification and sequencing of 1016 bp fragment of cytochrome oxidase subunit I from museum specimens.

    Science.gov (United States)

    Konopinski, Maciej K

    2008-05-01

    Four short, overlapping amplicons covering a 1016 bp fragment of mitochondrial cytochrome oxidase subunit I were developed. All four fragments were successfully amplified and sequenced in eight species of butterflies belonging to the genus Parnassius including over 100-year-old DNA from pinned museum specimens. The fragment contains sufficient variation for both inter- and intraspecific analyses. A total of 105 sites were polymorphic within 52 haplotypes found in 186 samples from Parnassius mnemosyne. © 2007 The Authors.

  10. Supply chain integration in the building industry : The emergence of integrated and repetitive strategies in a fragmented and project-driven industry

    NARCIS (Netherlands)

    Vrijhoef, R.

    2011-01-01

    The building industry is a fragmented and project-driven industry with specific characteristics, which can sometimes result in negative effects. Reference has often been made to other industries, particularly manufacturing, that would function more effectively and efficiently. Major differences

  11. Fragmentation of monoclonal antibodies

    Science.gov (United States)

    Vlasak, Josef

    2011-01-01

    Fragmentation is a degradation pathway ubiquitously observed in proteins despite the remarkable stability of peptide bond; proteins differ only by how much and where cleavage occurs. The goal of this review is to summarize reports regarding the non-enzymatic fragmentation of the peptide backbone of monoclonal antibodies (mAbs). The sites in the polypeptide chain susceptible to fragmentation are determined by a multitude of factors. Insights are provided on the intimate chemical mechanisms that can make some bonds prone to cleavage due to the presence of specific side-chains. In addition to primary structure, the secondary, tertiary and quaternary structures have a significant impact in modulating the distribution of cleavage sites by altering local flexibility, accessibility to solvent or bringing in close proximity side chains that are remote in sequence. This review focuses on cleavage sites observed in the constant regions of mAbs, with special emphasis on hinge fragmentation. The mechanisms responsible for backbone cleavage are strongly dependent on pH and can be catalyzed by metals or radicals. The distribution of cleavage sites are different under acidic compared to basic conditions, with fragmentation rates exhibiting a minimum in the pH range 5–6; therefore, the overall fragmentation pattern observed for a mAb is a complex result of structural and solvent conditions. A critical review of the techniques used to monitor fragmentation is also presented; usually a compromise has to be made between a highly sensitive method with good fragment separation and the capability to identify the cleavage site. The effect of fragmentation on the function of a mAb must be evaluated on a case-by-case basis depending on whether cleavage sites are observed in the variable or constant regions, and on the mechanism of action of the molecule. PMID:21487244

  12. Robustness of metacommunities with omnivory to habitat destruction: disentangling patch fragmentation from patch loss.

    Science.gov (United States)

    Liao, Jinbao; Bearup, Daniel; Wang, Yeqiao; Nijs, Ivan; Bonte, Dries; Li, Yuanheng; Brose, Ulrich; Wang, Shaopeng; Blasius, Bernd

    2017-06-01

    Habitat destruction, characterized by patch loss and fragmentation, is a major driving force of species extinction, and understanding its mechanisms has become a central issue in biodiversity conservation. Numerous studies have explored the effect of patch loss on food web dynamics, but ignored the critical role of patch fragmentation. Here we develop an extended patch-dynamic model for a tri-trophic omnivory system with trophic-dependent dispersal in fragmented landscapes. We found that species display different vulnerabilities to both patch loss and fragmentation, depending on their dispersal range and trophic position. The resulting trophic structure varies depending on the degree of habitat loss and fragmentation, due to a tradeoff between bottom-up control on omnivores (dominated by patch loss) and dispersal limitation on intermediate consumers (dominated by patch fragmentation). Overall, we find that omnivory increases system robustness to habitat destruction relative to a simple food chain. © 2017 by the Ecological Society of America.

  13. Fragmentation of Chitosan by Acids

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Kasaai

    2013-01-01

    Full Text Available Fragmentation of chitosan in aqueous solution by hydrochloric acid was investigated. The kinetics of fragmentation, the number of chain scissions, and polydispersity of the fragments were followed by viscometry and size exclusion chromatography. The chemical structure and the degree of N-acetylation (DA of the original chitosan and its fragments were examined by 1H NMR spectroscopy and elemental analysis. The kinetic data indicates that the reaction was of first order. The results of polydispersity and the DA suggest that the selected experimental conditions (temperature and concentration of acid were appropriate to obtain the fragments having the polydispersity and the DA similar to or slightly different from those of the original one. A procedure to estimate molecular weight of fragments as well as the number of chain scissions of the fragments under the experimental conditions was also proposed.

  14. 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.

  15. The form of causation in health, disease and intervention: biopsychosocial dispositionalism, conserved quantity transfers and dualist mechanistic chains.

    Science.gov (United States)

    Evans, David W; Lucas, Nicholas; Kerry, Roger

    2017-01-25

    Causation is important when considering: how an organism maintains health; why disease arises in a healthy person; and, how one may intervene to change the course of a disease. This paper explores the form of causative relationships in health, disease and intervention, with particular regard to the pathological and biopsychosocial models. Consistent with the philosophical view of dispositionalism, we believe that objects are the fundamental relata of causation. By accepting the broad scope of the biopsychosocial model, we argue that psychological and social constructs be considered objects. We think that this 'biopsychosocial dispositionalism' offers the flexibility required to describe causation throughout health, disease and intervention pathways. When constructing mechanistic chains to describe causative pathways, we argue that an object will causally connect with others through actions; transfers of energy from one object to another, initiated by the manifestation of one or more dispositional property. Finally, our analysis of causative interactions utilises the concept that a common form of interaction exists between disease and intervention pathways. This common form will always be an object, but the mode of interaction will vary with each disease. We describe how intervention may act through objects being shared between converging mechanistic chains, or through the removal and/or insertion of objects in such chains. We believe that this analysis provides novel insight to the forms of causative transactions that can occur. In addition, we hope that the findings of this analysis represent the first step towards developing a framework for appraising the composition of mechanistic theories.

  16. Lactobacilli-expressed single-chain variable fragment (scFv) specific for intercellular adhesion molecule 1 (ICAM-1) blocks cell-associated HIV-1 transmission across a cervical epithelial monolayer.

    Science.gov (United States)

    Chancey, Caren J; Khanna, Kristen V; Seegers, Jos F M L; Zhang, Guang Wen; Hildreth, James; Langan, Abigail; Markham, Richard B

    2006-05-01

    The vaginal and cervical epithelia provide an initial barrier to sexually acquired HIV-1 infection in women. To study the interactions between HIV-1-infected cells or cell-free HIV-1 and the reproductive epithelium, the transmission of HIV-1 by infected cells or cell-free virus across human cervical epithelial cells was examined using a Transwell culture system. Cell-associated HIV-1 was transmitted more efficiently than cell-free virus, and monocyte-associated virus was transmitted most efficiently. Abs to ICAM-1 added to the apical side of the epithelium blocked cell-mediated transepithelial HIV-1 transmission in vitro. When used in a previously described model of vaginal HIV-1 transmission in human PBL-SCID mice, anti-murine ICAM-1 Abs (0.4 microg/10 microl) also blocked vaginal transmission of cell-associated HIV-1 in vivo. To evaluate a candidate delivery system for the use of this Ab as an anti-HIV-1 microbicide, anti-ICAM single-chain variable fragment Abs secreted by transformed lactobacilli were evaluated for their protective efficacy in the Transwell model. Like the intact Ab and Fab derived from it, the single-chain variable fragment at a concentration of 6.7 microg/100 microl was able to reduce HIV-1 transmission by 70 +/- 5%. These data support the potential efficacy of an anti-ICAM Ab delivered by lactobacilli for use as an anti-HIV-1 microbicide.

  17. Wildlife habitat fragmentation.

    Science.gov (United States)

    John. Lehmkuhl

    2005-01-01

    A primary issue in forest wildlife management is habitat fragmentation and its effects on viability, which is the "bottom line" for plant and animal species of conservation concern. Population viability is the likelihood that a population will be able to maintain itself (remain viable) over a long period of time-usually 100 years or more. Though it is true...

  18. Multiparameter optimization method and enhanced production of secreted recombinant single-chain variable fragment against the HIV-1 P17 protein from Escherichia coli by fed-batch fermentation.

    Science.gov (United States)

    Paopang, Porntip; Kasinrerk, Watchara; Tayapiwatana, Chatchai; Seesuriyachan, Phisit; Butr-Indr, Bordin

    2016-01-01

    The single-chain fragment variable (scFv) was used to produce a completely functional antigen-binding fragment in bacterial systems. The advancements in antibody engineering have simplified the method of producing Fv fragments and made it more efficient and generally relevant. In a previous study, the scFv anti HIV-1 P17 protein was produced by a batch production system, optimized by the sequential simplex optimization method. This study continued that work in order to enhance secreted scFv production by fed-batch cultivation, which supported high volumetric productivity and provided a large amount of scFvs for diagnostic and therapeutic research. The developments in cell culture media and process parameter settings were required to realize the maximum production of cells. This study investigated the combined optimization methods, Plackett-Burman design (PBD) and sequential simplex optimization, with the aim of optimize feed medium. Fed-batch cultivation with an optimal feeding rate was determined. The result demonstrated that a 20-mL/hr feeding rate of the optimized medium can increase cell growth, total protein production, and scFv anti-p17 activity by 4.43, 1.48, and 6.5 times more than batch cultivation, respectively. The combined optimization method demonstrated novel power tools for the optimization strategy of multiparameter experiments.

  19. Characterization of the Native and Denatured Herceptin by ELISA and QCM using a High-Affinity Single Chain Fragment Variable (scFv) Recombinant Antibody

    Science.gov (United States)

    Shang, Yuqin; Mernaugh, Ray

    2012-01-01

    Herceptin/Trastuzumab is a humanized IgG1κ light chain antibody used to treat some forms of breast cancer. A phage-displayed recombinant antibody library was used to obtain an scFv (designated 2B4) to a linear synthetic peptide representing Herceptin’s heavy chain CDR3. ELISAs and piezoimmunosensor/quartz crystal microbalance (QCM) assays were used to characterize 2B4-binding activity to both native and heat denatured Herceptin. The 2B4 scFv specifically bound to heat denatured Herceptin in a concentration dependent manner over a wide (35–220.5 nM) dynamic range. Herceptin denatures and forms significant amount of aggregates when heated. UV-Vis characterization confirms that Herceptin forms aggregates as the temperature used to heat Herceptin increases. QCM affinity assay shows that binding stoichiometry between 2B4 scFv and Herceptin follows a 1:2 relationship proving that 2B4 scFv binds strongly to the dimers of heat denatured Herceptin aggregates and exhibits an affinity constant of 7.17 × 1013 M−2. The 2B4-based QCM assay was more sensitive than the corresponding ELISA. Combining QCM with ELISA can be used to more fully characterize non-specific binding events in assays. The potential theoretical and clinical implications of these results and the advantages of using QCM to characterize human therapeutic antibodies in samples are also discussed. PMID:22934911

  20. Surface molecular imprinting onto fluorescein-coated magnetic nanoparticlesvia reversible addition fragmentation chain transfer polymerization: A facile three-in-one system for recognition and separation of endocrine disrupting chemicals

    Science.gov (United States)

    Li, Ying; Dong, Cunku; Chu, Jia; Qi, Jingyao; Li, Xin

    2011-01-01

    In this study, we present a general protocol for the making of surface-imprinted magnetic fluorescence beads viareversible addition-fragmentation chain transfer polymerization. The resulting composites were characterized by X-ray diffraction analysis, transmission electron microscopy, scanning electron microscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy, and energy dispersive spectroscopy. The as-synthesized beads exhibited homogeneous polymer films (thickness of about 5.7 nm), spherical shape, high fluorescence intensity and magnetic property (Magnetization (Ms) = 3.67 emu g-1). The hybrids bind the original template 17β-estradiol with an appreciable selectivity over structurally related compounds. In addition, the resulting hybrids performed without obvious deterioration after five repeated cycles. This study therefore demonstrates the potential of molecularly imprinted polymers for the recognition and separation of endocrine disrupting chemicals.In this study, we present a general protocol for the making of surface-imprinted magnetic fluorescence beads viareversible addition-fragmentation chain transfer polymerization. The resulting composites were characterized by X-ray diffraction analysis, transmission electron microscopy, scanning electron microscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy, and energy dispersive spectroscopy. The as-synthesized beads exhibited homogeneous polymer films (thickness of about 5.7 nm), spherical shape, high fluorescence intensity and magnetic property (Magnetization (Ms) = 3.67 emu g-1). The hybrids bind the original template 17β-estradiol with an appreciable selectivity over structurally related compounds. In addition, the resulting hybrids performed without obvious deterioration after five repeated cycles. This study therefore demonstrates the potential of molecularly imprinted polymers for the recognition and separation of endocrine disrupting chemicals. Electronic

  1. Process Fragments

    Science.gov (United States)

    Eberle, Hanna; Unger, Tobias; Leymann, Frank

    The concepts presented in this paper are motivated by the assumption that process knowledge is distributed knowledge and not completely known just by one person. Driven by this assumption we deal in this paper with the following questions: How can partial process knowledge be represented? How can this partial knowledge be used to define something more complete? To use higher level artefacts as building blocks to new applications has a long tradition in software engineering to increase flexibility and reduce modeling costs. In this paper we take a first step in applying this concept to processes, by defining process building blocks and operations which compose process building blocks. The building blocks will be referred to as process fragments in the following. The process fragment composition may take place either at design or runtime of the process. The design time approach reduces design costs by reusing artefacts. However the runtime fragment composition approach realizes high flexibility due to the possibility in the dynamic selection of the fragments to be composed. The contribution of this work lies in a fragment definition that enables the fragment modeler to represent his 'local' and fragmentary knowledge in a formal way and which allows fragment models to be composed.

  2. A polymerase chain reaction-restriction fragment length polymorphism method based on the analysis of a 16S rRNA/tRNA(Val) mitochondrial region for species identification of commercial penaeid shrimps (Crustacea: Decapoda: Penaeoidea) of food interest.

    Science.gov (United States)

    Pascoal, Ananías; Barros-Velázquez, Jorge; Cepeda, Alberto; Gallardo, José M; Calo-Mata, Pilar

    2008-01-01

    A simple PCR-RFLP method has been developed for the identification of 19 penaeid shrimp species of food interest belonging to the superfamily Penaeoidea. Preliminary amplification, sequencing and alignment of a 960 bp fragment of the 16S rRNA/tRNA(Val)/12S rRNA mitochondrial region allowed the design of 16Scru4/16Scru4 primers, constructed on well-conserved mitochondrial sequences of the penaeid shrimp species considered. Such primers afforded the amplification of an internal 515-535 bp region of the 16S rRNA/tRNA(Val) genes that, when subjected to cleavage with AluI, TaqI and HinfI, provided species-specific restriction patterns. Moreover, the proposed method also allowed the definition of different intraspecific restriction types between different populations of Litopenaeus vannamei, Farfantepenaeus notialis, Fenneropenaeus merguiensis, Metapenaeus sp., Melicertus latisulcatus and Pleoticus muelleri of different origins. The method described here was also successfully applied for the identification of penaeid shrimps in complex processed precooked foods, where this type of shellfish is used as an added-value food ingredient. Sequencing analysis provided new information about the genetic relationships among shrimps not only at the levels of species and genus, but also among different populations at intraspecific level. The 16S rRNA/tRNA(Val) fragment considered in this study seems to be accurate for shrimp species identification in raw and processed foodstuffs and for phylogenetic analysis among penaeid shrimp species.

  3. Molecularly imprinted polymer coated solid-phase microextraction fiber prepared by surface reversible addition-fragmentation chain transfer polymerization for monitoring of Sudan dyes in chilli tomato sauce and chilli pepper samples.

    Science.gov (United States)

    Hu, Xiaogang; Fan, Yanan; Zhang, Yi; Dai, Guimei; Cai, Quanling; Cao, Yujuan; Guo, Changjuan

    2012-06-20

    Surface reversible addition-fragmentation chain transfer (RAFT) polymerization method was firstly applied to the preparation of molecularly imprinted polymer (MIP) coated silicon solid-phase microextraction (SPME) fibers. With Sudan I as template, an ultra-thin MIP coating with about 0.55-μm thickness was obtained with homogeneous structure and controlled composition, due to the controllable radical growing and chain propagation in surface RAFT polymerization. The MIP-coated fibers were found with enhanced selectivity coefficients (3.0-6.5) to Sudan I-IV dyes in contrast with those reported in our previous work. Furthermore, the ultra-thin thickness of MIP coating was helpful to the effective elution of template and fast adsorption/desorption kinetics, so only about 18 min was needed for MIP-coated SPME operation. The detection limits of 21-55 ng L(-1) were achieved for four Sudan dyes, when MIP-coated SPME was coupled with liquid chromatography (LC) and mass spectrometry (MS) detection. The MIP-coated SPME-LC-MS/MS method was tested for the monitoring of ultra trace Sudan dyes in spiked chilli tomato sauce and chilli pepper samples, and high enrichment effect, remarkable matrix peaks-removing capability, and consequent high sensitivities were achieved to four Sudan dyes. Copyright © 2012 Elsevier B.V. All rights reserved.

  4. Murine CR1/2 targeted antigenized single-chain antibody fragments induce transient low affinity antibodies and negatively influence an ongoing immune response.

    Science.gov (United States)

    Prechl, József; Molnár, Eszter; Szekeres, Zsuzsanna; Isaák, Andrea; Papp, Krisztián; Balogh, Péter; Erdei, Anna

    2007-01-01

    We have generated a single-chain antibody which recognizes murine CR1/2 and carries a genetically fused influenza hemagglutinin derived peptide. Theoretically such a construct is able to crosslink the B cell antigen receptor and CR1/2 on peptide specific B cells. The construct was able to reach its CR1/2 positive target cells, yet intraperitoneal delivery of the construct elicited an IgM response only slightly exceeding that induced by the free peptide. Providing T cell help by the injection of peptide specific lymphocytes did not alter the response in essence, that is anti-peptide IgG was not detectable even after booster immunizations. When used as a booster vaccine following injection of the peptide in adjuvant, the construct even inhibited the development of IgG1 and IgG3 anti-peptide antibodies. These data indicate that although targeting of antigen to CR1/2 on B cells can enhance transient proliferation or differentiation of antigen specific B cells it cannot induce strong, longlasting humoral immune responses. Furthermore, CR1/2 targeting constructs may negatively influence an ongoing immune reaction.

  5. Engineering of a recombinant trivalent single-chain variable fragment antibody directed against rabies virus glycoprotein G with improved neutralizing potency.

    Science.gov (United States)

    Turki, Imène; Hammami, Akil; Kharmachi, Habib; Mousli, Mohamed

    2014-02-01

    Human and equine rabies immunoglobulins are currently available for passive immunization against rabies. However, these are hampered by the limited supply and some drawbacks. Advances in antibody engineering have led to overcome issues of clinical applications and to improve the protective efficacy. In the present study, we report the generation of a trivalent single-chain Fv (scFv50AD1-Fd), that recognizes the rabies virus glycoprotein, genetically fused to the trimerization domain of the bacteriophage T4 fibritin, termed 'foldon' (Fd). scFv50AD1-Fd was expressed as soluble recombinant protein in bacterial periplasmic space and purified through affinity chromatography. The molecular integrity and stability were analyzed by polyacrylamide gradient-gel electrophoresis, size-exclusion chromatography and incubation in human sera. The antigen-binding properties of the trimeric scFv were analyzed by direct and competitive-ELISA. Its apparent affinity constant was estimated at 1.4 ± 0.25 × 10(9)M(-1) and was 75-fold higher than its monovalent scFv (1.9 ± 0.68 × 10(7)M(-1)). The scFv50AD1-Fd neutralized rabies virus in a standard in vitro and in vivo neutralization assay. We showed a high neutralization activity up to 75-fold compared with monovalent format and the WHO standard serum. The gain in avidity resulting from multivalency along with an improved biological activity makes the trivalent scFv50AD1-Fd construct an important reagent for rabies protection. The antibody engineering approach presented here may serve as a strategy for designing a new generation of anti-rabies for passive immunotherapy. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Optimal Economic Landscapes with Habitat Fragmentation Effects

    OpenAIRE

    Lewis, David J.; Wu, JunJie

    2005-01-01

    Habitat fragmentation is widely considered a primary threat to biodiversity. This paper develops a theoretical model of land use to analyze the optimal conservation of landscapes when land quality is spatially heterogeneous and wildlife habitat is fragmented and socially valuable. When agriculture is the primary cause of fragmentation, we show that reforestation efforts should be targeted to the most fragmented landscapes with an aggregate share of forest equal to a threshold, defined by the ...

  7. Chameleon fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Brax, Philippe [Institut de Physique Théorique, CEA, IPhT, CNRS, URA 2306, F-91191Gif/Yvette Cedex (France); Upadhye, Amol, E-mail: philippe.brax@cea.fr, E-mail: aupadhye@anl.gov [Institute for the Early Universe, Ewha University, International Education, Building #601, 11-1, Daehyun-Dong Seodaemun-Gu, Seoul 120-750 (Korea, Republic of)

    2014-02-01

    A scalar field dark energy candidate could couple to ordinary matter and photons, enabling its detection in laboratory experiments. Here we study the quantum properties of the chameleon field, one such dark energy candidate, in an ''afterglow'' experiment designed to produce, trap, and detect chameleon particles. In particular, we investigate the possible fragmentation of a beam of chameleon particles into multiple particle states due to the highly non-linear interaction terms in the chameleon Lagrangian. Fragmentation could weaken the constraints of an afterglow experiment by reducing the energy of the regenerated photons, but this energy reduction also provides a unique signature which could be detected by a properly-designed experiment. We show that constraints from the CHASE experiment are essentially unaffected by fragmentation for φ{sup 4} and 1/φ potentials, but are weakened for steeper potentials, and we discuss possible future afterglow experiments.

  8. Rock fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Brown, W.S.; Green, S.J.; Hakala, W.W.; Hustrulid, W.A.; Maurer, W.C. (eds.)

    1976-01-01

    Experts in rock mechanics, mining, excavation, drilling, tunneling and use of underground space met to discuss the relative merits of a wide variety of rock fragmentation schemes. Information is presented on novel rock fracturing techniques; tunneling using electron beams, thermocorer, electric spark drills, water jets, and diamond drills; and rock fracturing research needs for mining and underground construction. (LCL)

  9. HLA Class I and Class II Conserved Extended Haplotypes and Their Fragments or Blocks in Mexicans: Implications for the Study of Genetic Diversity in Admixed Populations

    Science.gov (United States)

    Ohashi, Marina; Lebedeva, Tatiana; Acuña-Alonzo, Víctor; Yunis, María; Granados-Montiel, Julio; Cruz-Lagunas, Alfredo; Vargas-Alarcón, Gilberto; Rodríguez-Reyna, Tatiana S.; Fernandez-Viña, Marcelo; Granados, Julio; Yunis, Edmond J.

    2013-01-01

    Major histocompatibility complex (MHC) genes are highly polymorphic and informative in disease association, transplantation, and population genetics studies with particular importance in the understanding of human population diversity and evolution. The aim of this study was to describe the HLA diversity in Mexican admixed individuals. We studied the polymorphism of MHC class I (HLA-A, -B, -C), and class II (HLA-DRB1, -DQB1) genes using high-resolution sequence based typing (SBT) method and we structured the blocks and conserved extended haplotypes (CEHs) in 234 non-related admixed Mexican individuals (468 haplotypes) by a maximum likelihood method. We found that HLA blocks and CEHs are primarily from Amerindian and Caucasian origin, with smaller participation of African and recent Asian ancestry, demonstrating a great diversity of HLA blocks and CEHs in Mexicans from the central area of Mexico. We also analyzed the degree of admixture in this group using short tandem repeats (STRs) and HLA-B that correlated with the frequency of most probable ancestral HLA-C/−B and -DRB1/−DQB1 blocks and CEHs. Our results contribute to the analysis of the diversity and ancestral contribution of HLA class I and HLA class II alleles and haplotypes of Mexican admixed individuals from Mexico City. This work will help as a reference to improve future studies in Mexicans regarding allotransplantation, immune responses and disease associations. PMID:24086347

  10. A Study on Campylobacter jejuni and Campylobacter coli through Commercial Broiler Production Chains in Thailand: Antimicrobial Resistance, the Characterization of DNA Gyrase Subunit A Mutation, and Genetic Diversity by Flagellin A Gene Restriction Fragment Length Polymorphism.

    Science.gov (United States)

    Thomrongsuwannakij, Thotsapol; Blackall, Patrick J; Chansiripornchai, Niwat

    2017-06-01

    chain reaction-restriction fragment length polymorphism of the flagellin A gene (flaA-RFLP) to determine their genetic relationships. Ten distinct clusters were recognized by flaA-RFLP typing. The results showed that horizontal transmission was the major route of Campylobacter transmission in this study. In conclusion, the emergence of MDR and high resistance rates to several antimicrobials are major concerns identified in this study. The prudent use of these agents and active surveillance of resistance at the farm level are essential steps to reduce the public health risks identified in this work.

  11. Binding of HIV-1 gp41-directed neutralizing and non-neutralizing fragment antibody binding domain (Fab and single chain variable fragment (ScFv antibodies to the ectodomain of gp41 in the pre-hairpin and six-helix bundle conformations.

    Directory of Open Access Journals (Sweden)

    John M Louis

    Full Text Available We previously reported a series of antibodies, in fragment antigen binding domain (Fab formats, selected from a human non-immune phage library, directed against the internal trimeric coiled-coil of the N-heptad repeat (N-HR of HIV-1 gp41. Broadly neutralizing antibodies from that series bind to both the fully exposed N-HR trimer, representing the pre-hairpin intermediate state of gp41, and to partially-exposed N-HR helices within the context of the gp41 six-helix bundle. While the affinities of the Fabs for pre-hairpin intermediate mimetics vary by only 2 to 20-fold between neutralizing and non-neutralizing antibodies, differences in inhibition of viral entry exceed three orders of magnitude. Here we compare the binding of neutralizing (8066 and non-neutralizing (8062 antibodies, differing in only four positions within the CDR-H2 binding loop, in Fab and single chain variable fragment (ScFv formats, to several pre-hairpin intermediate and six-helix bundle constructs of gp41. Residues 56 and 58 of the mini-antibodies are shown to be crucial for neutralization activity. There is a large differential (≥ 150-fold in binding affinity between neutralizing and non-neutralizing antibodies to the six-helix bundle of gp41 and binding to the six-helix bundle does not involve displacement of the outer C-terminal helices of the bundle. The binding stoichiometry is one six-helix bundle to one Fab or three ScFvs. We postulate that neutralization by the 8066 antibody is achieved by binding to a continuum of states along the fusion pathway from the pre-hairpin intermediate all the way to the formation of the six-helix bundle, but prior to irreversible fusion between viral and cellular membranes.

  12. Characterization and conservation of the inner E2 core domain structure of branched-chain alpha-keto acid dehydrogenase complex from bovine liver. Construction of a cDNA encoding the entire transacylase (E2b) precursor.

    Science.gov (United States)

    Griffin, T A; Lau, K S; Chuang, D T

    1988-10-05

    A cDNA clone encoding the entire transacylase (E2b) precursor of the bovine branched-chain alpha-keto acid dehydrogenase complex has been constructed from two overlapping incomplete cDNA clones which were isolated from a lambda ZAP library prepared from bovine liver poly(A)+ RNA. Nucleotide sequencing indicates that this bovine E2b cDNA insert (bE2-11) is 2701 base pairs in length with an open reading frame of 1446 base pairs. The bE2-11 cDNA insert encodes a leader peptide of 61 residues and a mature E2b polypeptide of 421 amino acid residues with a calculated monomeric molecular mass of 46,518 daltons. The molecular mass of the native E2b component isolated from bovine liver is 1,110,000 daltons as determined by sedimentation equilibrium. This value establishes the 24-subunit octahedral model for the quaternary structure of bovine E2b. The amino-terminal sequences of two tryptic fragments (A and B) of the E2b protein have been determined. Fragment A comprises residues 175 to 421 of the E2b protein and is the inner E2 core domain which contains the transacylase active site. Fragment B, produced by further tryptic cleavage of fragment, comprises residues 205 to 421, but does not have transacylase activity. Both fragments A and B confer the highly assembled 24-mer structure. The primary structure of the inner E2 core domain of bovine E2b (fragment A) is very similar to those of three other E2 proteins (human E2p, Escherichia coli E2p, and E. coli E2k). These similarities suggest that these E2 proteins are structurally and evolutionarily related.

  13. Differentiation among three species of bovine Thelazia (Nematoda: Thelaziidae) by polymerase chain reaction-restriction fragment length polymorphism of the first internal transcribed spacer ITS-1 (rDNA).

    Science.gov (United States)

    Otranto, D; Tarsitano, E; Traversa, D; Giangaspero, A; De Luca, F; Puccini, V

    2001-12-01

    Thelazia gulosa, Thelazia rhodesi and Thelazia skrjabini are nematodes transmitted by some species of Musca (Diptera: Muscidae) which cause ocular infestations in bovines. Differences in the rDNA of these species were determined by a PCR using different sets of relatively conserved oligonucleotide primers. PCR on the first internal transcribed spacer (ITS-1) revealed differences in size in Thelazia species (437 bp for T. gulosa, 370 bp for T. rhodesi and 506 bp for T. skrjabini) while the DNA control of Musca spp. was not amplified. The ITS-1 amplicons of the three species were sequenced and then analysed. The GC contents ranged from 26 to 36% and the level of differences in the nucleotide sequences of ITS-1 was lower between T. skrjabini and T. gulosa (39%) than the latter and T. rhodesi (49-56%). Restriction fragment length polymorphism (RFLP) of ITS-1 amplicons was also carried out and the restriction profiles compared. Clear genetic differences among the three Thelazia examined were demonstrated by using the enzymes HpaII, CpoI and SspI. This PCR-RFLP for the delineation of T. gulosa, T. rhodesi and T. skrjabini offers prospects as a molecular epidemiological tool to study parasite transmission patterns and prevalence.

  14. Bespoke Fragments

    DEFF Research Database (Denmark)

    Kruse Aagaard, Anders

    2017-01-01

    The PhD project Bespoke Fragments is investigating the space emerging in the exploration of the relationship between digital drawing and fabrication, and the field of materials and their properties and capacities. Through a series of different experiments, the project situates itself in a shuttling...... tangible experiments, the project discusses materiality and digitally controlled fabrication tools as a expansion of the architect’s tool box and workflow. Bespoke Fragments considers this expansion as an opportunity to establish a connection between forms of digital drawing and the specificities...... of materials. Through that connection, the project seeks to use the realisation to generate developments and findings and, through an iterative mode of thinking, establish a dialogue between drawing, materials, and fabrication. The use of digital fabrication tools through digital drawing opens up a new...

  15. Architectural fragments

    DEFF Research Database (Denmark)

    Bang, Jacob Sebastian

    2018-01-01

    . I try to invent the ways of drawing the models - that decode and unfold them into architectural fragments- into future buildings or constructions in the landscape. [1] Luigi Moretti: Italian architect, 1907 - 1973 [2] Man Ray: American artist, 1890 - 1976. in 2015, I saw the wonderful exhibition......I have created a large collection of plaster models: a collection of Obstructions, errors and opportunities that may develop into architecture. The models are fragments of different complex shapes as well as more simple circular models with different profiling and diameters. In this contect I have...... been studying Luigi Moretti's [1] plastermodel - "the Model of the inner spaces of the Saint Maria of the Divine Providence" - in which context I see my own models. In 1934, Man Ray [2] photographed mathematical rmodels (in plaster) at the Henri Poincaré Institute in Paris and later used...

  16. Fragmentation based

    Directory of Open Access Journals (Sweden)

    Shashank Srivastava

    2014-01-01

    Gaining the understanding of mobile agent architecture and the security concerns, in this paper, we proposed a security protocol which addresses security with mitigated computational cost. The protocol is a combination of self decryption, co-operation and obfuscation technique. To circumvent the risk of malicious code execution in attacking environment, we have proposed fragmentation based encryption technique. Our encryption technique suits the general mobile agent size and provides hard and thorny obfuscation increasing attacker’s challenge on the same plane providing better performance with respect to computational cost as compared to existing AES encryption.

  17. Discrimination between dog-related and vampire bat-related rabies viruses in Brazil by strain-specific reverse transcriptase-polymerase chain reaction and restriction fragment length polymorphism analysis.

    Science.gov (United States)

    Ito, Mikako; Itou, Takuya; Shoji, Youko; Sakai, Takeo; Ito, Fumio H; Arai, Yohko T; Takasaki, Tomohiko; Kurane, Ichiro

    2003-04-01

    There is a geographical overlap between the two main rabies epidemiological cycles maintained by dogs and vampire bats in Latin America. The geographical and temporal coincidence of rabies outbreaks of respective origins is not unusual in rural areas of Latin America. These circumstances make it difficult to discriminate the intraspecies and interspecies transmission pathways of rabies. This study was conducted to develop techniques to discriminate dog-related and vampire bat-related rabies virus isolates (DRRV and VRRV, respectively) in Brazil. The 1396 nucleotides of the nucleoprotein gene of a total of 27 DRRV and VRRV were sequenced. Strain-specific (SS) primers were developed based on these sequences. Forty-nine rabies virus strains isolated from animals and humans in several parts of Brazil were examined by reverse transcriptase-polymerase chain reaction (RT-PCR) with SS primers. These rabies viruses were also amplified by RT-PCR with general rabies primers and the PCR products were cut by three restriction enzymes, Blp I, Bsu36 I and BspE I. All the DRRV and VRRV were distinguished by RT-PCR with SS primers. The PCR products obtained from DRRV were cut at one site by Blp I, but not by Bsu36 I. The PCR products obtained from VRRV were cut at one or two sites by Bsu36 I, but not by Blp I. Blp I and Bsu36 I clearly discriminated DRRV and VRRV in restriction fragment length polymorphysim (RFLP) assays. The results of SS RT-PCR and RFLP were consistent. SS RT-PCR and RFLP assays have been developed for determining the origins of rabies virus isolates in Brazil. These assays are simple and rapid, and will be useful for identifying the rabies virus reservoirs of field isolates in Brazil, especially when used together.

  18. Generation of a rabbit single-chain fragment variable (scFv) antibody for specific detection of Bradyrhizobium sp. DOA9 in both free-living and bacteroid forms.

    Science.gov (United States)

    Vu, Nguyen Xuan; Pruksametanan, Natcha; Srila, Witsanu; Yuttavanichakul, Watcharin; Teamtisong, Kamonluck; Teaumroong, Neung; Boonkerd, Nantakorn; Tittabutr, Panlada; Yamabhai, Montarop

    2017-01-01

    A simple and reliable method for the detection of specific nitrogen-fixing bacteria in both free-living and bacteroid forms is essential for the development and application of biofertilizer. Traditionally, a polyclonal antibody generated from an immunized rabbit was used for detection. However, the disadvantages of using a polyclonal antibody include limited supply and cross-reactivity to related bacterial strains. This is the first report on the application of phage display technology for the generation of a rabbit recombinant monoclonal antibody for specific detection and monitoring of nitrogen-fixing bacteria in both free-living form and in plant nodules. Bradyrhizobium sp. DOA9, a broad host range soil bacteria, originally isolated from the root nodules of Aeschynomene americana in Thailand was used as a model in this study. A recombinant single-chain fragment variable (scFv) antibody library was constructed from the spleen of a rabbit immunized with DOA9. After three rounds of biopanning, one specific phage-displayed scFv antibody, designated bDOA9rb8, was identified. Specific binding of this antibody was confirmed by phage enzyme-linked immunosorbent assay (phage ELISA). The phage antibody could bind specifically to DOA9 in both free-living cells (pure culture) and bacteroids inside plant nodules. In addition to phage ELISA, specific and robust immunofluorescence staining of both free-living and bacteroid forms could also be observed by confocal-immunofluorescence imaging, without cross-reactivity with other tested bradyrhizobial strains. Moreover, specific binding of free scFv to DOA9 was also demonstrated by ELISA. This recombinant antibody can also be used for the study of the molecular mechanism of plant-microbe interactions in the future.

  19. Purification optimization for a recombinant single-chain variable fragment against type 1 insulin-like growth factor receptor (IGF-1R) by using design of experiment (DoE).

    Science.gov (United States)

    Song, Yong-Hong; Sun, Xue-Wen; Jiang, Bo; Liu, Ji-En; Su, Xian-Hui

    2015-12-01

    Design of experiment (DoE) is a statistics-based technique for experimental design that could overcome the shortcomings of traditional one-factor-at-a-time (OFAT) approach for protein purification optimization. In this study, a DoE approach was applied for optimizing purification of a recombinant single-chain variable fragment (scFv) against type 1 insulin-like growth factor receptor (IGF-1R) expressed in Escherichia coli. In first capture step using Capto L, a 2-level fractional factorial analysis and successively a central composite circumscribed (CCC) design were used to identify the optimal elution conditions. Two main effects, pH and trehalose, were identified, and high recovery (above 95%) and low aggregates ratio (below 10%) were achieved at the pH range from 2.9 to 3.0 with 32-35% (w/v) trehalose added. In the second step using cation exchange chromatography, an initial screening of media and elution pH and a following CCC design were performed, whereby the optimal selectivity of the scFv was obtained on Capto S at pH near 6.0, and the optimal conditions for fulfilling high DBC and purity were identified as pH range of 5.9-6.1 and loading conductivity range of 5-12.5 mS/cm. Upon a further gel filtration, the final purified scFv with a purity of 98% was obtained. Finally, the optimized conditions were verified by a 20-fold scale-up experiment. The purities and yields of intermediate and final products all fell within the regions predicted by DoE approach, suggesting the robustness of the optimized conditions. We proposed that the DoE approach described here is also applicable in production of other recombinant antibody constructs. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Genetic structure of fragmented November moth (Lepidoptera: Geometridae) populations in farmland

    DEFF Research Database (Denmark)

    Wynne, Ian Robert; Loxdale, Hugh D.; Brookes, Cliff P.

    2003-01-01

    allozymes, conservation genetics, Epirrita dilutata, Epirrita christyi, molecular markers, habitat fragmentation, population genetic structure......allozymes, conservation genetics, Epirrita dilutata, Epirrita christyi, molecular markers, habitat fragmentation, population genetic structure...

  1. Bespoke Fragments

    DEFF Research Database (Denmark)

    Kruse Aagaard, Anders

    2016-01-01

    the digital environment with the reality of materials – and use realisation and materialisation to generate architectural developments and findings through an iterative mode of thinking about the dialogue between drawing, materials and fabrication. The control of fabrication tools through digital drawing......The Ph.D. -project Bespoke Fragments seeks to explore and utilise the space emerging between the potentials of digital drawing and fabrication and the field of materials and their properties and capacities. Within this span, the project is situated in a shuttling between the virtual and the actual......, investigating levels of control and uncertainty encountering with these. Through tangible experiments, the project discusses materiality and digitally controlled fabrications tools as direct expansions of the architect's digital drawing and workflow. The project sees this expansion as an opportunity to connect...

  2. Framing Fragmentation

    DEFF Research Database (Denmark)

    Bundgaard, Charlotte

    2009-01-01

    Contemporary industrialized architecture based on advanced information technology and highly technological production processes, implies a radically different approach to architecture than what we have experienced in the past. Works of architecture composed of prefabricated building components......, contain distinctive architectural traits, not only based on rational repetition, but also supporting composition and montage as dynamic concepts. Prefab architecture is an architecture of fragmentation, individualization and changeability, and this sets up new challenges for the architect. This paper...... tries to develop a strategy for the architect dealing with industrially based architecture; a strategy which exploits architectural potentials in industrial building, which recognizes the rules of mass production and which redefines the architect’s position among the agents of building. If recent...

  3. In vivo distribution of single chain variable fragment (scFv) against atherothrombotic oxidized LDL/β2-glycoprotein I complexes into atherosclerotic plaques of WHHL rabbits: Implication for clinical PET imaging.

    Science.gov (United States)

    Sasaki, Takanori; Kobayashi, Kazuko; Kita, Shoichi; Kojima, Kazuo; Hirano, Hiroyuki; Shen, Lianhua; Takenaka, Fumiaki; Kumon, Hiromi; Matsuura, Eiji

    2017-02-01

    Oxidized LDL (oxLDL) can exist as a complex with β2-glycoprotein I (β2GPI) in plasma/serum of patients with non-autoimmune atherosclerotic disease or antiphospholipid syndrome (APS). Nonetheless, direct in vivo evidence supporting the pathophysiological involvement of oxLDL/β2GPI complexes and specific autoantibody against the complexes in developing atherothrombosis has yet been established. In the present study, we demonstrated in vivo distribution of single chain variable fragment of IgG anti-oxLDL/β2GPI complexes (3H3-scFv) in Watanabe heritable hyperlipidemic (WHHL) rabbits by PET/CT imaging. An antibody-based PET probe, 64Cu-3H3-scFv, was established, and WHHL rabbits were applied for a non-autoimmune atherosclerotic model to demonstrate in vivo distribution of the probe. 3H3-scFv has exhibits specificity towards β2GPI complexed with oxLDL but neither a free form of β2GPI nor oxLDL alone. Post-intravenous administration of 64Cu-3H3-scFv into WHHL rabbits has demonstrated a non-invasive approach for in vivo visualization of atherosclerotic lesion. The imaging probe achieved ideal blood clearance and distribution for optimal imaging capacity in 24h, significantly shorter than that of an intact IgG-based imaging probe. 64Cu-3H3-scFv targeted on atherosclerotic plaques in aortas of WHHL rabbits where extensive accumulation of lipid deposits was observed by lipid staining and autoradiography. The accumulation of 64Cu-3H3-scFv in aortic segments of WHHL rabbits was 2.8-folds higher than that of controls (p=0.0045). The present in vivo evidence supports the pathophysiological involvement of oxLDL/β2GPI complexes in atherosclerotic complications of WHHL rabbits. 64Cu-3H3-scFv represents a novel PET imaging probe for non-invasive pathophysiological assessment of oxLDL/β2GPI complexes accumulated in atherosclerotic plaques. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. The Flp double cross system a simple efficient procedure for cloning DNA fragments

    Directory of Open Access Journals (Sweden)

    Sadowski Paul D

    2003-07-01

    Full Text Available Abstract Background While conventional cloning methods using restriction enzymes and polynucleotide ligase are adequate for most DNAs, fragments made by the polymerase chain reaction are difficult to clone because the amplifying DNA polymerase tends to add untemplated nucleotides to the 3'-termini of the amplified strands. Conservative site-specific recombinases offer an efficient alternative to conventional cloning methods. Results In this paper I describe the use of the Flp site-specific recombinase for cloning PCR-amplified fragments. A DNA fragment is amplified with primers that contain at their ends inverted target sequences for Flp. Flp readily recombines these fragments in vitro into a vector that also contains two inverted Flp target sequences surrounding the α-complementing region of the lacZ gene of E. coli. The recombinants are conveniently detected as white colonies by the familiar blue/white screening test for lacZ activity. A useful feature of the system is that both orientations of the inserted DNA are usually obtained. If the recipient vector is cut between the two inverted Flp targets, Flp "heals" the double-strand break by inserting a linear fragment flanked by Flp targets. Conclusion This system ("The Flp Double Cross System" should be useful for cloning multiple PCR fragments into many sites in several vectors. It has certain advantages over other available recombinase-based cloning procedures.

  5. Fragmentation and Hadronization

    OpenAIRE

    Webber, B.R.

    1999-01-01

    Experimental data, theoretical ideas and models concerning jet fragmentation and the hadronization process are reviewed, concentrating on the following topics: factorization and small-x resummation of fragmentation functions, hadronization models, single-particle yields and spectra in Z decay, comparisons between quark and gluon jets, current and target fragmentation in deep inelastic scattering, heavy quark fragmentation, Bose-Einstein correlations and WW fragmentation.

  6. Fragmentation and Hadronization

    OpenAIRE

    Webber, B.R.

    2000-01-01

    Experimental data, theoretical ideas and models concerning jet fragmentation and the hadronization process are reviewed, concentrating on the following topics: factorization and small-x resummation of fragmentation functions, hadronization models, single-particle yields and spectra in Z decay, comparisons between quark and gluon jets, current and target fragmentation in deep inelastic scattering, heavy quark fragmentation, Bose-Einstein correlations and WW fragmentation.

  7. Altered specificity of single-chain antibody fragments bound to pandemic H1N1-2009 influenza virus after conversion of the phage-bound to the soluble form

    Directory of Open Access Journals (Sweden)

    Kaku Yoshihiro

    2012-09-01

    Full Text Available Abstract Background In 2009, a novel influenza A/H1N1 virus (H1N1pdm quickly spread worldwide and co-circulated with then-existing seasonal H1N1 virus (sH1N1. Distinguishing between these 2 viruses was necessary to better characterize the epidemiological properties of the emergent virus, including transmission patterns, pathogenesis, and anti-influenza drug resistance. This situation prompted us to develop a point-of-care virus differentiation system before entering the 2009–2010 influenza season. Aiming to establish H1N1pdm-specific detection tools rapidly, we employed phage display libraries to select H1N1pdm-specific single-chain variable fragments (scFvs. Findings Human single-fold scFv libraries (Tomlinson I + J underwent selection for the ability to bind H1N1pdm virus particles. Three rounds of panning brought 1152 phage-bound scFvs, of which 58 clones reacted with H1N1pdm specifically or preferentially over sH1N1 in an enzyme-linked immunosorbent assay (ELISA. After conversion of the scFvs to soluble form, 7 clones demonstrating high/stable expression were finally obtained. However, all the soluble scFvs except No. 29 were found to have lost their specificity/preference for H1N1pdm in ELISA. The specificity/preference of No. 29 was also confirmed by immunofluorescence assay and immunoprecipitation, and the viral nucleoprotein was identified by ELISA as its target protein. The change in specificity associated with scFv conversion from phage-bound to soluble form could be due to loss of phage scaffold pIII protein, which likely provides structural support for the scFv antigen-binding site. It is also possible that the similar antigenic properties of H1N1pdm and sH1N1 led to the observed alterations in scFv specificity. Discussion Using a phage display library, we obtained 7 soluble scFv clones reactive against H1N1pdm; however, only 1 showed specificity/preference toward H1N1pdm. Our results confirmed that using phage display

  8. The antiviral action of interferon is potentiated by removal of the conserved IRTAM domain of the IFNAR1 chain of the interferon alpha/beta receptor: effects on JAK-STAT activation and receptor down-regulation.

    Science.gov (United States)

    Basu, L; Yang, C H; Murti, A; Garcia, J V; Croze, E; Constantinescu, S N; Mullersman, J E; Pfeffer, L M

    1998-03-01

    The first cloned chain (IFNAR1) of the human interferon-alpha (IFN alpha) receptor acts as a species-specific transducer for type 1 IFN action when transfected into heterologous mouse cells. Stably transfected mouse L929 cell lines expressing truncation mutants of the intracellular domain of the human IFNAR1 chain were tested for biological responses to human IFN alpha. Deletion of the intracellular domain resulted in a complete loss of sensitivity to the biological activity of human IFN but markedly increased IFNAR1 cell surface expression, demonstrating that the intracellular domain is required for biological function and contains a domain that negatively regulates its cell surface expression. Removal of the conserved membrane distal 16-amino-acid IRTAM (Interferon Receptor Tyrosine Activation Motif) sequence: (1) increased sensitivity to IFN alpha's antiviral activity, (2) increased the rapid IFN alpha-dependent formation of STAT-containing DNA-binding complexes, (3) prolonged tyrosine phosphorylation kinetics of the JAK-STAT pathway, and (4) blocked the IFN-dependent down-regulation of the IFNAR1 chain. These results indicate that the IRTAM negatively regulates signalling events required for the induction of IFN's biological actions via regulating receptor down-regulation.

  9. Development of a multiplexed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay to identify common members of the Subgenera Culex (Culex) and Culex (Phenacomyia) in Guatemala

    National Research Council Canada - National Science Library

    Kent, Rebekah J; Deus, Stephen; Williams, Martin; Savage, Harry M

    2010-01-01

    .... (Cux.) nigripalpus/Cx. (Cux.) thriambus, and Cx. (Phc.) lactator were identified directly with a multiplexed primer cocktail comprising a conserved forward primer and specific reverse primers targeting ribosomal DNA (rDNA...

  10. Amino acid substitutions of conserved residues in the carboxyl-terminal domain of the [alpha]I(X) chain of type X collagen occur in two unrelated families with metaphyseal chondrodysplasia type Schmid

    Energy Technology Data Exchange (ETDEWEB)

    Wallis, G.A.; Rash, B.; Sweetman, W.A.; Thomas, J.T.; Grant, M.E.; Boot-Handford, R.P. (Univ. of Manchester (United Kingdom)); Super, M. (Royal Manchester Children' s Hospital, Manchester (United Kingdom)); Evans, G. (Robert Jones Orthopaedic Hospital, Oswestry (United Kingdom))

    1994-02-01

    Type X collagen is a homotrimeric, short-chain, nonfibrillar extracellular-matrix component that is specifically and transiently synthesized by hypertrophic chondrocytes at the site of endochondral ossification. The precise function of type X collagen is not known, but its specific pattern of expression suggests that mutations within the encoding gene (COL10A1) that alter the structure or synthesis of the protein may cause heritable forms of chondrodysplasia. The authors used the PCR and the SSCP techniques to analyze the coding and upstream promoter regions of the COL10A1 gene in a number of individuals with forms of chondrodysplasia. Using this approach, they identified two individuals with metaphyseal chondrodysplasia type Schmid (MCDS) with SSCP changes in the region of the gene encoding the carboxyl-terminal domain. Sequence analysis demonstrated that the individuals were heterozygous for two unique single-base-pair transitions that led to the substitution of the highly conserved amino acid residue tyrosine at position 598 by aspartic acid in one person and of leucine at position 614 by proline in the other. The substitution at residue 598 segregated with the phenotype in a family of eight (five affected and three unaffected) related persons. The substitutions at residue 614 occurred in a sporadically affected individual but not in her unaffected mother and brother. Additional members of this family were not available for further study. These results suggest that certain amino acid substitutions within the carboxyl-terminal domain of the chains of the type X collagen molecule cause MCDS. These amino acid substitutions are likely to alter either chain recognition or assembly of the type X collagen molecule, thereby depleting the amount of normal type X collagen deposited in the extracellular matrix, with consequent aberrations in bone growth and development. 36 refs., 5 figs.

  11. Inactivation of the conserved open reading frame ycf34 of Synechocystis sp. PCC 6803 interferes with the photosynthetic electron transport chain.

    Science.gov (United States)

    Wallner, Thomas; Hagiwara, Yoshinori; Bernát, Gábor; Sobotka, Roman; Reijerse, Edward J; Frankenberg-Dinkel, Nicole; Wilde, Annegret

    2012-11-01

    Ycf34 is a hypothetical chloroplast open reading frame that is present in the chloroplast genomes of several non-green algae. Ycf34 homologues are also encoded in all sequenced genomes of cyanobacteria. To evaluate the role of Ycf34 we have constructed and analysed a cyanobacterial mutant strain. Inactivation of ycf34 in Synechocystis sp. PCC 6803 showed no obvious phenotype under normal light intensity growth conditions. However, when the cells were grown under low light intensity they contained less and smaller phycobilisome antennae and showed a strongly retarded growth, suggesting an essential role of the Ycf34 polypeptide under light limiting conditions. Northern blot analysis revealed a very weak expression of the phycocyanin operon in the ycf34 mutant under light limiting growth in contrast to the wild type and to normal light conditions. Oxygen evolution and P(700) measurements showed impaired electron flow between photosystem II and photosystem I under these conditions which suggest that the impaired antenna size is most likely due to a highly reduced plastoquinone pool which triggers regulation on a transcriptional level. Using a FLAG-tagged Ycf34 we found that this protein is tightly bound to the thylakoid membranes. UV-vis and Mössbauer spectroscopy of the recombinant Ycf34 protein demonstrate the presence of an iron-sulphur cluster. Since Ycf34 lacks homology to known iron-sulphur cluster containing proteins, it might constitute a new type of iron-sulphur protein implicated in redox signalling or in optimising the photosynthetic electron transport chain. © 2012 Elsevier B.V. All rights reserved.

  12. Development of a one-tube multiplex reverse transcriptase-polymerase chain reaction assay for the simultaneous amplification of HIV type 1 group M gag and env heteroduplex mobility assay fragments

    OpenAIRE

    Cham, F.; Heyndrickx, L; Janssens, W; Vereecken, K.; Houwer, K.; Coppens, S.; Van Der Auwera, G.; Whittle, H; van der Groen, G

    2000-01-01

    The emergence of intersubtype recombinant HIV-1 isolates has made it imperative to analyze different regions of HIV-1 genomes. For this purpose a one-tube multiplex RT-PCR, coamplifying first-round amplicons that allow amplification of gag and env heteroduplex mobility assay (HMA) fragments from different HIV-1 group M isolates, was developed, starting with plasma samples. The multiplex RT-PCR assay is sensitive: 115 of 136 (84.5%) samples were positive for both gag and env, positive amplific...

  13. Identification of shrimp species in raw and processed food products by means of a polymerase chain reaction-restriction fragment length polymorphism method targeted to cytochrome b mitochondrial sequences.

    Science.gov (United States)

    Pascoal, Ananías; Barros-Velázquez, Jorge; Cepeda, Alberto; Gallardo, José M; Calo-Mata, Pilar

    2008-08-01

    A novel PCR-RFLP method has been developed for the identification of six commercially relevant penaeid shrimp species in raw and processed food products. The method can be completed within 8 h. To implement the method, PCR amplification with the crustF/crustR primers, targeted to the amplification of a ca. 181 bp region of the cytochrome b (cytb) mitochondrial gene in penaeid shrimps, was coupled to restriction analysis with CviJI, DdeI and NlaIV. The method was also applied successfully to the identification of shrimp species in complex processed foods, including this type of shellfish as an added-value food ingredient. The small size of this molecular target facilitates amplification from fresh, frozen, or precooked samples, where DNA fragmentation may be relevant and fragment size critical. We also report the first cytb mitochondrial sequences described to date for the species Farfantepenaeus notialis, Parapenaeus longirostris and Pleoticus muelleri, and these nearly triplicate current knowledge of reference nucleotide sequences in this mitochondrial region for this group of species. The cytb mitochondrial gene may also be considered as a molecular marker for identification and phylogenetic purposes in penaeid shrimp species.

  14. (DAD1) gene fragment of Chinese kale

    African Journals Online (AJOL)

    To clone the defective in anther dehiscence1 (DAD1) gene fragment of Chinese kale, about 700 bp product was obtained by PCR amplification using Chinese kale genomic DNA as the template and a pair of specific primers designed according to the conserved sequence of DAD1 genes of Arabidopsis thaliana and ...

  15. Anticlotting properties of fragments D from human fibrinogen and fibrin.

    Science.gov (United States)

    Haverkate, F; Timan, G; Nieuwenhuizen, W

    1979-08-01

    It appeared from our previous studies that Ca2+ concentrations comparable to those occurring in blood protect the C-terminal part of the gamma-chain remnants of fibrin(ogen) fragments D against further plasmin attack. This study shows that purified fibrin(ogen) fragments D formed in the presence of Ca2+ ions have anticlotting activity in vitro, whereas shortening of the gamma-chain remnants leads to loss of such activity.

  16. Aggregation Methods in Food Chains.

    NARCIS (Netherlands)

    Kooi, B.W.; Poggiale, J.C.; Auger, P.

    1998-01-01

    The aim of this paper is to apply aggregation methods to food chains under batch and chemostat conditions. These predator-prey systems are modelled using ODEs, one for each trophic level. Because the models are based on mass conservation laws, they are conservative and this allows perfect

  17. Cloning and expression of cell wall acid invertase gene fragment ...

    African Journals Online (AJOL)

    A fragment of invertase gene containing catalytic sites of cysteine was cloned from poinsettia (Euphorbia pulcherrima wild.) by using the polymerase chain reaction (PCR) method. The length of the fragment was 521 bp, encoding 173 amino acids and containing a part of open reading frames, but no intron. It had a high ...

  18. Cloning and expression of cell wall acid invertase gene fragment ...

    African Journals Online (AJOL)

    ONOS

    2010-01-25

    Jan 25, 2010 ... A fragment of invertase gene containing catalytic sites of cysteine was cloned from poinsettia. (Euphorbia pulcherrima wild.) by using the polymerase chain reaction (PCR) method. The length of the fragment was 521 bp, encoding 173 amino acids and containing a part of open reading frames, but no intron.

  19. Property-based design and synthesis of new chloroquine hybrids via simple incorporation of 2-imino-thiazolidine-4-one or 1h-pyrrol-2, 5-dione fragments on the 4-amino-7-chloroquinoline side chain

    Energy Technology Data Exchange (ETDEWEB)

    Rojas, Fernando A.; Kouznetsov, Vladimir V., E-mail: kouznet@uis.edu.co [Laboratorio de Quimica Organica y Biomolecular, Escuela de Quimica, Universidad Industrial de Santander, Bucaramanga (Colombia)

    2011-09-15

    In the present work, the syntheses of new 4-amino-7-chloroquinoline N-derivatives were performed by selective modification of the side chain amino group of N-(7-chloroquinoline-4-yl) alkyldiamines, basis framework of chloroquine (CQ) drug through the incorporation of heterocyclic 2-imino-thiazolidine-4-one and {sup 1}H-pyrrol-2,5-dione systems. These potential activity modulators were selected thanks to their characteristic properties, and evaluated by virtual screening employing the OSIRIS and Molinspirations platforms. Designed and synthesized quinolinic derivatives could increase the antimalarial activity of CQ analogues without affecting the lipophilicity as described in literature, suggesting them as candidates for further biological assessments. (author)

  20. Avian guild assemblages in forest fragments around Budongo ...

    African Journals Online (AJOL)

    The findings show that bird assemblages vary in their response to habitat fragmentation but within guilds the response to fragmentation can be consistent, and can make ecological sense. Forest bird conservation can therefore benefit from information on species ecology when deciding which bird species and which parts of ...

  1. The speed of range shifts in fragmented landscapes.

    Directory of Open Access Journals (Sweden)

    Jenny A Hodgson

    Full Text Available Species may be driven extinct by climate change, unless their populations are able to shift fast enough to track regions of suitable climate. Shifting will be faster as the proportion of suitable habitat in the landscape increases. However, it is not known how the spatial arrangement of habitat will affect the speed of range advance, especially when habitat is scarce, as is the case for many specialist species. We develop methods for calculating the speed of advance that are appropriate for highly fragmented, stochastic systems. We reveal that spatial aggregation of habitat tends to reduce the speed of advance throughout a wide range of species parameters: different dispersal distances and dispersal kernel shapes, and high and low extinction probabilities. In contrast, aggregation increases the steady-state proportion of habitat that is occupied (without climate change. Nonetheless, we find that it is possible to achieve both rapid advance and relatively high patch occupancy when the habitat has a "channeled" pattern, resembling corridors or chains of stepping stones. We adapt techniques from electrical circuit theory to predict the rate of advance efficiently for complex, realistic landscape patterns, whereas the rate cannot be predicted by any simple statistic of aggregation or fragmentation. Conservationists are already advocating corridors and stepping stones as important conservation tools under climate change, but they are vaguely defined and have so far lacked a convincing basis in fundamental population biology. Our work shows how to discriminate properties of a landscape's spatial pattern that affect the speed of colonization (including, but not limited to, patterns like corridors and chains of stepping stones, and properties that affect a species' probability of persistence once established. We can therefore point the way to better land use planning approaches, which will provide functional habitat linkages and also maintain local

  2. A new and improved method based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) for the determination of A1298C mutation in the methylenetetrahydrofolate reductase (MTHFR) gene.

    Science.gov (United States)

    Machnik, Grzegorz; Zapala, Malgorzata; Pelc, Ewa; Gasecka-Czapla, Monika; Kaczmarczyk, Grzegorz; Okopien, Boguslaw

    2013-01-01

    Intracellular folate homeostasis and metabolism is regulated by numerous genes. Among them, 5,10-methylenetetrahydrofolate reductase (MTHFR) is of special interest because of its involvement in regulation of the homocysteine level in the body as a result of folate metabolism. Moreover, some studies demonstrated that the homocysteine plasma level in individuals may be influenced by polymorphisms present in the MTHFR gene. Two common, clinically relevant mutations have been described: MTHFR C677T and MTHFR A1298C. Although several laboratory techniques allow genotyping of both polymorphisms, PCR-RFLP analysis is simple to perform, relatively cheap, and thus one of the most utilized. In the case of A1298C, the PCR-RFLP technique that utilizes MboII endonuclease class II requires an acrylamide gel electrophoresis, since agarose gel electrophoresis is unable to resolve short deoxyribonucleic acid (DNA) fragments after restriction digestion. Agarose gel electrophoresis is commonly preferred over that of acrylamide. To resolve this inconvenience, a novel PCR-RFLP, AjuI-based method to genotype A1298C alleles has been developed that can be performed on standard agarose gel.

  3. Fish responses to experimental fragmentation of seagrass habitat.

    Science.gov (United States)

    Macreadie, Peter I; Hindell, Jeremy S; Jenkins, Gregory P; Connolly, Rod M; Keough, Michael J

    2009-06-01

    Understanding the consequences of habitat fragmentation has come mostly from comparisons of patchy and continuous habitats. Because fragmentation is a process, it is most accurately studied by actively fragmenting large patches into multiple smaller patches. We fragmented artificial seagrass habitats and evaluated the impacts of fragmentation on fish abundance and species richness over time (1 day, 1 week, 1 month). Fish assemblages were compared among 4 treatments: control (single, continuous 9-m(2) patches); fragmented (single, continuous 9-m(2) patches fragmented to 4 discrete 1-m(2) patches); prefragmented/patchy (4 discrete 1-m(2) patches with the same arrangement as fragmented); and disturbance control (fragmented then immediately restored to continuous 9-m(2) patches). Patchy seagrass had lower species richness than actively fragmented seagrass (up to 39% fewer species after 1 week), but species richness in fragmented treatments was similar to controls. Total fish abundance did not vary among treatments and therefore was unaffected by fragmentation, patchiness, or disturbance caused during fragmentation. Patterns in species richness and abundance were consistent 1 day, 1 week, and 1 month after fragmentation. The expected decrease in fish abundance from reduced total seagrass area in fragmented and patchy seagrass appeared to be offset by greater fish density per unit area of seagrass. If fish prefer to live at edges, then the effects of seagrass habitat loss on fish abundance may have been offset by the increase (25%) in seagrass perimeter in fragmented and patchy treatments. Possibly there is some threshold of seagrass patch connectivity below which fish abundances cannot be maintained. The immediate responses of fish to experimental habitat fragmentation provided insights beyond those possible from comparisons of continuous and historically patchy habitat. ©2009 Society for Conservation Biology.

  4. Habitat fragmentation and its lasting impact on Earth's ecosystems.

    Science.gov (United States)

    Haddad, Nick M; Brudvig, Lars A; Clobert, Jean; Davies, Kendi F; Gonzalez, Andrew; Holt, Robert D; Lovejoy, Thomas E; Sexton, Joseph O; Austin, Mike P; Collins, Cathy D; Cook, William M; Damschen, Ellen I; Ewers, Robert M; Foster, Bryan L; Jenkins, Clinton N; King, Andrew J; Laurance, William F; Levey, Douglas J; Margules, Chris R; Melbourne, Brett A; Nicholls, A O; Orrock, John L; Song, Dan-Xia; Townshend, John R

    2015-03-01

    We conducted an analysis of global forest cover to reveal that 70% of remaining forest is within 1 km of the forest's edge, subject to the degrading effects of fragmentation. A synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. Effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. These findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services.

  5. Fragmentation trees reloaded.

    Science.gov (United States)

    Böcker, Sebastian; Dührkop, Kai

    2016-01-01

    Untargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds. One of the bottlenecks in this experimental setup is the interpretation of fragmentation spectra to accurately and efficiently identify compounds. Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. These trees are determined from the data using combinatorial optimization, and aim at explaining the experimental data via fragmentation cascades. Fragmentation tree computation does not require spectral or structural databases. To obtain biochemically meaningful trees, one needs an elaborate optimization function (scoring). We present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a Maximum A Posteriori estimator. We demonstrate the superiority of the new scoring for two tasks: both for the de novo identification of molecular formulas of unknown compounds, and for searching a database for structurally similar compounds, our method SIRIUS 3, performs significantly better than the previous version of our method, as well as other methods for this task. SIRIUS 3 can be a part of an untargeted metabolomics workflow, allowing researchers to investigate unknowns using automated computational methods.Graphical abstractWe present a new scoring for computing fragmentation trees from tandem mass spectrometry data based on Bayesian statistics. The best scoring fragmentation tree most likely explains the molecular formula of the measured parent ion.

  6. SCEDS: protein fragments for molecular replacement in Phaser

    Energy Technology Data Exchange (ETDEWEB)

    McCoy, Airlie J., E-mail: ajm201@cam.ac.uk [University of Cambridge, Hills Road, Cambridge CB2 0XY (United Kingdom); Nicholls, Robert A. [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Schneider, Thomas R. [Hamburg Unit c/o DESY, Notkestrasse 85, 22603 Hamburg (Germany); University of Cambridge, Hills Road, Cambridge CB2 0XY (United Kingdom)

    2013-11-01

    Protein fragments suitable for use in molecular replacement can be generated by normal-mode perturbation, analysis of the difference distance matrix of the original versus normal-mode perturbed structures, and SCEDS, a score that measures the sphericity, continuity, equality and density of the resulting fragments. A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models. The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model. The unperturbed structure is then compared with each perturbed structure in turn and the structurally invariant regions are identified by analysing the difference distance matrix. These fragments are scored with SCEDS, which is a combined measure of the sphericity of the fragments, the continuity of the fragments with respect to the polypeptide chain, the equality in number of atoms in the fragments and the density of C{sup α} atoms in the triaxial ellipsoid of the fragment extents. The fragment divisions with the highest SCEDS are then used as separate template models for MR. Test cases show that where the protein contains fragments that undergo a change in juxtaposition between template model and target, SCEDS can identify fragments that lead to a lower R factor after ten cycles of all-atom refinement with REFMAC5 than the original template structure. The method has been implemented in the software Phaser.

  7. Heavy Chain Diseases

    Science.gov (United States)

    ... heavy chain produced: Alpha Gamma Mu Alpha Heavy Chain Disease Alpha heavy chain disease (IgA heavy chain ... disease or lead to a remission. Gamma Heavy Chain Disease Gamma heavy chain disease (IgG heavy chain ...

  8. Habitat specialization predicts genetic response to fragmentation in tropical birds.

    Science.gov (United States)

    Khimoun, Aurélie; Eraud, Cyril; Ollivier, Anthony; Arnoux, Emilie; Rocheteau, Vincent; Bely, Marine; Lefol, Emilie; Delpuech, Martin; Carpentier, Marie-Laure; Leblond, Gilles; Levesque, Anthony; Charbonnel, Anaïs; Faivre, Bruno; Garnier, Stéphane

    2016-08-01

    Habitat fragmentation is one of the most severe threats to biodiversity as it may lead to changes in population genetic structure, with ultimate modifications of species evolutionary potential and local extinctions. Nonetheless, fragmentation does not equally affect all species and identifying which ecological traits are related to species sensitivity to habitat fragmentation could help prioritization of conservation efforts. Despite the theoretical link between species ecology and extinction proneness, comparative studies explicitly testing the hypothesis that particular ecological traits underlies species-specific population structure are rare. Here, we used a comparative approach on eight bird species, co-occurring across the same fragmented landscape. For each species, we quantified relative levels of forest specialization and genetic differentiation among populations. To test the link between forest specialization and susceptibility to forest fragmentation, we assessed species responses to fragmentation by comparing levels of genetic differentiation between continuous and fragmented forest landscapes. Our results revealed a significant and substantial population structure at a very small spatial scale for mobile organisms such as birds. More importantly, we found that specialist species are more affected by forest fragmentation than generalist ones. Finally, our results suggest that even a simple habitat specialization index can be a satisfying predictor of genetic and demographic consequences of habitat fragmentation, providing a reliable practical and quantitative tool for conservation biology. © 2016 John Wiley & Sons Ltd.

  9. A quantitative analysis of forest fragmentation in Los Tuxtlas, southeast Mexico: patterns and implications for conservation Un análisis cuantitativo de la fragmentación de la selva de Los Tuxtlas en el sudeste de México: patrones e implicaciones para la conservación

    Directory of Open Access Journals (Sweden)

    EDUARDO MENDOZA

    2005-09-01

    Full Text Available Habitat loss is a critical threat to tropical biodiversity and its quantification constitutes a central conservation issue. Typically, assessments have been based on deforestation rates statistics. However, this overlooks the effects brought about by the spatial reconfiguration of the remaining habitat: fragmentation. We present an analysis of fragmentation in a Neotropical site aimed at: (a devising a protocol for its quantification, (b using such protocol to provide insights on the ecological consequences of fragmentation, (c exploring its applicability to address the hypothesis that forest size-inequality decreases with elevation, an indicator of habitat accessibility. We applied the Gini coefficient (G and the Lorenz curve to analyze fragment-size variation using a satellite-generated map. We also estimated edge effect, fragment shape and isolation. Remaining forest includes 1,005 fragments, ranging from 0.5 to 9.356 ha (median = 0.89. Size inequality was very high (G = 0.928, producing a flattened Lorenz curve. Forty percent of the fragments did not maintain an area free of a 30-m edge effect, and larger fragments showed a marked deviation from ideal circular forms. Eighty-four percent of the fragments lay further than 500 m from the largest forest tract and their size decreased with distance. Fragment size distribution changed with altitude: the Gini coefficient was lowest and forest coverage was greatest at the highest altitude, but inequality peaked at an intermediate elevation. Given the current pace of habitat deterioration, application of similar analyses may improve global assessments of tropical ecosystems and their perspectives for biodiversity conservationLa destrucción del hábitat es la principal amenaza para la biodiversidad tropical, por lo que su cuantificación constituye un aspecto central para la biología de la conservación. Usualmente, esta cuantificación se basa en el cálculo de las tasas de deforestaci

  10. Embedded Fragments Registry (EFR)

    Data.gov (United States)

    Department of Veterans Affairs — In 2009, the Department of Defense estimated that approximately 40,000 service members who served in OEF/OIF may have embedded fragment wounds as the result of small...

  11. Fragmentation Main Model

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The fragmentation model combines patch size and patch continuity with diversity of vegetation types per patch and rarity of vegetation types per patch. A patch was...

  12. DNA fragmentation in spermatozoa

    DEFF Research Database (Denmark)

    Rex, A S; Aagaard, J.; Fedder, J

    2017-01-01

    Sperm DNA Fragmentation has been extensively studied for more than a decade. In the 1940s the uniqueness of the spermatozoa protein complex which stabilizes the DNA was discovered. In the fifties and sixties, the association between unstable chromatin structure and subfertility was investigated....... In the seventies, the impact of induced DNA damage was investigated. In the 1980s the concept of sperm DNA fragmentation as related to infertility was introduced as well as the first DNA fragmentation test: the Sperm Chromatin Structure Assay (SCSA). The terminal deoxynucleotidyl transferase nick end labelling...... (TUNEL) test followed by others was introduced in the nineties. The association between DNA fragmentation in spermatozoa and pregnancy loss has been extensively investigated spurring the need for a therapeutic tool for these patients. This gave rise to an increased interest in the aetiology of DNA damage...

  13. Fragmented Work Stories

    DEFF Research Database (Denmark)

    Humle, Didde Maria; Reff Pedersen, Anne

    2015-01-01

    stories. We argue that meaning by story making is not always created by coherence and causality; meaning is created by different types of fragmentation: discontinuities, tensions and editing. The objective of this article is to develop and advance antenarrative practice analysis of work stories......Following a strand of narrative studies pointing to the living conditions of storytelling and the micro-level implications of working within fragmented narrative perspectives, this article contributes to narrative research on work stories by focusing on how meaning is created from fragmented...... by exploring how different types of fragmentation create meanings. This is done by studying the work stories of job and personnel consultants and by drawing on the results of a narrative, ethnographic study of a consultancy. The analysis demonstrates how work stories are social practices negotiated, retold...

  14. Crystallographic fragment screening.

    Science.gov (United States)

    Badger, John

    2012-01-01

    Crystallographic fragment screening is a technique for initiating drug discovery in which protein crystals are soaked or grown with high concentrations of small molecule compounds (typically MW 110-250 Da) chosen to represent fragments of potential drugs. Specific binding of these compounds to the protein is subsequently visualized in electron density maps obtained from analysis of X-ray diffraction data collected from these crystals. Theoretical and practical experience indicate that a suitably diverse library of fragment compounds containing only a few hundred compounds may be sufficient to provide a comprehensive screen of the protein target. By soaking crystals in mixtures of 3-10 compounds a fragment screen may be completed within ∼100 diffraction data sets. This data collection requirement may be met given reproducible well-diffracting protein crystals and robotic sample handling equipment at a high flux X-ray source. The leading practical issue for most crystallography laboratories that wish to launch a fragment screening project is the design and/or procurement of an appropriate fragment library. Although several off-the-shelf fragment libraries are available from chemical suppliers, the numbers, sizes, and solubility of the compounds in relatively few of these libraries are well-match to the specific needs of the crystallographic screening experiment. Informed consideration of the properties of compounds in the screening library, possibly augmented by additional filtering of available compounds with appropriate search tools, is required to design a successful experiment. The analysis of results from crystallographic fragment screening involves highly repetitive application of routine image data processing and structure refinement calculations from many very similar crystals. Efficient handling of the data applies a high-throughput structure determination methodology that conveniently packages the structure solution calculations into a single process that

  15. Fragment Impact Toolkit (FIT)

    Energy Technology Data Exchange (ETDEWEB)

    Shevitz, Daniel Wolf [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Key, Brian P. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Garcia, Daniel B. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-09-05

    The Fragment Impact Toolkit (FIT) is a software package used for probabilistic consequence evaluation of fragmenting sources. The typical use case for FIT is to simulate an exploding shell and evaluate the consequence on nearby objects. FIT is written in the programming language Python and is designed as a collection of interacting software modules. Each module has a function that interacts with the other modules to produce desired results.

  16. Laminin alpha2 chain-deficient congenital muscular dystrophy: variable epitope expression in severe and mild cases

    DEFF Research Database (Denmark)

    Cohn, R D; Herrmann, R; Sorokin, L

    1998-01-01

    To characterize the expression of distinct fragments of laminin alpha2 chain in patients with partial laminin alpha2 chain deficiency and variable clinical severity.......To characterize the expression of distinct fragments of laminin alpha2 chain in patients with partial laminin alpha2 chain deficiency and variable clinical severity....

  17. To what extent does urbanisation affect fragmented grassland functioning?

    Science.gov (United States)

    van der Walt, L; Cilliers, S S; Kellner, K; Du Toit, M J; Tongway, D

    2015-03-15

    Urbanisation creates altered environments characterised by increased human habitation, impermeable surfaces, artificial structures, landscape fragmentation, habitat loss, resulting in different resource loss pathways. The vulnerable Rand Highveld Grassland vegetation unit in the Tlokwe Municipal area, South Africa, has been extensively affected and transformed by urbanisation, agriculture, and mining. Grassland fragments in urban areas are often considered to be less species rich and less functional than in the more untransformed or "natural" exurban environments, and are therefore seldom a priority for conservation. Furthermore, urban grassland fragments are often being more intensely managed than exurban areas, such as consistent mowing in open urban areas. Four urbanisation measures acting as indicators for patterns and processes associated with urban areas were calculated for matrix areas surrounding each selected grassland fragment to quantify the position of each grassland remnant along an urbanisation gradient. The grassland fragments were objectively classified into two classes of urbanisation, namely "exurban" and "urban" based on the urbanisation measure values. Grazing was recorded in some exurban grasslands and mowing in some urban grassland fragments. Unmanaged grassland fragments were present in both urban and exurban areas. Fine-scale biophysical landscape function was determined by executing the Landscape Function Analysis (LFA) method. LFA assesses fine-scale landscape patchiness (entailing resource conserving potential and erosion resistance) and 11 soil surface indicators to produce three main LFA parameters (stability, infiltration, and nutrient cycling), which indicates how well a system is functioning in terms of fine-scale biophysical soil processes and characteristics. The aim of this study was to determine the effects of urbanisation and associated management practices on fine-scale biophysical landscape function of urban and exurban

  18. Mass Spectral Fragmentation of VX

    National Research Council Canada - National Science Library

    Rohrbaugh, Dennis K

    2008-01-01

    The objective of this study was to provide structural identification of VX fragment ions formed during mass spectrometric analysis, elucidation of fragmentation pathways, and a compilation of tandem...

  19. Markov chains

    CERN Document Server

    Revuz, D

    1984-01-01

    This is the revised and augmented edition of a now classic book which is an introduction to sub-Markovian kernels on general measurable spaces and their associated homogeneous Markov chains. The first part, an expository text on the foundations of the subject, is intended for post-graduate students. A study of potential theory, the basic classification of chains according to their asymptotic behaviour and the celebrated Chacon-Ornstein theorem are examined in detail. The second part of the book is at a more advanced level and includes a treatment of random walks on general locally compact abelian groups. Further chapters develop renewal theory, an introduction to Martin boundary and the study of chains recurrent in the Harris sense. Finally, the last chapter deals with the construction of chains starting from a kernel satisfying some kind of maximum principle.

  20. Microbial platform technology for recombinant antibody fragment production: A review.

    Science.gov (United States)

    Gupta, Sanjeev Kumar; Shukla, Pratyoosh

    2017-02-01

    Recombinant antibody fragments are being used for the last few years as an important therapeutic protein to cure various critical and life threatening human diseases. Several expression platforms now days employed for the production of these recombinant fragments, out of which bacterial system has emerged a promising host for higher expression. Since, a small antibody fragment unlike full antibody does not require human-like post-translational modification therefore it is potentially expressed in prokaryotic production system. Recently, small antibody fragments such as scFvs (single-chain variable fragments) and Fabs (antibody fragments) which does not require glycosylation are successfully produced in bacteria and have commercially launched for therapeutic use as these fragments shows better tissue penetration and less immunogenic to human body compared to full-size antibody. Recently developed Wacker's ESETEC secretion technology is an efficient technology for the expression and secretion of the antibody fragment (Fab) exceeded up to 4.0 g/L while scFv up to 3.5 g/L into the fermentation broth. The Pfenex system and pOP prokaryotic expression vector are another platform used for the considerably good amount of antibody fragment production successfully. In this review, we summarize the recent progress on various expression platforms and cloning approaches for the production of different forms of antibody fragments in E. coli.

  1. based conservation

    African Journals Online (AJOL)

    http://dx.doi.org/10.4314/mcd.v10i2.1. Increasing women's par- ticipation in community- based conservation: key to success? Ensuring that both men and women benefit equitably from conservation and development programs is likely to increase the long-term success of both conservation and development goals. However ...

  2. Fragments of Time

    DEFF Research Database (Denmark)

    Christiansen, Steen Ledet

    Time travel films necessarily fragment linear narratives, as scenes are revisited with differences from the first time we saw it. Popular films such as Back to the Future mine comedy from these visitations, but there are many different approaches. One extreme is Chris Marker's La Jetée - a film...... made almost completely of still images, recounting the end of the world. These stills can be viewed as fragments that have survived the end of the world and now provide the only access to the events that occured. Shane Carruth's Primer has a different approach to time travel, the narrative diegesis...

  3. The Serendipity of Fragmentation

    DEFF Research Database (Denmark)

    Leixnering, Stephan; Meyer, Renate E.

    , it was the central government’s task to coordinate, steer and control the newly emerged decentralized organizations. This raises questions about the overall design of the public sector at present. Our paper engages with the prevalent public governance phenomenon of fragmentation from a design perspective in order...... form of organizing between networks and formal organization: lacking a single center and featuring multiplex and multifaceted relations within the politico-administrative apparatus and between government and PSOs, high fragmentation, local and robust action, but latent structures of significant formal...

  4. (FMO3) gene by polymerase chain reaction-restriction fragment ...

    African Journals Online (AJOL)

    Yomi

    2012-01-24

    Jan 24, 2012 ... 1National Engineering Laboratory for Animal Breeding, Ministry of Agriculture Key Laboratory of Animal Genetics and. Breeding, College of ... is a gene that is clustered on human chromosome 1. (HSA1) (Shephard et ... The procedure for extraction was modified from that of “Molecular Cloning” (Sambrook.

  5. Ecology. Three-Gorges Dam--experiment in habitat fragmentation?

    Science.gov (United States)

    Wu, Jianguo; Huang, Jianhui; Han, Xingguo; Xie, Zongqiang; Gao, Xianming

    2003-05-23

    Habitat fragmentation is the primary cause of the loss of biodiversity and ecosystem services, but its underlying processes and mechanisms remain poorly understood. Studies of islands and insular terrestrial habitats are essential for improving our understanding of habitat fragmentation. We argue that the Three-Gorges Dam, the largest that humans have ever created, presents a unique grand-scale natural experiment that allows ecologists to address a range of critical questions concerning the theory and practice of biodiversity conservation.

  6. Gene flow and effective population sizes of the butterfly Maculinea alcon in a highly fragmented, anthropogenic landscape

    DEFF Research Database (Denmark)

    Vanden Broeck, An; Maes, Dirk; Kelager, Andreas

    2017-01-01

    Understanding connectivity among populations in fragmented landscapes is of paramount importance in species conservation because it determines their long-term viability and helps to identify and prioritize populations to conserve. Rare and sedentary species are particularly vulnerable to habitat ...

  7. Stone fragmentation by ultrasound

    Indian Academy of Sciences (India)

    Some delicate nerves and fibres in the surrounding areas of the stones present in the kidney are also damaged by high ultrasonic intensity used in such systems. In the present work, enhancement of the kidney stone fragmentation by using ultrasound is studied. The cavitation bubbles are found to implode faster, with more ...

  8. Fragments of the Past

    Directory of Open Access Journals (Sweden)

    Peter Szende

    2016-10-01

    Full Text Available With travel being made more accessible throughout the decades, the hospitality industry constantly evolved their practices as society and technology progressed. Hotels looked for news ways up service their customers, which led to the invention of the Servidor in 1918. Once revolutionary innovations have gone extinct, merely becoming fragments of the past.

  9. A Cholera Conjugate Vaccine Containing O-specific Polysaccharide (OSP) of V. cholerae O1 Inaba and Recombinant Fragment of Tetanus Toxin Heavy Chain (OSP:rTTHc) Induces Serum, Memory and Lamina Proprial Responses against OSP and Is Protective in Mice.

    Science.gov (United States)

    Sayeed, Md Abu; Bufano, Meagan Kelly; Xu, Peng; Eckhoff, Grace; Charles, Richelle C; Alam, Mohammad Murshid; Sultana, Tania; Rashu, Md Rasheduzzaman; Berger, Amanda; Gonzalez-Escobedo, Geoffrey; Mandlik, Anjali; Bhuiyan, Taufiqur Rahman; Leung, Daniel T; LaRocque, Regina C; Harris, Jason B; Calderwood, Stephen B; Qadri, Firdausi; Vann, W F; Kováč, Pavol; Ryan, Edward T

    2015-01-01

    Vibrio cholerae is the cause of cholera, a severe watery diarrhea. Protection against cholera is serogroup specific. Serogroup specificity is defined by the O-specific polysaccharide (OSP) component of lipopolysaccharide (LPS). Here we describe a conjugate vaccine for cholera prepared via squaric acid chemistry from the OSP of V. cholerae O1 Inaba strain PIC018 and a recombinant heavy chain fragment of tetanus toxin (OSP:rTTHc). We assessed a range of vaccine doses based on the OSP content of the vaccine (10-50 μg), vaccine compositions varying by molar loading ratio of OSP to rTTHc (3:1, 5:1, 10:1), effect of an adjuvant, and route of immunization. Immunized mice developed prominent anti-OSP and anti-TT serum IgG responses, as well as vibriocidal antibody and memory B cell responses following intramuscular or intradermal vaccination. Mice did not develop anti-squarate responses. Intestinal lamina proprial IgA responses targeting OSP occurred following intradermal vaccination. In general, we found comparable immune responses in mice immunized with these variations, although memory B cell and vibriocidal responses were blunted in mice receiving the highest dose of vaccine (50 μg). We found no appreciable change in immune responses when the conjugate vaccine was administered in the presence or absence of immunoadjuvant alum. Administration of OSP:rTTHc resulted in 55% protective efficacy in a mouse survival cholera challenge model. We report development of an Inaba OSP:rTTHc conjugate vaccine that induces memory responses and protection against cholera in mice. Development of an effective cholera conjugate vaccine that induces high level and long-term immune responses against OSP would be beneficial, especially in young children who respond poorly to polysaccharide antigens.

  10. A Cholera Conjugate Vaccine Containing O-specific Polysaccharide (OSP of V. cholerae O1 Inaba and Recombinant Fragment of Tetanus Toxin Heavy Chain (OSP:rTTHc Induces Serum, Memory and Lamina Proprial Responses against OSP and Is Protective in Mice.

    Directory of Open Access Journals (Sweden)

    Md Abu Sayeed

    Full Text Available Vibrio cholerae is the cause of cholera, a severe watery diarrhea. Protection against cholera is serogroup specific. Serogroup specificity is defined by the O-specific polysaccharide (OSP component of lipopolysaccharide (LPS.Here we describe a conjugate vaccine for cholera prepared via squaric acid chemistry from the OSP of V. cholerae O1 Inaba strain PIC018 and a recombinant heavy chain fragment of tetanus toxin (OSP:rTTHc. We assessed a range of vaccine doses based on the OSP content of the vaccine (10-50 μg, vaccine compositions varying by molar loading ratio of OSP to rTTHc (3:1, 5:1, 10:1, effect of an adjuvant, and route of immunization.Immunized mice developed prominent anti-OSP and anti-TT serum IgG responses, as well as vibriocidal antibody and memory B cell responses following intramuscular or intradermal vaccination. Mice did not develop anti-squarate responses. Intestinal lamina proprial IgA responses targeting OSP occurred following intradermal vaccination. In general, we found comparable immune responses in mice immunized with these variations, although memory B cell and vibriocidal responses were blunted in mice receiving the highest dose of vaccine (50 μg. We found no appreciable change in immune responses when the conjugate vaccine was administered in the presence or absence of immunoadjuvant alum. Administration of OSP:rTTHc resulted in 55% protective efficacy in a mouse survival cholera challenge model.We report development of an Inaba OSP:rTTHc conjugate vaccine that induces memory responses and protection against cholera in mice. Development of an effective cholera conjugate vaccine that induces high level and long-term immune responses against OSP would be beneficial, especially in young children who respond poorly to polysaccharide antigens.

  11. Modified mismatch polymerase chain reaction-restriction fragment length polymorphism detected mutations in codon 12 and 13 of exon 2 of K-ras gene in colorectal cancer patients and its association with liver metastases: Data from a South Asian country.

    Science.gov (United States)

    Faleel, Fathima Dhilhani Mohamed; Zoysa, M I M De; Lokuhetti, M D S; Gunawardena, Y I N S; Chandrasekharan, Vishvanath Naduviladath; Dassanayake, Ranil Samantha

    2016-01-01

    Mutations in K-ras codon 12 and 13 of exon 2 are known to affect prognosis and impart resistance to anti-epidermal growth factor monoclonal antibody therapy in colorectal carcinoma (CRC). Our aim was to investigate the utility value of modified mismatch polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay to detect mutation in K-ras codons of CRC patients and to relate the mutational status to liver metastasis. Mismatch PCR-RFLP was developed to detect K-ras mutations in DNA isolated from paraffinized tumor tissue of thirty CRC patients. All patients had 5 year follow-up data to detect liver metastasis. Cross-tabulations were generated between K-ras mutations and the metastatic status. The Chi-square test was used to indicate statistical significance of the association. Of the 30 CRC patients investigated, K-ras mutations of codons 12 and/or 13 of exon 2 were detected in 14 (46.6%). Meanwhile, 13 patients (43.3%) were observed to have developed liver metastases. There was a significant association between the presence of the K-ras mutation in codon 12 and the occurrence of liver metastasis (χ2 = 4.693, P = 0.030) on the contrary to the mutation in codon 13 to which such occurrence of liver metastases was not seen (χ2 = 1.884, P = 0.169). Codon 12 of exon 2 of K--ras gene detected by modified mismatch PCR-RFLP assay is significantly associated with liver metastasis in CRC patients during the first 5 years after surgery. Thus, modified mismatch PCR-RFLP protocol is a suitable method in this setting to detect K-ras gene mutations predicting liver metastasis in CRC patients.

  12. Heavy-Quark Fragmentation

    CERN Document Server

    Cacciari, M; Cacciari, Matteo; Gardi, Einan

    2003-01-01

    We study perturbative and non-perturbative aspects of heavy-quark fragmentation into hadrons, emphasizing the large-x region, where x is the energy fraction of the detected hadron. We first prove that when the moment index N and the quark mass m get large simultaneously with the ratio (N Lambda/m) fixed, the fragmentation function depends on this ratio alone. This opens up the way to formulate the non-perturbative contribution to the fragmentation function at large N as a shape function of m(1-x) which is convoluted with the Sudakov-resummed perturbative result. We implement this resummation and the parametrization of the corresponding shape function using Dressed Gluon Exponentiation. The Sudakov exponent is calculated in a process independent way from a generalized splitting function which describes the emission probability of an off-shell gluon off a heavy quark. Non-perturbative corrections are parametrized based on the renormalon structure of the Sudakov exponent. They appear in moment space as an expone...

  13. Fracture, failure, and fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Dienes, J.K.

    1984-01-01

    Though continuum descriptions of material behavior are useful for many kinds of problems, particularly those involving plastic flow, a more general approach is required when the failure is likely to involve growth and coalescence of a large number of fractures, as in fragmentation. Failures of this kind appear frequently in rapid dynamic processes such as those resulting from impacts and explosions, particularly in the formation of spall fragments. In the first part of this paper an approach to formulating constitutive relations that accounts for the opening, shear and growth of an ensemble of cracks is discussed. The approach also accounts for plastic flow accompanying fragmentation. The resulting constitutive relations have been incorporated into a Lagrangean computer program. In the second part of this paper a theoretical approach to coalescence is described. The simplest formulation makes use of a linear Liouville equation, with crack growth limited by the mean free path of cracks, assumed constant. This approach allows for an anisotropic distribution of cracks. An alternative approach is also described in which the decrease of the mean free path with increasing crack size is accounted for, but the crack distribution is assumed isotropic. A reduction of the governing Liouville equation to an ordinary differential equation of third order is possible, and the result can be used to determine how mean-free-path decreases with increasing crack size.

  14. Ecosystem extent and fragmentation

    Science.gov (United States)

    Sayre, Roger; Hansen, Matt

    2017-01-01

    One of the candidate essential biodiversity variable (EBV) groups described in the seminal paper by Pereira et al. (2014) concerns Ecosystem Structure. This EBV group is distinguished from another EBV group which encompasses aspects of Ecosystem Function. While the Ecosystem Function EBV treats ecosystem processes like nutrient cycling, primary production, trophic interactions, etc., the Ecosystem Structure EBV relates to the set of biophysical properties of ecosystems that create biophysical environmental context, confer biophysical structure, and occur geographically. The Ecosystem Extent and Fragmentation EBV is one of the EBVs in the Ecosystem Structure EBV group.Ecosystems are understood to exist at multiple scales, from very large areas (macro-ecosystems) like the Arctic tundra, for example, to something as small as a tree in an Amazonian rain forest. As such, ecosystems occupy space and therefore can be mapped across any geography of interest, whether that area of interest be a site, a nation, a region, a continent, or the planet. One of the most obvious and seemingly straightforward EBVs is Ecosystem Extent and Fragmentation. Ecosystem extent refers to the location and geographic distribution of ecosystems across landscapes or in the oceans, while ecosystem fragmentation refers to the spatial pattern and connectivity of ecosystem occurrences on the landscape.

  15. Artificial Synthesis of Conserved Segment S Gene Fragment of Rift ...

    African Journals Online (AJOL)

    1College of Veterinary Medicine, Sichuan Agricultural University, Yaan 625014, 2Changde Entry-Exit Inspection and Quarantine. Bureau, Changde .... eye. Due to these advantages, LAMP has become a new and important research direction for the detection and diagnosis of many pathogens [11,12]. EXPERIMENTAL.

  16. Who wants to conserve remaining forest fragments in the ...

    African Journals Online (AJOL)

    Most tropical landscapes are not only confronted with severe deforestation but also with forest frag-. I. Groupe de foresterie pour le développement, Department of Environmental Sciences, ETH Zurich, Zurich, Switzlerand. II. NADEL, Department of Humanities, Social and Political Sciences, ETH Zurich, Zurich, Switzerland.

  17. Artificial Synthesis of Conserved Segment S Gene Fragment of Rift ...

    African Journals Online (AJOL)

    trade in animal and animal products, population migration, and climate change, the risk of RVFV spreading increases continually. Due to the fact that there are no efficient vaccines for humans or animals [5], controlling and conducting research on RVF have becoming more urgent and significant. Since RVFV infections do ...

  18. Sperm DNA fragmentation and its role in wildlife conservation.

    Science.gov (United States)

    Gosálvez, Jaime; Holt, William V; Johnston, Stephen D

    2014-01-01

    Until about 20 years ago, sperm assessment in the laboratory was focused on motility, morphology and acrosomal integrity. Then came the gradual realisation that, because the main objective of a spermatozoon is to deliver an intact genetic payload of DNA to the egg, being able to check DNA quality of spermatozoa would be equally important, if not more so. Research over the last two decades has therefore led to the development of several techniques for reliably detecting DNA strand breaks, and the more recent focus has been directed towards understanding the fertility implications of DNA damage. It is now clear that evolutionary history has played an important role in determining the stability of sperm DNA under stressful conditions, and that the nature of the DNA-protein interactions also influence the extent to which fertility is affected by both technical procedures involved in sperm preservation and the basic biology of the species concerned. Here we present an overview of the principles involved in DNA assessment and also provide some cases studies that illustrate the influences of species diversity.

  19. CONTROL OF FRAGMENTATION BY BLASTING

    OpenAIRE

    Božić, Branko

    1998-01-01

    The degree of fragmentation influences the economy of the excavation operations. Characteristics of blasted rock such as fragment size, volume and mass are fundamental variables effecting the economics of a mining operation and are in effect the basis for evaluating the quality of a blast. The properties of fragmentation, such as size and shape, are very important information for the optimization of production. Three factors control the fragment size distribution: the rock structure, the q...

  20. SCALING AND 4-QUARK FRAGMENTATION

    NARCIS (Netherlands)

    SCHOLTEN, O; BOSVELD, GD

    1991-01-01

    The conditions for a scaling behaviour from the fragmentation process leading to slow protons are discussed- The scaling referred to implies that the fragmentation functions depend on the light-cone momentum fraction only. It is shown that differences in the fragmentation functions for valence- and

  1. Charge distribution in the ternary fragmentation of {sup 252}Cf

    Energy Technology Data Exchange (ETDEWEB)

    Senthil Kannan, M.T.; Balasubramaniam, M. [Bharathiar University, Department of Physics, Coimbatore (India)

    2017-08-15

    We present here, for the first time, a study on ternary fragmentation charge distribution of {sup 252}Cf using the convolution integral method and the statistical theory. The charge distribution for all possible charge combinations of a ternary breakup are grouped as a bin containing different mass partitions. Different bins corresponding to various third fragments with mass numbers from A{sub 3} = 16 to 84 are identified with the available experimental masses. The corresponding potential energy surfaces are calculated using the three cluster model for the two arrangements A{sub 1} + A{sub 2} + A{sub 3} and A{sub 1} + A{sub 3} + A{sub 2}. The ternary fragmentation yield values are calculated for the ternary combination from each bin possessing minimum potential energy. The yields of the resulting ternary combinations as a function of the charge numbers of the three fragments are analyzed for both the arrangements. The calculations are carried out at different excitation energies of the parent nucleus. For each excitation energy the temperature of the three fragments are iteratively computed conserving the total energy. The distribution of fragment temperatures corresponding to different excitation energies for some fixed third fragments are discussed. The presence of the closed shell nucleus Sn in the favourable ternary fragmentation is highlighted. (orig.)

  2. Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals.

    Science.gov (United States)

    Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; King, Sarah R B; Di Marco, Moreno; Rondinini, Carlo; Boitani, Luigi

    2017-07-18

    Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world's terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, and most high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world's terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation.

  3. Synthesis of arabinoxylan fragments

    DEFF Research Database (Denmark)

    Underlin, Emilie Nørmølle; Böhm, Maximilian F.; Madsen, Robert

    The cell wall of plants can be termed the skeleton of the plant. One of the parts making up the cell wall is hemicellulose. Hemicellulose is composed of a number of saccharides where one of the most abundant are the arabinoxylan-oligosaccharides. In many instances the biosynthesis and degration...... of arabinoxylan oligosaccharides remain elusive. As a consequence defined arabinoxylan fragments have been chosen as synthetic targets which subsequently will be submitted to enzymatic studies. A better understanding of these processes could lead to e.g. better utilisation of the biomass for biofuel production...

  4. An Archeology of Fragments

    Directory of Open Access Journals (Sweden)

    Gerald L. Bruns

    2014-10-01

    Full Text Available This is a short (fragmentary history of fragmentary writing from the German Romantics (F. W. Schlegel, Friedrich Hölderlin to modern and contemporary concrete or visual poetry. Such writing is (often deliberately a critique of the logic of subsumption that tries to assimilate whatever is singular and irreducible into totalities of various categorical or systematic sorts. Arguably, the fragment (parataxis is the distinctive feature of literary Modernism, which is a rejection, not of what precedes it, but of what Max Weber called “the rationalization of the world” (or Modernity whose aim is to keep everything, including all that is written, under surveillance and control.

  5. Reshaping conservation

    DEFF Research Database (Denmark)

    Funder, Mikkel; Danielsen, Finn; Ngaga, Yonika

    2013-01-01

    members strengthen the monitoring practices to their advantage, and to some extent move them beyond the reach of government agencies and conservation and development practitioners. This has led to outcomes that are of greater social and strategic value to communities than the original 'planned' benefits......, although the monitoring scheme has also to some extent become dominated by local 'conservation elites' who negotiate the terrain between the state and other community members. Our findings suggest that we need to move beyond simplistic assumptions of community strategies and incentives in participatory...... conservation and allow for more adaptive and politically explicit governance spaces in protected area management....

  6. Spontaneously disappearing large herniated lumbar disc fragment

    Directory of Open Access Journals (Sweden)

    Umamaheswara V. Reddy

    2014-01-01

    Full Text Available There are reports of spontaneous regression of large extruded disc; however, the exact underlying mechanism and management of such cases remains controversial. We report a 40-year-old female who opted for conservative management for a large extruded lumbar disc. Follow-up magnetic resonance imaging (MRI showed complete disappearance of the disc fragment; however, there were degenerative changes in the upper and lower adjacent margins of the vertebral body. Spine surgeons should be aware of spontaneous regression of the disc phenomenon as a patient with a large extruded disc who opted for the conservative management initially can have persistence pain, but there may not be an underlying protruded disc.

  7. Comparing binding modes of analogous fragments using NMR in fragment-based drug design: application to PRDX5.

    Directory of Open Access Journals (Sweden)

    Clémentine Aguirre

    Full Text Available Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD experiment and the protein-observed 15N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model.

  8. Hearing Conservation

    Science.gov (United States)

    1995-01-01

    the federal standard. Footnote** See Title 29 Code of Federal Regulations (CFR) 1910.95 "Occupational Noise Exposure." (Back to text) | USDOL | CONTACT INFORMATION | DISCLAIMER | 15 of 15 OSHA 3074 - Hearing Conservation

  9. Wildlife Conservation

    OpenAIRE

    Spash, Clive L.; Aldred, Jonathan

    1998-01-01

    In this paper we consider how conservation has arisen as a key aspect of the reaction to human-initiated degradation and disappearance of ecosystems, wild lands. and wildlife. Concern over species extinction is given an historical perspective which shows the way in which pressure on wild and natural aspects of global ecology have changed in recent centuries. The role of conservation in the struggle to protect the environment is then analysed using underlying ethical arguments behind the econo...

  10. Austere conservation

    DEFF Research Database (Denmark)

    Bluwstein, Jevgeniy; Moyo, Francis; Kicheleri, Rose Peter

    2016-01-01

    . Our findings suggest that WMAs foster very limited ownership, participation and collective action at the community level, because WMA governance follows an austere logic of centralized control over key resources. Thus, we suggest that it is difficult to argue that WMAs are community-owned conservation...... initiatives until a genuinely devolved and more flexible conservation model is implemented to give space for popular participation in rule-making....

  11. A Mini-Library of Sequenced Human DNA Fragments: Linking Bench Experiments with Informatics

    Science.gov (United States)

    Dalgleish, Raymond; Shanks, Morag E.; Monger, Karen; Butler, Nicola J.

    2012-01-01

    We describe the development of a mini-library of human DNA fragments for use in an enquiry-based learning (EBL) undergraduate practical incorporating "wet-lab" and bioinformatics tasks. In spite of the widespread emergence of the polymerase chain reaction (PCR), the cloning and analysis of DNA fragments in "Escherichia coli"…

  12. Stereoselective synthesis and absolute configuration of the C1'-C25' fragment of symbiodinolide.

    Science.gov (United States)

    Takamura, Hiroyoshi; Murata, Takeshi; Asai, Takahiro; Kadota, Isao; Uemura, Daisuke

    2009-09-04

    Stereoselective synthesis of the C1'-C25' fragment of symbiodinolide, which was obtained as a degraded product from symbiodinolide by alkaline hydrolysis, has been accomplished. The synthetic route features Kotsuki coupling and Julia-Kocienski olefination in the introduction of the side chains. This enantio- and stereoselective synthesis has established the absolute configuration of the C1'-C25' fragment.

  13. The production of antibody fragments and antibody fusion proteins by yeasts and filamentous fungi

    NARCIS (Netherlands)

    Joosten, V.; Lokman, C.; Hondel, C.A.M.J.J. van den; Punt, P.J.

    2003-01-01

    In this review we will focus on the current status and views concerning the production of antibody fragments and antibody fusion proteins by yeasts and filamentous fungi. We will focus on single-chain antibody fragment production (scFv and VHH) by these lower eukaryotes and the possible applications

  14. Adaptation and Fatigue Model for Neuron Networks and Large Time Asymptotics in a Nonlinear Fragmentation Equation

    National Research Council Canada - National Science Library

    Pakdaman, Khashayar; Perthame, Benoît; Salort, Delphine

    2014-01-01

    Motivated by a model for neural networks with adaptation and fatigue, we study a conservative fragmentation equation that describes the density probability of neurons with an elapsed time s after its last...

  15. The relative effects of habitat loss, fragmentation, and degradation on population extinction

    Science.gov (United States)

    The most prominent conservation concerns are typically habitat loss and habitat fragmentation. The role of habitat degradation has received comparatively little attention. But research has shown that the quality of habitat patches can significantly influence wildlife population d...

  16. Deforestation and Forest Fragmentation in South Ecuador since the 1970s - Losing a Hotspot of Biodiversity

    National Research Council Canada - National Science Library

    Tapia-Armijos, María Fernanda; Homeier, Jürgen; Espinosa, Carlos Iván; Leuschner, Christoph; de la Cruz, Marcelino

    2015-01-01

    Deforestation and fragmentation are major components of global change; both are contributing to the rapid loss of tropical forest area with important implications for ecosystem functioning and biodiversity conservation...

  17. Cold chain management: Knowledge and practices in primary ...

    African Journals Online (AJOL)

    Administrator

    Abstract. Background: To maintain vaccines perfectly conserved from its manufacture through administration requires an adequate could chain infrastructure. At the end of the chain, primary health care providers must have adequate knowledge to manage the cold chain. Objective: The study describes an observed audit of ...

  18. Cold chain management: Knowledge and practices in primary ...

    African Journals Online (AJOL)

    Background: To maintain vaccines perfectly conserved from its manufacture through administration requires an adequate could chain infrastructure. At the end of the chain, primary health care providers must have adequate knowledge to manage the cold chain. Objective: The study describes an observed audit of the ...

  19. Deforestation and Forest Fragmentation in South Ecuador since the 1970s - Losing a Hotspot of Biodiversity.

    OpenAIRE

    María Fernanda Tapia-Armijos; Jürgen Homeier; Carlos Iván Espinosa; Christoph Leuschner; Marcelino de la Cruz

    2015-01-01

    Deforestation and fragmentation are major components of global change; both are contributing to the rapid loss of tropical forest area with important implications for ecosystem functioning and biodiversity conservation. The forests of South Ecuador are a biological 'hotspot' due to their high diversity and endemism levels. We examined the deforestation and fragmentation patterns in this area of high conservation value using aerial photographs and Aster satellite scenes. The registered annual ...

  20. Intermittency in {sup 197}Au fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Dabrowska, A.; Holynski, R.; Olszewski, A.; Szarska, M.; Wilczynska, B.; Wolter, W.; Wosiek, B. [Institute of Nuclear Physics, Cracow (Poland); Cherry, M.L.; Deines-Jones, P.; Jones, W.V.; Sengupta, K.; Wefel, B. [Louisiana State Univ., Baton Rouge, LA (United States). Dept. of Physics and Astronomy; Waddington, C.J. [Minnesota Univ., Minneapolis, MN (United States). School of Physics and Astronomy; Pozharova, E.A.; Skorodko, T.Yu. [Inst. of Theoretical and Experimental Physics, Moscow (Russian Federation); KLMM Collaboration

    1995-07-01

    The concept of factorial moments was applied to an analysis of the dynamical fluctuations in the charge distributions of the fragments emitted from gold nuclei with energies 10.6 and < 1.0 GeV/n interacting with emulsion nuclei. Clear evidence for intermittent fluctuations has been found in an analysis using all the particles released from the gold projectile, with a stronger effect observed below 1 GeV/n than at 10.6 GeV/n. For the full data sets, however, the intermittency effect was found to be very sensitive to the singly charged particles, and neglecting these particles strongly reduces the intermittency signal. When the analysis is restricted to the multiply charged fragments, an intermittency effect is revealed only for multifragmentation events, although one that is enhanced as compared to the analysis of all, singly and multiply charged, particles. The properties of the anomalous fractal dimensions suggest a sequential decay mechanism, rather than the existence of possible critical behaviour in the process of nuclear fragmentation. The likely influence of the charge conservation effects and the finite size of decaying systems on the observed intermittency signals was pointed out. (author). 37 refs, 9 figs, 5 tabs.

  1. A multi-method analysis of forest fragmentation and loss: The case ...

    African Journals Online (AJOL)

    Lazie

    2014-02-01

    Feb 1, 2014 ... Forest fragmentation and loss seriously affect biodiversity. There is need to monitor and assess forest fragmentation and loss in communal areas for effective biodiversity management. In this study, we analysed the ... conservation of biodiversity and ecological functions of forests (Harris, 1984; Forman, ...

  2. Restoring habitat corridors in fragmented landscapes using optimization and percolation models

    Science.gov (United States)

    Justin C. Williams; Stephanie A. Snyder

    2005-01-01

    Landscape fragmentation and habitat loss are significant threats to the conservation of biological diversity. Creating and restoring corridors between isolated habitat patches can help mitigate or reverse the impacts of fragmentation. It is important that restoration and protection efforts be undertaken in the most efficient and effective way possible because...

  3. Global patterns of fragmentation and connectivity of mammalian carnivore habitat.

    Science.gov (United States)

    Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; Rondinini, Carlo; Boitani, Luigi

    2011-09-27

    Although mammalian carnivores are vulnerable to habitat fragmentation and require landscape connectivity, their global patterns of fragmentation and connectivity have not been examined. We use recently developed high-resolution habitat suitability models to conduct comparative analyses and to identify global hotspots of fragmentation and connectivity for the world's terrestrial carnivores. Species with less fragmentation (i.e. more interior high-quality habitat) had larger geographical ranges, a greater proportion of habitat within their range, greater habitat connectivity and a lower risk of extinction. Species with higher connectivity (i.e. less habitat isolation) also had a greater proportion of high-quality habitat, but had smaller, not larger, ranges, probably reflecting shorter distances between habitat patches for species with restricted distributions; such species were also more threatened, as would be expected given the negative relationship between range size and extinction risk. Fragmentation and connectivity did not differ among Carnivora families, and body mass was associated with connectivity but not fragmentation. On average, only 54.3 per cent of a species' geographical range comprised high-quality habitat, and more troubling, only 5.2 per cent of the range comprised such habitat within protected areas. Identification of global hotspots of fragmentation and connectivity will help guide strategic priorities for carnivore conservation.

  4. Development of a simple restriction fragment length polymorphism assay for subtyping of coxsackie B viruses.

    Science.gov (United States)

    Patel, D D; Kapoor, A; Ayyagari, A; Dhole, T N

    2004-09-15

    Coxsackie B viruses (genus, Enterovirus; family, Picornaviridae) can cause aseptic meningitis, encephalitis, pleurodynia, myocarditis and are implicated in the pathogenesis of dilated cardiomyopathy. The differentiation of the group B coxsackieviruses into their subtypes has potential clinical and epidemiological implications. In the present study, a simple restriction fragment length polymorphism (RFLP) assay was developed for typing of group B coxsackieviruses into subtypes 1-6. It is a two step process, first, virus isolation and identification by virus neutralization assay, using pools of polyclonal antisera, second, the reverse transcription polymerase chain reaction (RT-PCR) using a single primer pair selected from the conserved 5'-untranslated region (5'-UTR) of enterovirus genome followed by RFLP. A 440 bp product was amplified from the reference strains of each subtype of group B coxsackievirus and 29 clinical isolates (positive for group B coxsackieviruses by neutralization assay). The amplified products were subjected to restriction endonuclease digestion by enzyme BsaJI. The assay was able to distinguish all six serotypes of coxsackie B viruses. The results were comparable to serotyping and showed that due to the relatively conserved nature of 5'-UTR in enterovirus genome, this region can be used for subgeneric molecular identification of enteroviruses.

  5. CONTROL OF FRAGMENTATION BY BLASTING

    Directory of Open Access Journals (Sweden)

    Branko Božić

    1998-12-01

    Full Text Available The degree of fragmentation influences the economy of the excavation operations. Characteristics of blasted rock such as fragment size, volume and mass are fundamental variables effecting the economics of a mining operation and are in effect the basis for evaluating the quality of a blast. The properties of fragmentation, such as size and shape, are very important information for the optimization of production. Three factors control the fragment size distribution: the rock structure, the quantity of explosive and its distribution within the rock mass. Over the last decade there have been considerable advances in our ability to measure and analyze blasting performance. These can now be combined with the continuing growth in computing power to develop a more effective description of rock fragmentation for use by future blasting practitioners. The paper describes a view of the fragmentation problem by blasting and the need for a new generation of engineering tools to guide the design and implementation of blasting operations.

  6. Genetic consequences of habitat fragmentation in plant populations: susceptible signals in plant traits and methodological approaches.

    Science.gov (United States)

    Aguilar, Ramiro; Quesada, Mauricio; Ashworth, Lorena; Herrerias-Diego, Yvonne; Lobo, Jorge

    2008-12-01

    Conservation of genetic diversity, one of the three main forms of biodiversity, is a fundamental concern in conservation biology as it provides the raw material for evolutionary change and thus the potential to adapt to changing environments. By means of meta-analyses, we tested the generality of the hypotheses that habitat fragmentation affects genetic diversity of plant populations and that certain life history and ecological traits of plants can determine differential susceptibility to genetic erosion in fragmented habitats. Additionally, we assessed whether certain methodological approaches used by authors influence the ability to detect fragmentation effects on plant genetic diversity. We found overall large and negative effects of fragmentation on genetic diversity and outcrossing rates but no effects on inbreeding coefficients. Significant increases in inbreeding coefficient in fragmented habitats were only observed in studies analyzing progenies. The mating system and the rarity status of plants explained the highest proportion of variation in the effect sizes among species. The age of the fragment was also decisive in explaining variability among effect sizes: the larger the number of generations elapsed in fragmentation conditions, the larger the negative magnitude of effect sizes on heterozygosity. Our results also suggest that fragmentation is shifting mating patterns towards increased selfing. We conclude that current conservation efforts in fragmented habitats should be focused on common or recently rare species and mainly outcrossing species and outline important issues that need to be addressed in future research on this area.

  7. Conservation endocrinology

    Science.gov (United States)

    McCormick, Stephen; Romero, L. Michael

    2017-01-01

    Endocrinologists can make significant contributions to conservation biology by helping to understand the mechanisms by which organisms cope with changing environments. Field endocrine techniques have advanced rapidly in recent years and can provide substantial information on the growth, stress, and reproductive status of individual animals, thereby providing insight into current and future responses of populations to changes in the environment. Environmental stressors and reproductive status can be detected nonlethally by measuring a number of endocrine-related endpoints, including steroids in plasma, living and nonliving tissue, urine, and feces. Information on the environmental or endocrine requirements of individual species for normal growth, development, and reproduction will provide critical information for species and ecosystem conservation. For many taxa, basic information on endocrinology is lacking, and advances in conservation endocrinology will require approaches that are both “basic” and “applied” and include integration of laboratory and field approaches.

  8. An Algebra for Program Fragments

    DEFF Research Database (Denmark)

    Kristensen, Bent Bruun; Madsen, Ole Lehrmann; Møller-Pedersen, Birger

    1985-01-01

    Program fragments are described either by strings in the concrete syntax or by constructor applications in the abstract syntax. By defining conversions between these forms, both may be intermixed. Program fragments are constructed by terminal and nonterminal symbols from the grammar and by variab......Program fragments are described either by strings in the concrete syntax or by constructor applications in the abstract syntax. By defining conversions between these forms, both may be intermixed. Program fragments are constructed by terminal and nonterminal symbols from the grammar...

  9. Global priorities for national carnivore conservation under land use change

    NARCIS (Netherlands)

    Di Minin, E.; Slotow, R.; Hunter, L.T.B.; Montesino Pouzols, F.; Toivonen, T.; Verburg, P.H.; Leader-Williams, N.; Petracca, L.; Moilanen, A.

    2016-01-01

    Mammalian carnivores have suffered the biggest range contraction among all biodiversity and are particularly vulnerable to habitat loss and fragmentation. Therefore, we identified priority areas for the conservation of mammalian carnivores, while accounting for species-specific requirements for

  10. Antibody elbow angles are influenced by their light chain class

    Energy Technology Data Exchange (ETDEWEB)

    Stanfield, R; Zemla, A; Wilson, I; Rupp, B

    2006-01-12

    We have examined the elbow angles for 365 different Fab fragments, and observe that Fabs with lambda light chains have adopted a wider range of elbow angles than their kappa-chain counterparts, and that the lambda light chain Fabs are frequently found with very large (>195{sup o}) elbow angles. This apparent hyperflexibility of lambda-chain Fabs may be due to an insertion in their switch region, which is one residue longer than in kappa chains, with glycine occurring most frequently at the insertion position. A new, web-based computer program that was used to calculate the Fab elbow angles is also described.

  11. Colorful Conservation

    Science.gov (United States)

    Skophammer, Karen

    2011-01-01

    Some people only think about conservation on Earth Day. Being in the "art business" however, this author is always conscious of the many products she thinks get wasted when they could be reused, recycled, and restored--especially in a school building and art room. In this article, she describes an art lesson that allows students to paint…

  12. Creative conservation

    NARCIS (Netherlands)

    Bentham, Roelof J.

    1968-01-01

    The increasing exploitation of our natural resources, the unlimited occupation of ever more new areas, and the intensification of land-use, make it necessary for us to expand the concept of conservation. But we also need to reconsider that concept itself. For the changing conditions in the

  13. [Conservation Units.

    Science.gov (United States)

    Texas Education Agency, Austin.

    Each of the six instructional units deals with one aspect of conservation: forests, water, rangeland, minerals (petroleum), and soil. The area of the elementary school curriculum with which each correlates is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the…

  14. Thermodynamical string fragmentation

    Science.gov (United States)

    Fischer, Nadine; Sjöstrand, Torbjörn

    2017-01-01

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from the LHC. While some improvements can be noted, it turns out to be nontrivial to obtain effects as big as required, and further work is called for.

  15. Meta-analysis of the effects of forest fragmentation on interspecific interactions.

    Science.gov (United States)

    Magrach, Ainhoa; Laurance, William F; Larrinaga, Asier R; Santamaria, Luis

    2014-10-01

    Forest fragmentation dramatically alters species persistence and distribution and affects many ecological interactions among species. Recent studies suggest that mutualisms, such as pollination and seed dispersal, are more sensitive to the negative effects of forest fragmentation than antagonisms, such as predation or herbivory. We applied meta-analytical techniques to evaluate this hypothesis and quantified the relative contributions of different components of the fragmentation process (decreases in fragment size, edge effects, increased isolation, and habitat degradation) to the overall effect. The effects of fragmentation on mutualisms were primarily driven by habitat degradation, edge effects, and fragment isolation, and, as predicted, they were consistently more negative on mutualisms than on antagonisms. For the most studied interaction type, seed dispersal, only certain components of fragmentation had significant (edge effects) or marginally significant (fragment size) effects. Seed size modulated the effect of fragmentation: species with large seeds showed stronger negative impacts of fragmentation via reduced dispersal rates. Our results reveal that different components of the habitat fragmentation process have varying impacts on key mutualisms. We also conclude that antagonistic interactions have been understudied in fragmented landscapes, most of the research has concentrated on particular types of mutualistic interactions such as seed dispersal, and that available studies of interspecific interactions have a strong geographical bias (arising mostly from studies carried out in Brazil, Chile, and the United States). © 2014 Society for Conservation Biology.

  16. Fragmentation of exotic oxygen isotopes

    Energy Technology Data Exchange (ETDEWEB)

    Leistenschneider, A.; Elze, Th.W.; Gruenschloss, A.; Palit, R. [Johann Wolfgang Goethe-Univ., Frankfurt (Germany). Inst. fuer Kernphysik; Aumann, T.; Cortina, D.; Datta Pramanik, U.; Emling, H.; Geissel, H.; Helariutta, K.; Hellstroem, M.; Ilievski, S.; Jones, K.; Muenzenberg, G.; Scheidenberger, C.; Schmidt, K.-H.; Suemmerer, K. [Gesellschaft fuer Schwerionenforschung (GSI), Darmstadt (Germany); Boretzky, K.; Kratz, J.V.; Le Hong, Khiem [Johannes Gutenberg-Univ., Mainz (Germany). Inst. fue Kernchemie; Canto, L.F. [Universidade Federal, Rio de Janeiro, RJ (Brazil). Inst. de Fisica; Carlson, B.V. [Centro Tecnico Aeroespacial (CTA), Sao Jose dos Campos, SP (Brazil). Inst. Tecnologico de Aeronautica (ITA). Dept. de Fisica; Hussein, M.S. [Sao Paulo Univ. (USP), SP (Brazil). Inst. de Fisica; Kulessa, R.; Lubkiewicz, E.; Wajda, E.; Walus, W. [Uniwersytet Jagellonski, Krakow (Poland). Instytut Fizyki; Reiter, P. [Ludwig-Maximilians-Univ., Garching (Germany). Sektion Physik; Simon, H. [Technische Univ., Darmstadt (Germany). Inst. fuer Kernphysik

    2003-06-01

    Abrasion-ablation models and the empirical EPAX parametrization of projectile fragmentation are described. Their cross section predictions are compared to recent data of the fragmentation of secondary beams of neutron-rich, unstable {sup 19,20,21} O isotopes at beam energies near 600 MeV/nucleon as well as data for stable {sup 17,18} O beams. (author)

  17. Polymer fragmentation in extensional flow

    Energy Technology Data Exchange (ETDEWEB)

    Maroja, Armando M.; Oliveira, Fernando A.; Ciesla, Michal; Longa, Lech

    2001-06-01

    In this paper we present an analysis of fragmentation of dilute polymer solutions in extensional flow. The transition rate is investigated both from theoretical and computational approaches, where the existence of a Gaussian distribution for the breaking bonds has been controversial. We give as well an explanation for the low fragmentation frequency found in DNA experiments.

  18. Mass spectrometry for fragment screening.

    Science.gov (United States)

    Chan, Daniel Shiu-Hin; Whitehouse, Andrew J; Coyne, Anthony G; Abell, Chris

    2017-11-08

    Fragment-based approaches in chemical biology and drug discovery have been widely adopted worldwide in both academia and industry. Fragment hits tend to interact weakly with their targets, necessitating the use of sensitive biophysical techniques to detect their binding. Common fragment screening techniques include differential scanning fluorimetry (DSF) and ligand-observed NMR. Validation and characterization of hits is usually performed using a combination of protein-observed NMR, isothermal titration calorimetry (ITC) and X-ray crystallography. In this context, MS is a relatively underutilized technique in fragment screening for drug discovery. MS-based techniques have the advantage of high sensitivity, low sample consumption and being label-free. This review highlights recent examples of the emerging use of MS-based techniques in fragment screening. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  19. Exporting conservation

    OpenAIRE

    LTRA-12

    2012-01-01

    Metadata only record Soil degradation represents a major threat to food security, particularly in mountainous regions of Southeast Asia, where rainfall can wash away inches of topsoil. This article presents conservation agriculture as a potential solution, focusing on the work that North Carolina Agricultural and Technical State University conducts in Southeast Asia in conjunction with regional partners as part of the Sustainable Agriculture and Natural Resource Management (SANREM) collabo...

  20. National Assessment of the Fragmentation Levels and Fragmentation-Class Transitions of the Forests in Mexico for 2002, 2008 and 2013

    Directory of Open Access Journals (Sweden)

    Elizabeth Clay

    2016-02-01

    Full Text Available Landscape modification and habitat fragmentation are key drivers of global species and biodiversity loss, as well as a major threat to the conservation of forest ecosystems. Mexico is one of the five biologically richest countries in the world. This study first generated a national level assessment of the fragmentation of temperate and tropical forests in Mexico for 2002, 2008, and 2013. Then, using these results, it explores how transitions to non-forest or to other fragmentation classes have evolved within the previous date fragmentation classes for the 2002–2008 and 2008–2013 periods. The Morphological Spatial Pattern Analysis (MSPA method was used to assess the forest fragmentation. The results show that high fragmentation classes are more likely to transition to no-forest land covers in tropical than in temperate forests and that these conversions were larger during 2002–2008 than during the 2008–2013 period in both forest types. When analyzing the transitions between fragmentation classes, a higher percent of the forest area remained the same fragmentation class between 2008 and 2013 than from 2002 to 2008. Transitions between forest fragmentation classes were relatively small compared to transitions to no-forest land covers, and transitions to higher fragmentation classes were slightly larger in tropical than in temperate forests.

  1. The spectroscopy of fission fragments

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, W.R. [Department of Physics and Astronomy, University of Manchester, Manchester, M13 9PL (United Kingdom); Collaboration: La Direction des Sciences de la Matiere du CEA (FR); Le Fonds National de la Recherche Scientifique de Belgique (BE)

    1998-12-31

    High-resolution measurements on {gamma} rays from fission fragments have provided a rich source of information, unobtainable at the moment in any other way, on the spectroscopy of neutron-rich nuclei. In recent years important data have been obtained on the yrast- and near yrast-structure of neutron-rich fission fragments. We discuss the scope of measurements which can be made on prompt gamma rays from secondary fission fragments, the techniques used in the experiments and some results recently obtained. (author) 24 refs., 8 figs., 1 tab.

  2. Marginal AMP chain graphs

    OpenAIRE

    Pena, Jose M.

    2014-01-01

    We present a new family of models that is based on graphs that may have undirected, directed and bidirected edges. We name these new models marginal AMP (MAMP) chain graphs because each of them is Markov equivalent to some AMP chain graph under marginalization of some of its nodes. However, MAMP chain graphs do not only subsume AMP chain graphs but also multivariate regression chain graphs. We describe global and pairwise Markov properties for MAMP chain graphs and prove their equivalence for...

  3. The relative influence of habitat loss and fragmentation: do tropical mammals meet the temperate paradigm?

    Science.gov (United States)

    Thornton, Daniel H; Branch, Lyn C; Sunquist, Melvin E

    2011-09-01

    The relative influence of habitat loss vs. habitat fragmentation per se (the breaking apart of habitat) on species distribution and abundance is a topic of debate. Although some theoretical studies predict a strong negative effect of fragmentation, consensus from empirical studies is that habitat fragmentation has weak effects compared with habitat loss and that these effects are as likely to be positive as negative. However, few empirical investigations of this issue have been conducted on tropical or wide-ranging species that may be strongly influenced by changes in patch size and edge that occur with increasing fragmentation. We tested the relative influence of habitat loss and fragmentation by examining occupancy of forest patches by 20 mid- and large-sized Neotropical mammal species in a fragmented landscape of northern Guatemala. We related patch occupancy of mammals to measures of habitat loss and fragmentation and compared the influence of these two factors while controlling for patch-level variables. Species responded strongly to both fragmentation and loss, and response to fragmentation generally was negative. Our findings support previous assumptions that conservation of large mammals in the tropics will require conservation strategies that go beyond prevention of habitat loss to also consider forest cohesion or other aspects of landscape configuration.

  4. Rehydration of a reattached fractured tooth fragment after prolonged dehydration.

    Science.gov (United States)

    Arhun, Neslihan; Onay, Emel Olga; Ungor, Mete

    2012-01-01

    Crown fractures of the anterior teeth are one of the most common outcomes of trauma to the orofacial region. The reattachment of dental fragments is a conservative treatment and should be considered a primary treatment choice in the restoration of anterior tooth fractures. This article presents a clinical technique for the restoration of a fractured maxillary lateral incisor by reattaching the tooth fragment that was kept in dry conditions for five days with the aid of adhesive dentistry. The esthetic compromise of white color (due to excessive dehydration of the segment) was reconciled after one month of service in the mouth by regaining the natural color by rehydration. The one-year clinical evaluation revealed a successful outcome for this technique, and the patient was pleased with the esthetic results of the conservative treatment modality.

  5. Jet mass dependence of fragmentation in positron-proton collisions

    Energy Technology Data Exchange (ETDEWEB)

    Urmossy, K. [Shandong University, School of Physics and Key Laboratory of Particle Physics and Particle Irradiation (MOE), Jinan, Shandong (China)

    2017-02-15

    We propose the characterization of fragmentation functions by the energy fraction x a hadron takes away from the energy of the jet measured in the frame co-moving with the jet. Besides, we propose the usage of the jet mass as the fragmentation scale Q. We show that these two Lorentz-invariant variables emerge naturally in a microcanonical ensemble with conserved four-momentum. Then, we construct a statistical hadronisation model, in which, two features of the hadronic final states in various high-energy reactions (power law spectra and negative-binomial multiplicity distributions) can be connected simply. Finally, we analyse the scale dependence of the parameters of the model (power of the spectrum and mean energy per hadron) in the φ{sup 3} theory. Fitting fragmentation functions in diffractive positron-proton collisions, we obtain a prediction for the jet mass dependence of the hadron multiplicity distribution inside jets. (orig.)

  6. Fragment Reattachment after Atypical Crown Fracture in Maxillary Central Incisor

    Directory of Open Access Journals (Sweden)

    Vanessa Torraca Peraro Vaz

    2014-01-01

    Full Text Available Background. Fracture by trauma is one of the most common types of dental injury in the permanent dentition among children and teenagers. Aim. The aim of this study was to report the treatment performed to an atypical dental trauma case in a maxillary central incisor of a young patient by means of reattachment of the tooth fragment. Case Description. A 12-year-old male patient suffered a vertical crown fracture to the maxillary right central incisor. After clinical and radiographic examinations, a conservative restorative treatment which consisted in the reattachment of the tooth fragment with flow resin was performed in order to preserve the dental element and to obtain maximum aesthetics. Conclusion. The reattachment of fractured fragment is a fast and easy technique that can be used successfully as an option to restore dental element which suffered trauma. Clinical Significance. This technique restores the aesthetics and function of the dental element with minimal discomfort to the patient.

  7. A importância da ordem Ciconiiformes na cadeia epidemiológica de Salmonella spp. para a saúde pública e a conservação da diversidade biológica The role of order Ciconiiformes in the epidemiological chain of Salmonella spp. for public health and biological diversity conservation

    Directory of Open Access Journals (Sweden)

    Marcio A. Silva

    2010-07-01

    Full Text Available A diversidade biológica é representada por todas as unidades da natureza e sua conservação diz respeito à sobrevivência da própria espécie humana. Uma das ameaças à sua conservação são as doenças infecciosas que afetam a fauna, dentre as quais se podee incluir a salmonelose como uma das mais importantes, especialmente para a avifauna. Aves de topo de cadeia alimentar como os Ciconiiformes podem ser potenciais reservatórios e disseminadores da Salmonella spp. para outras espécies silvestres e também para populações humanas e animais domésticos, podendo causar prejuízos à saúde pública e ao meio ambiente. Objetivou-se descrever a infecção ou doença por Salmonella sp., o seu agente etiológico e sua ocorrência em Ciconiiformes, bem como demonstrar a importância destas aves na cadeia epidemiológica silvestre desta zoonose, verificando os riscos para a saúde pública e para a conservação da diversidade biológica.Biological diversity is represented by all nature units and its conservation is about the survival of human beings. Infectious diseases are one of the possible threats for wildlife conservation, which includes salmonellosis as a most important disease, especially for the avifauna. Top alimentary chain birds such as Ciconiiformes can be reservoirs and disseminators of Salmonella spp. to other wild and domestic animals, and also for human populations, with serious risks to public and environmental health. This review describes infection by Salmonella spp., its etiological agent and occurrence in Ciconiiformes, as well as the importance of these wild birds for the epidemiological chain of the zoonosis, and discusses the risks for public health and biological diversity conservation.

  8. Efficient Expression of Antibody Fragments with the Brevibacillus Expression System

    Directory of Open Access Journals (Sweden)

    Hiroshi Hanagata

    2014-05-01

    Full Text Available Antibodies, owing to their capability to bind specifically to a target molecule, have been and will continue to be applied in various areas, including research, diagnosis and therapy. In particular, antibody fragments, which are size-reduced antibodies comprising functional variable domains, are suited for production in bacteria. They also are useful in applications requiring intracellular delivery and for further engineering toward molecules possessing multiple custom functions. An expression system based on Brevibacillus is characterized by high efficiency and simple genetic recombination for secretory production. The Brevibacillus expression system has been successfully utilized for the efficient production of antibody fragments, e.g., scFvs (single-chain antibody fragments comprising heavy-chain and light-chain variable domains, linked by a spacer sequence. Expression in fusion with a Halobacterium-derived secretory protein was shown to confer enhanced productivity. In the case of Fabs, productivity as high as 100 mg/L was accomplished in a simple system, i.e., shake flask cultures. The Brevibacillus expression system offers several advantages, shared by other bacterial systems, such as E. coli, in particular, for the ease in genetic engineering and culture production.

  9. Fragmentation studies on metastable diethylaniline derivatives using mass-analyzed ion kinetic energy spectrometry.

    Science.gov (United States)

    Seulen, Sarah; Grotemeyer, Jürgen

    2018-02-01

    It is well known that small substituted aromatic amines lose their substituents after electron ionization in a multistep fragmentation mechanism. In this contribution, the fragmentation reactions of N,N-diethyl-aniline and different methyl-substituted N,N-diethyl-methyl-aniline isomers are investigated with respect to the position of the methyl group attached to the aromatic ring system. Metastable ion decay reveals a complicated fragmentation mechanism leading to an interplay of the aromatic methyl group and the ethyl substituents at the amine function. A small change in the substitution leads to a significant change of the observed fragments indicating a participation of o-methyl groups in the fragmentation mechanism of the diethyl amino side chain. Because the underlying mechanisms are not fully understood, the presented investigations deliver through 13C isotopic labeling a deep insight into the hidden rearrangement and fragmentation mechanisms in these compounds.

  10. Conservation implications when the next predators are known. Chapter 2

    Science.gov (United States)

    Frank R., III Thompson; Christine A. Ribic

    2012-01-01

    Conservation and management of passerines has largely focused on habitat manipulation or restoration because the natural communities on which these birds depend have been destroyed and fragmented. However, productivity is another important aspect of avian conservation, and nest predation can be a large source of nesting mortality for passerines. Recent studies using...

  11. Light quark fragmentations into pions

    Science.gov (United States)

    Edemskaya, A. K.; Naumov, D. V.; Samoylov, O. B.

    2011-12-01

    We discuss a process of hadronization of light quarks into charged pions in e + e - annihilations and in deep inelastic scatering of charged leptons and neutrino off nucleons. The corresponding semi-inclusive cross-sections of pions production we write in terms of quark fragmentation functions and fracture functions. We suggest a new method of measurements of fragmentation and fracture functions based on analysis of semiinclusive data.

  12. QGP and Modified Jet Fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xin-Nian

    2005-04-18

    Recent progresses in the study of jet modification in hotmedium and their consequences in high-energy heavy-ion collisions are reviewed. In particular, I will discuss energy loss for propagating heavy quarks and the resulting modified fragmentation function. Medium modification of the parton fragmentation function due to quark recombination are formulated within finite temperature field theory and their implication on the search for deconfined quark-gluon plasma is also discussed.

  13. The Greening of Global Value Chains

    DEFF Research Database (Denmark)

    De Marchi, Valentina; Maria, Eleonora Di; Ponte, Stefano

    2013-01-01

    With increasing fragmentation of production between independent firms that are spatially dispersed and are responsible for different steps of the production process, a Global Value Chain approach is employed to examine how ‘lead firms’ shape the green features of upstream activities. Comparative......-off’ mechanisms embedded in standards and design. Two governing approaches to the greening of value chains are identified: standard-driven and mentoring-driven, and these are used to provide some reflections on when we are likely to observe one or the other, and also to develop a future research agenda....

  14. The effect of habitat fragmentation on cyclic population dynamics: a numerical study.

    Science.gov (United States)

    Strohm, S; Tyson, R

    2009-08-01

    Through four spatially explicit models, we investigate how habitat fragmentation affects cyclic predator-prey population dynamics. We use a Partial Differential Equation (PDE) framework to describe the dispersal of predators and prey in a heterogeneous landscape made of high quality and low quality habitat patches, subject to increasing fragmentation through habitat separation and/or habitat loss. Our results show that habitat fragmentation decreases the amplitude of the predator-prey population cycles while average population density is not as strongly affected in general. Beyond these simple trends however, the four models show differing responses to fragmentation, indicating that when making predictions about population survival and persistence in the face of habitat fragmentation, the choice of model is important. Our results may inform conservation efforts in fragmented habitats for cyclic species such as the snowshoe hare and Canada lynx.

  15. Logistic chain modelling

    NARCIS (Netherlands)

    Slats, P.A.; Bhola, B.; Evers, J.J.M.; Dijkhuizen, G.

    1995-01-01

    Logistic chain modelling is very important in improving the overall performance of the total logistic chain. Logistic models provide support for a large range of applications, such as analysing bottlenecks, improving customer service, configuring new logistic chains and adapting existing chains to

  16. Health supply chain management.

    Science.gov (United States)

    Zimmerman, Rolf; Gallagher, Pat

    2010-01-01

    This chapter gives an educational overview of: * The actual application of supply chain practice and disciplines required for service delivery improvement within the current health environment. * A rationale for the application of Supply Chain Management (SCM) approaches to the Health sector. * The tools and methods available for supply chain analysis and benchmarking. * Key supply chain success factors.

  17. Chains and identity

    NARCIS (Netherlands)

    Grijpink, J.H.A.M.

    2012-01-01

    This article is available in English and DutchGuidelines are presented to cope with identity problems in chains. A chain is a collaboration of a great number of autonomous organisations and professionals to tackle a dominant chain problem. In many chains identity fraud is an aspect of the dominant

  18. Silicone chain extender

    DEFF Research Database (Denmark)

    2015-01-01

    The present invention relates to a silicone chain extender, more particularly a chain extender for silicone polymers and copolymers, to a chain extended silicone polymer or copolymer and to a functionalized chain extended silicone polymer or copolymer, to a method for the preparation thereof...

  19. Bicistronic DNA display for in vitro selection of Fab fragments.

    Science.gov (United States)

    Sumida, Takeshi; Doi, Nobuhide; Yanagawa, Hiroshi

    2009-12-01

    In vitro display methods are superior tools for obtaining monoclonal antibodies. Although totally in vitro display methods, such as ribosome display and mRNA display, have the advantages of larger library sizes and quicker selection procedures compared with phage display, their applications have been limited to single-chain Fvs due to the requirement for linking of the mRNA and the nascent protein on the ribosome. Here we describe a different type of totally in vitro method, DNA display, that is applicable to heterodimeric Fab fragments: in vitro compartmentalization in water-in-oil emulsions allows the linking of an oligomeric protein and its encoding DNA with multiple ORFs. Since previously used emulsions impaired the synthesis of functional Fab fragments, we modified conditions for preparing emulsions, and identified conditions under which it was possible to enrich Fab fragments 10(6)-fold per three rounds of affinity selection. Furthermore, we confirmed that genes encoding stable Fab fragments could be selected from a Fab fragment library with a randomized hydrophobic core in the constant region by applying heat treatment as a selection pressure. Since this method has all advantages of both phage display and totally in vitro display, it represents a new option for many applications using display methods.

  20. Anticoagulant and calcium-binding properties of high molecular weight derivatives of human fibrinogen, produced by plasmin (fragments X)

    NARCIS (Netherlands)

    Nieuwenhuizen, W.; Gravesen, M.

    1981-01-01

    Early plasmin degradation products (X fragments) of human fibrinogen were prepared in the presence of calcium-ions or EGTA, and purified on Sepharose 6B-CL. X fragments were characterized with respect to amino-terminal amino acids, polypeptide-chain composition, anticlotting properties and

  1. Detecting fragmentation extinction thresholds for forest understory plant species in peninsular Spain.

    Directory of Open Access Journals (Sweden)

    Marta Rueda

    Full Text Available Ecological theory predicts that fragmentation aggravates the effects of habitat loss, yet empirical results show mixed evidences, which fail to support the theory instead reinforcing the primary importance of habitat loss. Fragmentation hypotheses have received much attention due to their potential implications for biodiversity conservation, however, animal studies have traditionally been their main focus. Here we assess variation in species sensitivity to forest amount and fragmentation and evaluate if fragmentation is related to extinction thresholds in forest understory herbs and ferns. Our expectation was that forest herbs would be more sensitive to fragmentation than ferns due to their lower dispersal capabilities. Using forest cover percentage and the proportion of this percentage occurring in the largest patch within UTM cells of 10-km resolution covering Peninsular Spain, we partitioned the effects of forest amount versus fragmentation and applied logistic regression to model occurrences of 16 species. For nine models showing robustness according to a set of quality criteria we subsequently defined two empirical fragmentation scenarios, minimum and maximum, and quantified species' sensitivity to forest contraction with no fragmentation, and to fragmentation under constant forest cover. We finally assessed how the extinction threshold of each species (the habitat amount below which it cannot persist varies under no and maximum fragmentation. Consistent with their preference for forest habitats probability occurrences of all species decreased as forest cover contracted. On average, herbs did not show significant sensitivity to fragmentation whereas ferns were favored. In line with theory, fragmentation yielded higher extinction thresholds for two species. For the remaining species, fragmentation had either positive or non-significant effects. We interpret these differences as reflecting species-specific traits and conclude that although

  2. Detecting fragmentation extinction thresholds for forest understory plant species in peninsular Spain.

    Science.gov (United States)

    Rueda, Marta; Moreno Saiz, Juan Carlos; Morales-Castilla, Ignacio; Albuquerque, Fabio S; Ferrero, Mila; Rodríguez, Miguel Á

    2015-01-01

    Ecological theory predicts that fragmentation aggravates the effects of habitat loss, yet empirical results show mixed evidences, which fail to support the theory instead reinforcing the primary importance of habitat loss. Fragmentation hypotheses have received much attention due to their potential implications for biodiversity conservation, however, animal studies have traditionally been their main focus. Here we assess variation in species sensitivity to forest amount and fragmentation and evaluate if fragmentation is related to extinction thresholds in forest understory herbs and ferns. Our expectation was that forest herbs would be more sensitive to fragmentation than ferns due to their lower dispersal capabilities. Using forest cover percentage and the proportion of this percentage occurring in the largest patch within UTM cells of 10-km resolution covering Peninsular Spain, we partitioned the effects of forest amount versus fragmentation and applied logistic regression to model occurrences of 16 species. For nine models showing robustness according to a set of quality criteria we subsequently defined two empirical fragmentation scenarios, minimum and maximum, and quantified species' sensitivity to forest contraction with no fragmentation, and to fragmentation under constant forest cover. We finally assessed how the extinction threshold of each species (the habitat amount below which it cannot persist) varies under no and maximum fragmentation. Consistent with their preference for forest habitats probability occurrences of all species decreased as forest cover contracted. On average, herbs did not show significant sensitivity to fragmentation whereas ferns were favored. In line with theory, fragmentation yielded higher extinction thresholds for two species. For the remaining species, fragmentation had either positive or non-significant effects. We interpret these differences as reflecting species-specific traits and conclude that although forest amount is of

  3. Fragmentation and ablation during entry

    Energy Technology Data Exchange (ETDEWEB)

    Canavan, G.H.

    1997-09-01

    This note discusses objects that both fragment and ablate during entry, using the results of previous reports to describe the velocity, pressure, and fragmentation of entering objects. It shows that the mechanisms used there to describe the breakup of non-ablating objects during deceleration remain valid for most ablating objects. It treats coupled fragmentation and ablation during entry, building on earlier models that separately discuss the entry of objects that are hard, whose high heat of ablation permits little erosion, and those who are strong whose strength prevents fragmentation, which are discussed in ``Radiation from Hard Objects,`` ``Deceleration and Radiation of Strong, Hard, Asteroids During Atmospheric Impact,`` and ``Meteor Signature Interpretation.`` This note provides a more detailed treatment of the further breakup and separation of fragments during descent. It replaces the constraint on mass per unit area used earlier to determine the altitude and magnitude of peak power radiation with a detailed analytic solution of deceleration. Model predictions are shown to be in agreement with the key features of numerical calculations of deceleration. The model equations are solved for the altitudes of maximum radiation, which agree with numerical integrations. The model is inverted analytically to infer object size and speed from measurements of peak power and altitude to provide a complete model for the approximate inversion of meteor data.

  4. Diets of swift foxes (Vulpes velox) in continuous and fragmented prairie in Northwestern Texas

    Science.gov (United States)

    Kamler, J.F.; Ballard, W.B.; Wallace, M.C.; Gipson, P.S.

    2007-01-01

    Distribution of the swift fox (Vulpes velox) has declined dramatically since the 1800s, and suggested causes of this decline are habitat fragmentation and transformation due to agricultural expansion. However, impacts of fragmentation and human-altered habitats on swift foxes still are not well understood. To better understand what effects these factors have on diets of swift foxes, scats were collected in northwestern Texas at two study sites, one of continuous native prairie and one representing fragmented native prairie interspersed with agricultural and fields in the Conservation Reserve Program. Leporids, a potential food source, were surveyed seasonally on both sites. Diets of swift foxes differed between sites; insects were consumed more on continuous prairie, whereas mammals, birds, and crops were consumed more on fragmented prairie. Size of populations of leporids were 2-3 times higher on fragmented prairie, and swift foxes responded by consuming more leporids on fragmented (11.1% frequency occurrence) than continuous (3.8%) prairie. Dietary diversity was greater on fragmented prairie during both years of the study. Differences in diets between sites suggested that the swift fox is an adaptable and opportunistic feeder, able to exploit a variety of food resources, probably in relation to availability of food. We suggest that compared to continuous native prairie, fragmented prairie can offer swift foxes a more diverse prey base, at least within the mosaic of native prairie, agricultural, and fields that are in the Conservation Reserve Program.

  5. Effects of protected area downsizing on habitat fragmentation in Yosemite National Park (USA, 1864 - 2014

    Directory of Open Access Journals (Sweden)

    Rachel E. Golden Kroner

    2016-09-01

    Full Text Available Protected area downgrading, downsizing, and degazettement (PADDD has been documented worldwide, but its impacts on biodiversity are poorly understood. To fill this knowledge gap, we reviewed historical documents to identify legal changes that altered the boundaries of Yosemite National Park. We identified two downsizes and five additions between 1905 and 1937 that reduced the size of Yosemite National Park by 30%. To examine the effects of these downsizing events on habitat fragmentation by roads, we compared protected, never-protected, and downsized lands at three spatial scales using four habitat fragmentation metrics: road density, fragment (land surrounded by roads area-to-perimeter ratio, fragment area, and fragment density. In general, lands that were removed from protection, e.g., downsized, were more highly fragmented than protected lands and indistinguishable from never-protected lands. Lands where downsizes were reversed were less fragmented than lands where downsizes were not reversed. These results suggest that protected area downsizing may exacerbate habitat fragmentation, a key contributor to biodiversity loss globally. Furthermore, the case study in Yosemite National Park demonstrates that iconic protected areas in developed countries are not immune to downsizing. These findings underscore the need to account for PADDD and governance histories in ecological research, monitoring, and evaluation. As we move toward more evidence-based conservation policy, a rigorous understanding of PADDD is essential to ensure that protected areas fulfill their promise as a strategy for conserving global biodiversity.

  6. Leptospira spp detection by Polymerase Chain Reaction (PCR in clinical samples of captive black-capped Capuchin monkey (Cebus apella

    Directory of Open Access Journals (Sweden)

    Scarcelli Eliana

    2003-01-01

    Full Text Available Leptospirosis is a widely distributed zoonosis that affects domestic and wild animals, and that has the man as the end point of its epidemiological chain. Leptospirosis diagnosis in primates is more difficult than in other animal species, as clinical signs and lesions are less evident and antibody response is detected only for short periods. The aim of this article was to describe the detection of Leptospira spp using polymerase chain reaction (PCR, in clinical samples from one captive black-capped Capuchin monkey (Cebus apella, which presented characteristics compatible with leptospirosis (jaundice and haemorrhagic kdney in the macroscopic post-mortem examination. A friable kidney fragment and urine sample were cultured and submitted to experimental inoculation in guinea pigs and PCR using genus specific primer pair targeting the 16S rRNA region from Leptospira interrogans serovar canicola. Isolation of the agent was negative both in culture and experimental inoculation. The PCR amplification of the clinical samples showed a 330 pb amplified fragment that corresponds to the Leptospira genus. Based on these results PCR was considered an important tool for leptospira detection in nonhumam primates, more sensitive and specific than other techniques, especially considering that the viability of the pathogen was not possible. These advantages enable the detection of the leptospiras in urine and kidney, even when autolysed, frozen or badly conserved, which prevented the isolation and experimental inoculation from positive results.

  7. Alternative Techniques to Remove Fractured Instrument Fragments from the Apical Third of Root Canals: Report of Two Cases

    OpenAIRE

    Brito-Júnior,Manoel; Normanha,João Américo; Camilo,Carla Cristina; Faria-e-Silva,André Luis; Saquy,Paulo César; Ferraz,Maria Ãngela Arêa Leão; Silva-Sousa,Yara Teresinha Correa

    2015-01-01

    This paper describes two cases of instrument fragment removal from the apical thirds of root canals using a customized extractor and a modified needle technique, respectively. In case 1, a customized extractor was manufactured to remove a bur fragment located in the apical root canal of a maxillary central incisor. The use of this extractor enabled successful and conservative removal of the instrument fragment. In case...

  8. Therapeutic Anti-Methamphetamine Antibody Fragment-Nanoparticle Conjugates: Synthesis and In Vitro Characterization

    OpenAIRE

    Nanaware-Kharade, Nisha; Gonzalez, Guillermo A.; Lay, Jackson O.; Hendrickson, Howard P.; Peterson, Eric C.

    2012-01-01

    Treatments specific to the medical problems caused by methamphetamine (METH) abuse are greatly needed. Towards this goal, we are developing new multivalent anti-METH antibody fragment-nanoparticle conjugates with customizable pharmacokinetic properties. We have designed a novel anti-METH single chain antibody fragment with an engineered terminal cysteine (scFv6H4Cys). Generation 3 (G3) polyamidoamine dendrimer nanoparticles were chosen for conjugation due to their monodisperse properties and ...

  9. An efficient method for isolating antibody fragments against small peptides by antibody phage display

    DEFF Research Database (Denmark)

    Duan, Zhi; Siegumfeldt, Henrik

    2010-01-01

    We generated monoclonal scFv (single chain variable fragment) antibodies from an antibody phage display library towards three small synthetic peptides derived from the sequence of s1-casein. Key difficulties for selection of scFv-phages against small peptides were addressed. Small peptides do....... The scFvs were sequenced and characterized, and specificity was characterized by ELISA. The methods developed in this study are universally applicable for antibody phage display to efficiently produce antibody fragments against small peptides....

  10. Sustainable Supply Chain Design

    DEFF Research Database (Denmark)

    Bals, Lydia; Tate, Wendy

    A significant conceptual and practical challenge is how to integrate triple bottom line (TBL; including economic, social and environmental) sustainability into global supply chains. Although this integration is necessary to slow down global resource depletion, understanding is limited of how...... to implement TBL goals across the supply chain. In supply chain design, the classic economic perspective still dominates, although the idea of the TBL is more widely disseminated. The purpose of this research is to add to the sustainable supply chain management literature (SSCM) research agenda...... by incorporating the physical chain, and the (information and financial) support chains into supply chain design. This manuscript tackles issues of what the chains are designed for and how they are designed structurally. Four sustainable businesses are used as illustrative case examples of innovative supply chain...

  11. A thermodynamic theory of dynamic fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Yew, Ching H. [Texas Univ., Austin, TX (United States); Taylor, P.A. [Sandia National Labs., Albuquerque, NM (United States)

    1993-08-01

    We present a theory of dynamic fragmentation of brittle materials based on thermodynamic arguments. We recover the expressions for average fragment size and number as originally derived by Grady. We extend the previous work by obtaining descriptions of fragment size distribution and compressibility change due to the fragmentation process. The size distribution is assumed to be proportional to the spectral power of the strain history and a sample distribution is presented for a fragmentation process corresponding to a constant rate strain history. The description of compressibility change should be useful in computational studies of fragmentation. These results should provide insight into the process of fragmentation of brittle materials from hypervelocity impact.

  12. Water Conservation and Water Storage

    Science.gov (United States)

    Narayanan, M.

    2014-12-01

    Water storage can be a viable part of the solution to water conservation. This means that we should include reservoirs. Regardless, one should evaluate all aspects of water conservation principles. Recent drought in California indicates that there is an urgent need to re-visit the techniques used to maintain the water supply-chain mechanism in the entire state. We all recognize the fact that fish and wildlife depend on the streams, rivers and wetlands for survival. It is a well-known fact that there is an immediate need to provide solid protection to all these resources. Laws and regulations should help meet the needs of natural systems. Farmers may be forced to drilling wells deeper than ever. But, they will be eventually depleting groundwater reserves. Needless to say that birds, fish and wildlife cannot access these groundwater table. California is talking a lot about conservation. Unfortunately, the conservation efforts have not established a strong visible hold. The Environmental Protection Agency has a plan called E2PLAN (Narayanan, 2012). It is EPA's plan for achieving energy and environmental performance, leadership, accountability, and carbon neutrality. In June 2011, the EPA published a comprehensive, multi-year planning document called Strategic Sustainability Performance Plan. The author has previously reported these in detail at the 2012 AGU fall meeting. References: Ziegler, Jay (15 JUNE 2014). The Conversation: Water conservation efforts aren't taking hold, but there are encouraging signs. THE SACRAMENTO BEE. California. Narayanan, Mysore. (2012). The Importance of Water Conservation in the 21st Century. 72nd AGU International Conference. Eos Transactions: American Geophysical Union, Vol. 92, No. 56, Fall Meeting Supplement, 2012. H31I - 1255.http://www.sacbee.com/2014/06/15/6479862/jay-ziegler-water-conservation.html#storylink=cpy

  13. Population pressure and farm fragmentation:

    African Journals Online (AJOL)

    user

    Small farmers play a dominant role in rural area in Rwanda according to many researchers. These farmers have some particular characteristics: most of them have tiny farms, while purchasing and borrowing of land are frequent. In addition, the size of farms is not only very small but farms are further fragmented into ...

  14. Fragmentation of stretched liquid ligaments

    NARCIS (Netherlands)

    Marmottant, P.G.M.; Villermaux, Emmanuel

    2004-01-01

    The dynamics and fragmentation of stretched liquid ligaments is investigated. The ligaments are produced by the withdrawal of a tube initially dipping at a free surface. Time resolved high speed motion experiments reveal two different elongation behaviors, depending on the nondimensional number t,

  15. Fragmented nature: consequences for biodiversity

    NARCIS (Netherlands)

    Olff, H.; Ritchie, M.E.

    2002-01-01

    We discuss how fragmentation of resources and habitat operate differently on species diversity across spatial scales, ranging from positive effects on local species coexistence to negative effect on intermediate spatial scales, to again positive effects on large spatial and temporal scales. Species

  16. Fragmented nature : consequences for biodiversity

    NARCIS (Netherlands)

    Olff, Han; Ritchie, Mark E.

    2002-01-01

    We discuss how fragmentation of resources and habitat operate differently on species diversity across spatial scales, ranging from positive effects on local species coexistence to negative effect on intermediate spatial scales, to again positive effects on large spatial and temporal scales. Species

  17. Factors Affecting Entry into Supply Chain Trade: An Analysis of Firms in Southeast Asia

    National Research Council Canada - National Science Library

    Wignaraja, Ganeshan

    2015-01-01

    This article undertakes a comparative, firm‐level analysis of joining supply chain trade in five S outheast A sian economies to improve our understanding of fragmentation of manufacturing across borders...

  18. Antiretroviral procurement and supply chain management.

    Science.gov (United States)

    Ripin, David J; Jamieson, David; Meyers, Amy; Warty, Umesh; Dain, Mary; Khamsi, Cyril

    2014-01-01

    Procurement, the country-level process of ordering antiretrovirals (ARVs), and supply chain management, the mechanism by which they are delivered to health-care facilities, are critical processes required to move ARVs from manufacturers to patients. To provide a glimpse into the ARV procurement and supply chain, the following pages provide an overview of the primary stakeholders, principal operating models, and policies and regulations involved in ARV procurement. Also presented are key challenges that need to be addressed to ensure that the supply chain is not a barrier to the goal of universal coverage. This article will cover the steps necessary to order and distribute ARVs, including different models of delivery, key stakeholders involved, strategic considerations that vary depending on context and policies affecting them. The single drug examples given illustrate the complications inherent in fragmented supply and demand-driven models of procurement and supply chain management, and suggest tools for navigating these hurdles that will ultimately result in more secure and reliable ARV provision. Understanding the dynamics of ARV supply chain is important for the global health community, both to ensure full and efficient treatment of persons living with HIV as well as to inform the supply chain decisions for other public health products.

  19. The VERDI fission fragment spectrometer

    Directory of Open Access Journals (Sweden)

    Frégeau M.O.

    2013-12-01

    Full Text Available The VERDI time-of-flight spectrometer is dedicated to measurements of fission product yields and of prompt neutron emission data. Pre-neutron fission-fragment masses will be determined by the double time-of-flight (TOF technique. For this purpose an excellent time resolution is required. The time of flight of the fragments will be measured by electrostatic mirrors located near the target and the time signal coming from silicon detectors located at 50 cm on both sides of the target. This configuration, where the stop detector will provide us simultaneously with the kinetic energy of the fragment and timing information, significantly limits energy straggling in comparison to legacy experimental setup where a thin foil was usually used as a stop detector. In order to improve timing resolution, neutron transmutation doped silicon will be used. The high resistivity homogeneity of this material should significantly improve resolution in comparison to standard silicon detectors. Post-neutron fission fragment masses are obtained form the time-of-flight and the energy signal in the silicon detector. As an intermediary step a diamond detector will also be used as start detector located very close to the target. Previous tests have shown that poly-crystalline chemical vapour deposition (pCVD diamonds provides a coincidence time resolution of 150 ps not allowing complete separation between very low-energy fission fragments, alpha particles and noise. New results from using artificial single-crystal diamonds (sCVD show similar time resolution as from pCVD diamonds but also sufficiently good energy resolution.

  20. A probabilistic fragment-based protein structure prediction algorithm.

    Science.gov (United States)

    Simoncini, David; Berenger, Francois; Shrestha, Rojan; Zhang, Kam Y J

    2012-01-01

    Conformational sampling is one of the bottlenecks in fragment-based protein structure prediction approaches. They generally start with a coarse-grained optimization where mainchain atoms and centroids of side chains are considered, followed by a fine-grained optimization with an all-atom representation of proteins. It is during this coarse-grained phase that fragment-based methods sample intensely the conformational space. If the native-like region is sampled more, the accuracy of the final all-atom predictions may be improved accordingly. In this work we present EdaFold, a new method for fragment-based protein structure prediction based on an Estimation of Distribution Algorithm. Fragment-based approaches build protein models by assembling short fragments from known protein structures. Whereas the probability mass functions over the fragment libraries are uniform in the usual case, we propose an algorithm that learns from previously generated decoys and steers the search toward native-like regions. A comparison with Rosetta AbInitio protocol shows that EdaFold is able to generate models with lower energies and to enhance the percentage of near-native coarse-grained decoys on a benchmark of [Formula: see text] proteins. The best coarse-grained models produced by both methods were refined into all-atom models and used in molecular replacement. All atom decoys produced out of EdaFold's decoy set reach high enough accuracy to solve the crystallographic phase problem by molecular replacement for some test proteins. EdaFold showed a higher success rate in molecular replacement when compared to Rosetta. Our study suggests that improving low resolution coarse-grained decoys allows computational methods to avoid subsequent sampling issues during all-atom refinement and to produce better all-atom models. EdaFold can be downloaded from http://www.riken.jp/zhangiru/software.html [corrected].

  1. Monoclonal antibody fragment removal mediated by mixed mode resins.

    Science.gov (United States)

    O'Connor, Ellen; Aspelund, Matthew; Bartnik, Frank; Berge, Mark; Coughlin, Kelly; Kambarami, Mutsa; Spencer, David; Yan, Huiming; Wang, William

    2017-05-26

    Efforts to increase monoclonal antibody expression in cell culture can result in the presence of fragmented species requiring removal in downstream processing. Capto adhere, HEA Hypercel, and PPA Hypercel anion exchange/hydrophobic interaction mixed mode resins were evaluated for their fragment removal capabilities and found to separate large hinge IgG1 antibody fragment (LHF) from monomer. Removal of greater than 75% of LHF population occurred at pH 8 and low conductivity. The mechanism of fragment removal was investigated in two series of experiments. The first experimental series consisted of comparison to chromatographic behavior on corresponding single mode resins. Both single mode anion exchange and hydrophobic interaction resins failed to separate LHF. The second experimental series studied the impact of phase modifiers, ethylene glycol, urea, and arginine on the mixed mode mediated removal. The addition of ethylene glycol decreased LHF removal by half. Further decreases in LHF separation were seen upon incubation with urea and arginine. Therefore, it was discovered that the purification is the result of a mixed mode phenomena dominated by hydrophobic interaction and hydrogen bonding effects. The site of interaction between the LHF and mixed mode resin was determined by chemical labeling of lysine residues with sulfo-NHS acetate. The labeling identified the antibody hinge and light chain regions as mediating the fragment separation. Sequence analysis showed that under separation conditions, a hydrophobic proline patch and hydrogen bonding serine and threonine residues mediate the hinge interaction with the Capto adhere ligand. Additionally, a case study is presented detailing the optimization of fragment removal using Capto adhere resin to achieve purity and yield targets in a manufacturing facility. This study demonstrated that mixed mode resins can be readily integrated into commercial antibody platform processes when additional chromatographic abilities

  2. Gastrointestinal parasites of Howler monkeys (Alouatta palliata) inhabiting the fragmented landscape of the Santa Marta mountain range, Veracruz, Mexico.

    Science.gov (United States)

    Valdespino, Carolina; Rico-Hernández, Guillermo; Mandujano, Salvador

    2010-06-01

    In recent years populations of howler monkeys (Alouatta palliata) in southeastern Mexico have decreased substantially due to the transformation and loss of natural habitats. This is especially evident in the Santa Marta mountain range, Veracruz, Mexico where several studies have evaluated the impact of fragmentation on howler monkey populations in order to propose management programs for their conservation. The conditions generated by fragmentation likely change the rates of parasitic infection and could decrease howler survival. In this study, gastrointestinal parasite species richness, prevalence, and egg density of infection were determined in howler groups inhabiting five forest fragments at the Santa Marta mountain range. Two hundred and seventy-eight fresh fecal samples were collected between October 2002 and April 2003. Three parasite species were found during the dry and the wet season in all forest fragments sampled: one unidentified species of Eimeriidae; Trypanoxyuris minutus (Oxyuridae); and Controrchis biliophilus (Dicrocoeliidae). Both the prevalence of T. minutus and infection density for all parasites differed between seasons and fragments (the largest fragment consistently differed from other fragments). Host density, distance to the nearest town, fragment size, fragment shape, and total basal area of food trees explained parasite prevalence, but each species had a different pattern. Although parasite richness was lower, prevalence and density were higher than values reported for howlers in conserved forests. These results suggest that the establishment of biological corridors and animal translocation programs must take into account the parasite ecology of each fragment to avoid higher infection rates and preclude potential consequent mortality.

  3. The Global Value Chain

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull

    The conference paper aims to develop the global value chain concept by including corporate internal value adding activities and competition to the basic framework in order to turn the global value chain into a strategic management tool......The conference paper aims to develop the global value chain concept by including corporate internal value adding activities and competition to the basic framework in order to turn the global value chain into a strategic management tool...

  4. Importance of riparian remnants for frog species diversity in a highly fragmented rainforest

    Science.gov (United States)

    Rodríguez-Mendoza, Clara; Pineda, Eduardo

    2010-01-01

    Tropical forests undergo continuous transformation to other land uses, resulting in landscapes typified by forest fragments surrounded by anthropogenic habitats. Small forest fragments, specifically strip-shaped remnants flanking streams (referred to as riparian remnants), can be particularly important for the maintenance and conservation of biodiversity within highly fragmented forests. We compared frog species diversity between riparian remnants, other forest fragments and cattle pastures in a tropical landscape in Los Tuxtlas, Mexico. We found similar species richness in the three habitats studied and a similar assemblage structure between riparian remnants and forest fragments, although species composition differed by 50 per cent. Frog abundance was halved in riparian remnants compared with forest fragments, but was twice that found in pastures. Our results suggest that riparian remnants play an important role in maintaining a portion of frog species diversity in a highly fragmented forest, particularly during environmentally stressful (hot and dry) periods. In this regard, however, the role of riparian remnants is complementary, rather than substitutive, with respect to the function of other forest fragments within the fragmented forest. PMID:20554561

  5. Fragmentation

    Science.gov (United States)

    K.H. Riitters

    2009-01-01

    Effective resource management takes into account the administrative and biophysical settings within which natural resources occur. A setting may be described in many ways; for example, by forest land ownership, by reserved and roadless designation, or by the distribution of human populations in relation to forest (chapter 3). The physical arrangement of forest in a...

  6. Biogeographical and taxonomic biases in tropical forest fragmentation research.

    Science.gov (United States)

    Deikumah, Justus P; McAlpine, Clive A; Maron, Martine

    2014-12-01

    Despite several decades of research on the effects of fragmentation and habitat change on biodiversity, there remain strong biases in the geographical regions and taxonomic species studied. The knowledge gaps resulting from these biases are of particular concern if the forests most threatened with modification are also those for which the effects of such change are most poorly understood. To quantify the nature and magnitude of such biases, we conducted a systematic review of the published literature on forest fragmentation in the tropics for the period 1980-2012. Studies included focused on any type of response of single species, communities, or assemblages of any taxonomic group to tropical forest fragmentation and on fragmentation-related changes to forests. Of the 853 studies we found in the SCOPUS database, 64% were conducted in the Neotropics, 13% in Asia, 10% in the Afrotropics, and 5% in Australasia. Thus, although the Afrotropics is subject to the highest rates of deforestation globally, it was the most disproportionately poorly studied biome. Significant taxonomic biases were identified. Of the taxonomic groups considered, herpetofauna was the least studied in the tropics, particularly in Africa. Research examining patterns of species distribution was by far the most common type (72%), and work focused on ecological processes (28%) was rare in all biomes, but particularly in the Afrotropics and for fauna. We suggest research efforts be directed toward less-studied biogeographic regions, particularly where the threat of forest fragmentation continues to be high. Increased research investment in the Afrotropics will be important to build knowledge of threats and inform responses in a region where almost no efforts to restore its fragmented landscapes have yet begun and forest protection is arguably most tenuous. © 2014 Society for Conservation Biology.

  7. Beyond the fragmentation threshold hypothesis: regime shifts in biodiversity across fragmented landscapes.

    Directory of Open Access Journals (Sweden)

    Renata Pardini

    Full Text Available Ecological systems are vulnerable to irreversible change when key system properties are pushed over thresholds, resulting in the loss of resilience and the precipitation of a regime shift. Perhaps the most important of such properties in human-modified landscapes is the total amount of remnant native vegetation. In a seminal study Andrén proposed the existence of a fragmentation threshold in the total amount of remnant vegetation, below which landscape-scale connectivity is eroded and local species richness and abundance become dependent on patch size. Despite the fact that species patch-area effects have been a mainstay of conservation science there has yet to be a robust empirical evaluation of this hypothesis. Here we present and test a new conceptual model describing the mechanisms and consequences of biodiversity change in fragmented landscapes, identifying the fragmentation threshold as a first step in a positive feedback mechanism that has the capacity to impair ecological resilience, and drive a regime shift in biodiversity. The model considers that local extinction risk is defined by patch size, and immigration rates by landscape vegetation cover, and that the recovery from local species losses depends upon the landscape species pool. Using a unique dataset on the distribution of non-volant small mammals across replicate landscapes in the Atlantic forest of Brazil, we found strong evidence for our model predictions--that patch-area effects are evident only at intermediate levels of total forest cover, where landscape diversity is still high and opportunities for enhancing biodiversity through local management are greatest. Furthermore, high levels of forest loss can push native biota through an extinction filter, and result in the abrupt, landscape-wide loss of forest-specialist taxa, ecological resilience and management effectiveness. The proposed model links hitherto distinct theoretical approaches within a single framework

  8. Radiation-induced protein fragmentation and inactivation in liquid and solid aqueous solutions. Role of OH and electrons

    Energy Technology Data Exchange (ETDEWEB)

    Audette-Stuart, Marilyne [Atomic Energy of Canada Limited, CANDU Life Sciences Center, Chalk River Laboratories, Chalk River Ont., K0J 1J0 (Canada); Houee-Levin, Chantal [Laboratoire de Chimie Physique, UMR-8000 CNRS-Universite Paris XI, Centre Universitaire, F-91405 Orsay Cedex (France)]. E-mail: chantal.houee-levin@lcp.u-psud.fr; Potier, Michel [Service de genetique medicale, Hopital Sainte-Justine, Universite de Montreal, Montreal Que., H3 T 1C5 (Canada)

    2005-02-01

    Irradiation of proteins in diluted liquid aqueous solutions produces cleavages and polymerizations of the peptidic chains. In frozen solutions, fragmentation is observed but polymerization products are absent. Loss of activity occurs in both cases. In the solid state, yields of fragmentation do not vary with the quantity of water. The use of scavengers indicates that hydroxyl radical does not contribute significantly to fragmentation and to inactivation in the solid state. Electrons within the water molecules closely associated with the protein are involved in the processes leading to protein fragmentation.

  9. Diverse Effects of a Seven-Year Experimental Grassland Fragmentation on Major Invertebrate Groups.

    Directory of Open Access Journals (Sweden)

    Brigitte Braschler

    Full Text Available Habitat fragmentation is a major driver of biodiversity loss, but observed effects vary and may depend on the group examined. Time since fragmentation may explain some differences between taxonomical groups, as some species and thus species composition respond with a delay to changes in their environment. Impacts of drivers of global change may thus be underestimated in short-term studies. In our study we experimentally fragmented nutrient-poor dry calcareous grasslands and studied the response of species richness, individual density and species composition of various groups of invertebrates (gastropods, ants, ground beetles, rove beetles, orthoptera, spiders, woodlice in 12 small (1.5 m * 1.5 m and 12 large (4.5 m * 4.5 m fragments and their corresponding control plots after 7 years. We further examined responses to fragmentation in relation to body size and habitat preferences. Responses to fragmentation varied between taxonomical groups. While spider species richness and individual density were lower in fragments, the opposite was true for an orthopteran species and woodlice. Species composition and β-diversity differed between fragments and control plots for some groups. However, the interaction treatment*plot size was rarely significant. Species with high occupancy rates in undisturbed control plots responded more negatively to the fragmentation, while species with large body size were relatively more abundant in fragments in some groups. No effect of the fragmentation was found for ants, which may have the longest lag times because of long-lived colonies. However, relationships between abundance and the species' preferences for environmental factors affected by edge effects indicate that ant diversity too may be affected in the longer-term. Our results show the importance of considering different groups in conservation management in times of widespread fragmentation of landscapes. While species richness may respond slowly, changes in

  10. Diverse Effects of a Seven-Year Experimental Grassland Fragmentation on Major Invertebrate Groups.

    Science.gov (United States)

    Braschler, Brigitte; Baur, Bruno

    2016-01-01

    Habitat fragmentation is a major driver of biodiversity loss, but observed effects vary and may depend on the group examined. Time since fragmentation may explain some differences between taxonomical groups, as some species and thus species composition respond with a delay to changes in their environment. Impacts of drivers of global change may thus be underestimated in short-term studies. In our study we experimentally fragmented nutrient-poor dry calcareous grasslands and studied the response of species richness, individual density and species composition of various groups of invertebrates (gastropods, ants, ground beetles, rove beetles, orthoptera, spiders, woodlice) in 12 small (1.5 m * 1.5 m) and 12 large (4.5 m * 4.5 m) fragments and their corresponding control plots after 7 years. We further examined responses to fragmentation in relation to body size and habitat preferences. Responses to fragmentation varied between taxonomical groups. While spider species richness and individual density were lower in fragments, the opposite was true for an orthopteran species and woodlice. Species composition and β-diversity differed between fragments and control plots for some groups. However, the interaction treatment*plot size was rarely significant. Species with high occupancy rates in undisturbed control plots responded more negatively to the fragmentation, while species with large body size were relatively more abundant in fragments in some groups. No effect of the fragmentation was found for ants, which may have the longest lag times because of long-lived colonies. However, relationships between abundance and the species' preferences for environmental factors affected by edge effects indicate that ant diversity too may be affected in the longer-term. Our results show the importance of considering different groups in conservation management in times of widespread fragmentation of landscapes. While species richness may respond slowly, changes in abundance related to

  11. Diverse Effects of a Seven-Year Experimental Grassland Fragmentation on Major Invertebrate Groups

    Science.gov (United States)

    Braschler, Brigitte; Baur, Bruno

    2016-01-01

    Habitat fragmentation is a major driver of biodiversity loss, but observed effects vary and may depend on the group examined. Time since fragmentation may explain some differences between taxonomical groups, as some species and thus species composition respond with a delay to changes in their environment. Impacts of drivers of global change may thus be underestimated in short-term studies. In our study we experimentally fragmented nutrient-poor dry calcareous grasslands and studied the response of species richness, individual density and species composition of various groups of invertebrates (gastropods, ants, ground beetles, rove beetles, orthoptera, spiders, woodlice) in 12 small (1.5 m * 1.5 m) and 12 large (4.5 m * 4.5 m) fragments and their corresponding control plots after 7 years. We further examined responses to fragmentation in relation to body size and habitat preferences. Responses to fragmentation varied between taxonomical groups. While spider species richness and individual density were lower in fragments, the opposite was true for an orthopteran species and woodlice. Species composition and β-diversity differed between fragments and control plots for some groups. However, the interaction treatment*plot size was rarely significant. Species with high occupancy rates in undisturbed control plots responded more negatively to the fragmentation, while species with large body size were relatively more abundant in fragments in some groups. No effect of the fragmentation was found for ants, which may have the longest lag times because of long-lived colonies. However, relationships between abundance and the species’ preferences for environmental factors affected by edge effects indicate that ant diversity too may be affected in the longer-term. Our results show the importance of considering different groups in conservation management in times of widespread fragmentation of landscapes. While species richness may respond slowly, changes in abundance related

  12. Fragment separator momentum compression schemes

    Energy Technology Data Exchange (ETDEWEB)

    Bandura, Laura, E-mail: bandura@anl.gov [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); National Superconducting Cyclotron Lab, Michigan State University, 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Erdelyi, Bela [Argonne National Laboratory, Argonne, IL 60439 (United States); Northern Illinois University, DeKalb, IL 60115 (United States); Hausmann, Marc [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Kubo, Toshiyuki [RIKEN Nishina Center, RIKEN, Wako (Japan); Nolen, Jerry [Argonne National Laboratory, Argonne, IL 60439 (United States); Portillo, Mauricio [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Sherrill, Bradley M. [National Superconducting Cyclotron Lab, Michigan State University, 1 Cyclotron, East Lansing, MI 48824-1321 (United States)

    2011-07-21

    We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.

  13. Fragment separator momentum compression schemes.

    Energy Technology Data Exchange (ETDEWEB)

    Bandura, L.; Erdelyi, B.; Hausmann, M.; Kubo, T.; Nolen, J.; Portillo, M.; Sherrill, B.M. (Physics); (MSU); (Northern Illinois Univ.); (RIKEN)

    2011-07-21

    We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.

  14. Fragment separator momentum compression schemes

    Science.gov (United States)

    Bandura, Laura; Erdelyi, Bela; Hausmann, Marc; Kubo, Toshiyuki; Nolen, Jerry; Portillo, Mauricio; Sherrill, Bradley M.

    2011-07-01

    We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.

  15. Fragmentering og korridorer i landskabet

    DEFF Research Database (Denmark)

    Hammershøj, M.; Madsen, A. B.

    , at fragmentering af habitater resulterer i en reduktion og isolering af mange plante- og dyrepopulationer. Det er desuden vist, at korridorer har en funktion som habitater, hvilket er medvirkende til, at et område med korridorer kan huse flere arter og individer end et tilsvarende område uden korridorer. Der......Rapporten indeholder en litteraturudredning, der er baseret på en bearbejdning af den tilgængelige nationale og internationale litteratur omhandlende fragmentering og korridorer på det botaniske og zoologiske område. I alt 1.063 titler ligger til grund for udredningen. Udredningen har vist...... mangler dog entydige beviser for, at korridorer kan være af afgørende betydning for rekolonisering af habitater, i hvilke en given art er forsvundet. Afslutningsvis gives en liste med forskningsbehov samt en række anbefalinger....

  16. Fragmentation in the biopharmaceutical industry.

    Science.gov (United States)

    Goldsmith, Andrew D; Varela, Francisco E

    2017-02-01

    The large number of biopharmaceutical mergers and acquisitions (M&A) that occurred over the past decade has generated questions about whether the industry is consolidating around too-few players, negatively impacting both the number of medicines developed and overall innovation. However, closer examination of the level of biopharmaceutical consolidation by prescription sales shows that the industry was more fragmented in 2015 than in 2003. The trend towards increasing fragmentation is also observed across noncommercial and independent metrics over the same time period. The number and size of M&A deals has masked an active and competitive marketplace in which market growth and the number of companies entering the market exceeded the apparent reduction in the number of players caused by acquisitions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Carcinogenesis of Depleted Uranium Fragments.

    Science.gov (United States)

    1996-02-01

    29 of 54 Chinese hamsters injected intravenously with a relatively high dose of Thorotrast (> 0.4 Bq/g) developed fibrosarcomas from perivascular...leakage of some injections (Guilmette et al., 1989). Plutonium fragments have been injected into the footpads of dogs to simulate the plutonium...extensively studied in animals, particularly in rats (Haley, 1982; Haley et al., 1982; Diamond et al., 1987; Morrow et al., 1982) and dogs (Morrow et al

  18. Modeling of Fragmentation of Asteroids

    Science.gov (United States)

    Agrawal, Parul; Prabhu, Dinesh K.; Carlozzi, Alexander; Hart, Kenneth; Bryson, Katie; Sears, Derek

    2015-01-01

    The objective of this study is to understand fragmentation and fracture of a given asteroid and mechanisms of break-up. The focus of the present work is to develop modeling techniques for stony asteroids in 10m-100m range to answer two questions: 1) What is the role of material makeup of an asteroid in the stress distribution? 2)How is stress distribution altered in the presence of pre-existing defects?

  19. Structure, fragmentation and fracture functions

    CERN Document Server

    Canal-Garcia, C A

    2000-01-01

    We address the partonic description of the proton, the photon and the "color singlet, " as seen in inclusive and semi-inclusive DIS, in e /sup +/e/sup $/collisions, and in diffractive processes, respectively. Their formal treatment using structure, fragmentation, and fracture functions is outlined giving an insight into the perturbative QCD framework for these functions. Examples and comparisons with experimental data from LEP, HERA, and Tevatron are also covered. (52 refs).

  20. Fibril fragmentation enhances amyloid cytotoxicity.

    Science.gov (United States)

    Xue, Wei-Feng; Hellewell, Andrew L; Gosal, Walraj S; Homans, Steve W; Hewitt, Eric W; Radford, Sheena E

    2009-12-04

    Fibrils associated with amyloid disease are molecular assemblies of key biological importance, yet how cells respond to the presence of amyloid remains unclear. Cellular responses may not only depend on the chemical composition or molecular properties of the amyloid fibrils, but their physical attributes such as length, width, or surface area may also play important roles. Here, we report a systematic investigation of the effect of fragmentation on the structural and biological properties of amyloid fibrils. In addition to the expected relationship between fragmentation and the ability to seed, we show a striking finding that fibril length correlates with the ability to disrupt membranes and to reduce cell viability. Thus, despite otherwise unchanged molecular architecture, shorter fibrillar samples show enhanced cytotoxic potential than their longer counterparts. The results highlight the importance of fibril length in amyloid disease, with fragmentation not only providing a mechanism by which fibril load can be rapidly increased but also creating fibrillar species of different dimensions that can endow new or enhanced biological properties such as amyloid cytotoxicity.

  1. Residual Fragments after Percutaneous Nephrolithotomy

    Directory of Open Access Journals (Sweden)

    Kaan Özdedeli

    2012-09-01

    Full Text Available Clinically insignificant residual fragments (CIRFs are described as asymptomatic, noninfectious and nonobstructive stone fragments (≤4 mm remaining in the urinary system after the last session of any intervention (ESWL, URS or PCNL for urinary stones. Their insignificance is questionable since CIRFs could eventually become significant, as their presence may result in recurrent stone growth and they may cause pain and infection due to urinary obstruction. They may become the source of persistent infections and a significant portion of the patients will have a stone-related event, requiring auxilliary interventions. CT seems to be the ultimate choice of assessment. Although there is no concensus about the timing, recent data suggests that it may be performed one month after the procedure. However, imaging can be done in the immediate postoperative period, if there are no tubes blurring the assessment. There is some evidence indicating that selective medical therapy may have an impact on decreasing stone formation rates. Retrograde intrarenal surgery, with its minimally invasive nature, seems to be the best way to deal with residual fragments.

  2. Species specific polymerase chain reaction (PCR) assay for ...

    African Journals Online (AJOL)

    A highly specific single step polymerase chain reaction (PCR) is described for the detection of pig (Sus domesticus) meat. A PCR assay was successfully optimized for amplification of 629 and 322-bp DNA fragment extracted from pig meat using designed species-specific primer pairs based on mitochondrial D-loop and 12S ...

  3. Expression, production and renaturation of a functional single-chain ...

    African Journals Online (AJOL)

    The single-chain variable antibody fragment (scFv) against human intercellular adhesion molecule-1 (ICAM-1) was expressed at a high level in Escherichia coli as inclusion bodies. We attempted to refold the scFv by ion-exchange chromatography (IEC), dialysis and dilution. The results show that the column ...

  4. OECD Skills Outlook 2017: Skills and Global Value Chains

    Science.gov (United States)

    OECD Publishing, 2017

    2017-01-01

    Since the 1990s, the world has entered a new phase of globalisation. Information and communication technology, trade liberalisation and lower transport costs have enabled firms and countries to fragment the production process into global value chains (GVCs). Many products are now designed in one country and assembled in another country from parts…

  5. Conservation of plant genetic resources | Olorode | African Journal ...

    African Journals Online (AJOL)

    Survey, collection and conservation are important starting points in the genetic resources impact chain and in sustainable environmental protection strategies. Collection of plant genetic resources provides materials for herbaria, field gene banks, seed banks and in vitro conservation which are all important and crucial for ...

  6. A Method for Predicting Fragmentation Characteristics of Natural and Performed Explosive Fragmentation Munitions

    National Research Council Canada - National Science Library

    Gold, Vladimir

    2001-01-01

    New methodology for simulating performance of explosive fragmentation munitions presented in this work integrates three-dimensional axisymmetric hydrocode analyses with analytical fragmentation modeling...

  7. 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.

  8. Fragmentation of small carbon clusters, a review

    Energy Technology Data Exchange (ETDEWEB)

    Beroff, K. [Laboratoire des Collisions Atomiques et Moleculaires, CNRS and Universite Paris-Sud, batiment 351, 91405 Orsay Cedex (France)], E-mail: karine.beroff@u-psud.fr; Chabot, M. [Institut de Physique Nucleaire, CNRS-IN2P3 and Universite Paris-Sud, 91405 Orsay Cedex (France); Mezdari, F. [Laboratoire des Collisions Atomiques et Moleculaires, CNRS and Universite Paris-Sud, batiment 351, 91405 Orsay Cedex (France); Martinet, G.; Tuna, T. [Institut de Physique Nucleaire, CNRS-IN2P3 and Universite Paris-Sud, 91405 Orsay Cedex (France); Desesquelles, P. [Centre de Spectrometrie Nucleaire et Spectrometrie de Masse, Universite Paris-Sud and CNRS-IN2P3, batiment 104, 91405 Orsay Cedex (France); LePadellec, A. [Institut de Recherche sur les Systemes Atomiques et Moleculaires Complexes, Universite Paul Sabatier and CNRS, batiment 3R1B4, 31062 Toulouse Cedex 9 (France); Barat, M. [Laboratoire des Collisions Atomiques et Moleculaires, CNRS and Universite Paris-Sud, batiment 351, 91405 Orsay Cedex (France)

    2009-03-15

    An overview of the works devoted to fragmentation of small carbon clusters is given in a first part. Fragmentation of swift neutral and (multi) charged carbon clusters studied with the AGAT spectrometer is presented and discussed in a second part.

  9. Fragmentation of small carbon clusters, a review

    OpenAIRE

    Béroff, K.; Chabot, M.; Mezdari, F.; Martinet, G.; Tuna, T.; Désesquelles, P.; Le Padellec, Arnaud; Barat, M.

    2008-01-01

    An overview of the works devoted to fragmentation of small carbon clusters is given in a first part. Fragmentation of swift neutral and (multi) charged carbon clusters studied with the AGAT spectrometer is presented and discussed in a second part.

  10. Identification of amplified fragment length polymorphism (AFLP ...

    African Journals Online (AJOL)

    Identification of amplified fragment length polymorphism (AFLP) fragments linked to soybean mosaic virus resistance gene in Glycine soja and conversion to a sequence characterized amplified regions (SCAR) marker for rapid selection.

  11. Fragment Kinetic Energies and Modes of Fragment Formation

    Science.gov (United States)

    Odeh, T.; Bassini, R.; Begemann-Blaich, M.; Fritz, S.; Gaff-Ejakov, S. J.; Gourio, D.; Groß, C.; Immé, G.; Iori, I.; Kleinevoß, U.; Kunde, G. J.; Kunze, W. D.; Lynen, U.; Maddalena, V.; Mahi, M.; Möhlenkamp, T.; Moroni, A.; Müller, W. F.; Nociforo, C.; Ocker, B.; Petruzzelli, F.; Pochodzalla, J.; Raciti, G.; Riccobene, G.; Romano, F. P.; Saija, A.; Schnittker, M.; Schüttauf, A.; Schwarz, C.; Seidel, W.; Serfling, V.; Sfienti, C.; Trautmann, W.; Trzcinski, A.; Verde, G.; Wörner, A.; Xi, Hongfei; Zwieglinski, B.

    2000-05-01

    Kinetic energies of light fragments ( A<=10) from the decay of target spectators in 197Au+197Au collisions at 1000 MeV per nucleon have been measured with high-resolution telescopes at backward angles. Except for protons and apart from the observed evaporation components, the kinetic-energy spectra exhibit slope temperatures of about 17 MeV, independent of the particle species, but not corresponding to the thermal or chemical degrees of freedom at breakup. It is suggested that these slope temperatures may reflect the intrinsic Fermi motion and thus the bulk density of the spectator system at the instant of becoming unstable.

  12. A recombinant, fully human monoclonal antibody with antitumor activity constructed from phage-displayed antibody fragments

    NARCIS (Netherlands)

    Huls, GA; Heijnen, IAFM; Cuomo, ME; Koningsberger, JC; Boel, E; de Vries, ARV; Loyson, SAJ; Helfrich, W; Henegouwen, GPV; van Meijer, M; de Kruif, J; Logtenberg, T

    A single-chain Fv antibody fragment specific for the tumor-associated Ep-CAM molecule was isolated from a semisynthetic phage display library and converted into an intact, fully human IgG1 monoclonal antibody (huMab), The purified huMab had an affinity of 5 nM and effectively mediated tumor cell

  13. cDNA sequencing of fragments from fibrinolytic gene (F-4) from ...

    African Journals Online (AJOL)

    A fibrinolytic anticoagulant (F-4) was previously isolated by Daoud et al; (1986) from Cerastes cerastes venom. In this study, isolation and sequencing of gene fragments of this F-4 protein was attempted. Primers utilized in the polymerase chain reactions were obtained from two sources: P1, a primer that was previously used ...

  14. Properties, production and applications of camelid single-domain antibody fragments

    NARCIS (Netherlands)

    Harmsen, M.M.; Haard, de H.J.

    2007-01-01

    Camelids produce functional antibodies devoid of light chains of which the single N-terminal domain is fully capable of antigen binding. These single-domain antibody fragments (VHHs or Nanobodies®) have several advantages for biotechnological applications. They are well expressed in microorganisms

  15. Supply Chain Management og Supply Chain costing

    DEFF Research Database (Denmark)

    Nielsen, Steen; Mortensen, Ole

    2002-01-01

    Formålet med denne artikel er at belyse de muligheder som ligger i at integrere virksomhedens økonomiske styring med begrebet Supply Chain Management (SCM). Dette søges belyst ved først at beskrive den teoretiske ramme, hvori SCM indgår. Herefter analyseres begrebet Supply Chain Costing (SCC) som...... Århus. Et resultat er, at via begrebet Supply Chain Costing skabes der mulighed for at måle logistikkædens aktiviteter i kr./øre. Anvendelsen af denne information har også strategisk betydning for at kunne vælge kunde og leverandør. Ved hjælp af integrationen skabes der også helt nye mulighed...

  16. Energy conservation options for cooking with biomass in Ghana

    DEFF Research Database (Denmark)

    Nielsen, Per Sieverts; Næraa, Rikke; Karlsson, Kenneth

    1996-01-01

    . An energy chain for the cooking process is established and the possible conservation options are surveyed in kitchen performance tests in Abodom in the tropical zone of Ghana. The energy consumption for the food preparation has been measured and energy saving options have been determined for some parts...... of the energy chain. The results show that the possible options for energy conservation through the entire energy chain of the present technology are at least of the same magnitude as that involved in just switching to a more efficient biomass stove. The heat loss is largest while simmering when the boiling...

  17. Self-organized criticality in fragmenting

    DEFF Research Database (Denmark)

    Oddershede, L.; Dimon, P.; Bohr, J.

    1993-01-01

    The measured mass distributions of fragments from 26 fractured objects of gypsum, soap, stearic paraffin, and potato show evidence of obeying scaling laws; this suggests the possibility of self-organized criticality in fragmenting. The probability of finding a fragment scales inversely to a power...

  18. Scaling and four-quark fragmentation

    NARCIS (Netherlands)

    Scholten, O.; Bosveld, G. D.

    1991-01-01

    The conditions for a scaling behaviour from the fragmentation process leading to slow protons are discussed. The scaling referred to implies that the fragmentation functions depend on the light-cone momentum fraction only. It is shown that differences in the fragmentation functions for valence- and

  19. Population pressure and farm fragmentation: Challenges facing ...

    African Journals Online (AJOL)

    In addition, the size of farms is not only very small but farms are further fragmented into diminutive size fields due to increasing population pressure. The magnitude of fragmentation has increased overtime. Effects of population pressure and farm fragmentation are studied based on a survey of 200 households from Rusatira ...

  20. Editorial: Supply Chain Management

    Directory of Open Access Journals (Sweden)

    Dimitrios Aidonis

    2017-05-01

    Full Text Available This special issue has followed up the 3rd Olympus International Conference on Supply Chains held on Athens Metropolitan Expo, November 7 & 8 2015, Greece. The Conference was organized by the Department of Logistics Technological Educational Institute of Central Macedonia, in collaboration with the: a Laboratory of Quantitative Analysis, Logistics and Supply Chain Management of the Department of Mechanical Engineering, Aristotle University of Thessaloniki (AUTH, b Greek Association of Supply Chain Management (EEL of Northern Greece and the c Supply Chain & Logistics Journal. During the 2-Days Conference more than 60 research papers were presented covering the following thematic areas: (i Transportation, (ii Best Practices in Logistics, (iii Information and Communication Technologies in Supply Chain Management, (iv Food Logistics, (v New Trends in Business Logistics, and (vi Green Supply Chain Management. Three keynote invited speakers addressed interesting issues for the Operational Research, the Opportunities and Prospects of Greek Ports chaired Round Tables with other Greek and Foreign Scientists and Specialists.

  1. Understanding the Chain Fountain

    CERN Document Server

    Biggins, John Simeon

    2013-01-01

    If a chain is initially at rest in a beaker at a height h1 above the ground, and the end of the chain is pulled over the rim of the beaker and down towards the ground and then released, the chain will spontaneously "flow" out of the beaker under gravity. Furthermore, if h1 is sufficient, the beads do not simply drag over the edge of the beaker but form a fountain reaching a height h2 above it. We show that the formation of a fountain requires that the beads come into motion not only by being pulled upwards by the part of the chain immediately above the pile, but also by being pushed upwards by an anomalous reaction force from the pile of stationary chain. We propose possible origins for this force, argue that its magnitude will be proportional to the square of the chain velocity, and predict and verify experimentally that h2 is proportional to h1.

  2. Supply chain components

    Directory of Open Access Journals (Sweden)

    Vieraşu, T.

    2011-01-01

    Full Text Available In this article I will go through three main logistics components, which are represented by: transportation, inventory and facilities, and the three secondary logistical components: information, production location, price and how they determine performance of any supply chain. I will discuss then how these components are used in the design, planning and operation of a supply chain. I will also talk about some obstacles a supply chain manager may encounter.

  3. Application of a GIS-BIOLOCO tool for the design and assessment of biomass delivery chains

    NARCIS (Netherlands)

    Geijzendorffer, I.R.; Annevelink, E.; Elbersen, B.S.; Smidt, R.A.; Mol, de R.M.

    2008-01-01

    The spatial fragmentation of different biomass sources in one or more regions makes design and assessment of sustainable biomass delivery chains rather complicated. This paper presents a GIS tool that supports the design and facilitates a sustainability assessment of biomass delivery chains at a

  4. Human beta 2 chain of laminin (formerly S chain): cDNA cloning, chromosomal localization, and expression in carcinomas

    DEFF Research Database (Denmark)

    Wewer, U M; Gerecke, D R; Durkin, M E

    1994-01-01

    Overlapping cDNA clones that encode the full-length human laminin beta 2 chain, formerly called the S chain, were isolated. The cDNA of 5680 nt contains a 5391-nt open reading frame encoding 1797 amino acids. At the amino terminus is a 32-amino-acid signal peptide that is followed by the mature...... beta 2 chain polypeptide of 1765 amino acids with a calculated molecular mass of 192,389 Da. The human beta 2 chain is predicted to have all of the seven structural domains typical of the beta chains of laminin, including the short cysteine-rich alpha region. The amino acid sequence of human beta 2...... chain showed 86.1% sequence identity to the rat beta 2 chain, 50.0% to the human beta 1 chain, and 36.3% to the human beta 3 chain. The greatest sequence identity was in domains VI, V, and III. The sequence of a 24-amino-acid peptide fragment isolated from the beta 2 chain of laminin purified from human...

  5. Plasmon-Polariton Properties in Metallic Nanosphere Chains

    Directory of Open Access Journals (Sweden)

    Witold Aleksander Jacak

    2015-06-01

    Full Text Available The propagation of collective wave type plasmonic excitations along infinite chains of metallic nanospheres has been analyzed, including near-, medium- and far-field contributions to the plasmon dipole interaction with all retardation effects taken into account. It is proven that there exist weakly-damped self-modes of plasmon-polaritons in the chain for which the propagation range is limited by relatively small Ohmic losses only. In this regime, the Lorentz friction irradiation losses on each nanosphere in the chain are ideally compensated by the energy income from the rest of the chain. The completely undamped collective waves were identified in the case of the presence of persistent external excitation of some fragment of the chain. The obtained characteristics of these excitations fit the experimental observations well.

  6. Formation of amyloid fibers by monomeric light chain variable domains.

    Science.gov (United States)

    Brumshtein, Boris; Esswein, Shannon R; Landau, Meytal; Ryan, Christopher M; Whitelegge, Julian P; Phillips, Martin L; Cascio, Duilio; Sawaya, Michael R; Eisenberg, David S

    2014-10-03

    Systemic light chain amyloidosis is a lethal disease characterized by excess immunoglobulin light chains and light chain fragments composed of variable domains, which aggregate into amyloid fibers. These fibers accumulate and damage organs. Some light chains induce formation of amyloid fibers, whereas others do not, making it unclear what distinguishes amyloid formers from non-formers. One mechanism by which sequence variation may reduce propensity to form amyloid fibers is by shifting the equilibrium toward an amyloid-resistant quaternary structure. Here we identify the monomeric form of the Mcg immunoglobulin light chain variable domain as the quaternary unit required for amyloid fiber assembly. Dimers of Mcg variable domains remain stable and soluble, yet become prone to assemble into amyloid fibers upon disassociation into monomers. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Augmented generation of protein fragments during wakefulness as the molecular cause of sleep: a hypothesis

    Science.gov (United States)

    Varshavsky, Alexander

    2012-01-01

    Despite extensive understanding of sleep regulation, the molecular-level cause and function of sleep are unknown. I suggest that they originate in individual neurons and stem from increased production of protein fragments during wakefulness. These fragments are transient parts of protein complexes in which the fragments were generated. Neuronal Ca2+ fluxes are higher during wakefulness than during sleep. Subunits of transmembrane channels and other proteins are cleaved by Ca2+-activated calpains and by other nonprocessive proteases, including caspases and secretases. In the proposed concept, termed the fragment generation (FG) hypothesis, sleep is a state during which the production of fragments is decreased (owing to lower Ca2+ transients) while fragment-destroying pathways are upregulated. These changes facilitate the elimination of fragments and the remodeling of protein complexes in which the fragments resided. The FG hypothesis posits that a proteolytic cleavage, which produces two fragments, can have both deleterious effects and fitness-increasing functions. This (previously not considered) dichotomy can explain both the conservation of cleavage sites in proteins and the evolutionary persistence of sleep, because sleep would counteract deleterious aspects of protein fragments. The FG hypothesis leads to new explanations of sleep phenomena, including a longer sleep after sleep deprivation. Studies in the 1970s showed that ethanol-induced sleep in mice can be strikingly prolonged by intracerebroventricular injections of either Ca2+ alone or Ca2+ and its ionophore (Erickson et al., Science 1978;199:1219–1221; Harris, Pharmacol Biochem Behav 1979;10:527–534; Erickson et al., Pharmacol Biochem Behav 1980;12:651–656). These results, which were never interpreted in connection to protein fragments or the function of sleep, may be accounted for by the FG hypothesis about molecular causation of sleep. PMID:22930402

  8. Strategic rat control for restoring populations of native species in forest fragments.

    Science.gov (United States)

    Armstrong, Doug P; Gorman, Nic; Pike, Rhonda; Kreigenhofer, Brigitte; McArthur, Nikki; Govella, Susanne; Barrett, Paul; Richard, Yvan

    2014-06-01

    hierarchical modeling for fragmentation studies. © 2014 Society for Conservation Biology.

  9. Resilient networks of ant-plant mutualists in Amazonian forest fragments.

    Directory of Open Access Journals (Sweden)

    Heather A Passmore

    Full Text Available The organization of networks of interacting species, such as plants and animals engaged in mutualisms, strongly influences the ecology and evolution of partner communities. Habitat fragmentation is a globally pervasive form of spatial heterogeneity that could profoundly impact the structure of mutualist networks. This is particularly true for biodiversity-rich tropical ecosystems, where the majority of plant species depend on mutualisms with animals and it is thought that changes in the structure of mutualist networks could lead to cascades of extinctions.We evaluated effects of fragmentation on mutualistic networks by calculating metrics of network structure for ant-plant networks in continuous Amazonian forests with those in forest fragments. We hypothesized that networks in fragments would have fewer species and higher connectance, but equal nestedness and resilience compared to forest networks. Only one of the nine metrics we compared differed between continuous forest and forest fragments, indicating that networks were resistant to the biotic and abiotic changes that accompany fragmentation. This is partially the result of the loss of only specialist species with one connection that were lost in forest fragments.We found that the networks of ant-plant mutualists in twenty-five year old fragments are similar to those in continuous forest, suggesting these interactions are resistant to the detrimental changes associated with habitat fragmentation, at least in landscapes that are a mosaic of fragments, regenerating forests, and pastures. However, ant-plant mutualistic networks may have several properties that may promote their persistence in fragmented landscapes. Proactive identification of key mutualist partners may be necessary to focus conservation efforts on the interactions that insure the integrity of network structure and the ecosystems services networks provide.

  10. Fragmentation in massive star formation.

    Science.gov (United States)

    Beuther, Henrik; Schilke, Peter

    2004-02-20

    Studies of evolved massive stars indicate that they form in a clustered mode. During the earliest evolutionary stages, these regions are embedded within their natal cores. Here we present high-spatial-resolution interferometric dust continuum observations disentangling the cluster-like structure of a young massive star-forming region. The derived protocluster mass distribution is consistent with the stellar initial mass function. Thus, fragmentation of the initial massive cores may determine the initial mass function and the masses of the final stars. This implies that stars of all masses can form via accretion processes, and coalescence of intermediate-mass protostars appears not to be necessary.

  11. DRAG COEFFICIENTS FOR IRREGULAR FRAGMENTS

    Science.gov (United States)

    1986-08-01

    regular fragments.were studied In the report, I.e., a sphere, a c-ibe and a bar. Th.a bar length, 1530) 77= pp. P width and thickness were. in the ratio...measurements for the 96 fragmento are contained in Tables A-1, A-2 and A-3 of Appendix A. The esiential aspects of the vertical wind tunnel are shown...THICKNESS L’ MAXIMUM LENGTH P ..UPS AVERAGE LENGTH W’ M AXIMUM WIDTH PLUS AVERAGE WIDTH T’ M I’XIX1MUM THICKNESS PLUS AVERAIE THICKNESS i -- STANDARO DEVIATION

  12. 7 CFR 12.23 - Conservation plans and conservation systems.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 1 2010-01-01 2010-01-01 false Conservation plans and conservation systems. 12.23... CONSERVATION Highly Erodible Land Conservation § 12.23 Conservation plans and conservation systems. (a) Use of field office technical guide. A conservation plan or conservation system developed for the purposes of...

  13. Alternative techniques to remove fractured instrument fragments from the apical third of root canals: report of two cases.

    Science.gov (United States)

    Brito-Júnior, Manoel; Normanha, João Américo; Camilo, Carla Cristina; Faria-e-Silva, André Luis; Saquy, Paulo César; Ferraz, Maria Ãngela Arêa Leão; Silva-Sousa, Yara Teresinha Correa

    2015-01-01

    This paper describes two cases of instrument fragment removal from the apical thirds of root canals using a customized extractor and a modified needle technique, respectively. In case 1, a customized extractor was manufactured to remove a bur fragment located in the apical root canal of a maxillary central incisor. The use of this extractor enabled successful and conservative removal of the instrument fragment. In case 2, a modified injection needle was used as a trepan to gain access around an instrument fragment located in the curved apical portion of the mesiobuccal canal of a mandibular molar. A segment of steel wire was inserted into the needle lumen to engage the metallic fragment, enabling its removal with counter-clockwise rotation and a simultaneous pull-out motion. Alternative and creative methods are useful for the management of intracanal metallic fragments during root canal treatment.

  14. Dihadron fragmentation functions for large invariant mass.

    Science.gov (United States)

    Zhou, J; Metz, A

    2011-04-29

    Using perturbative quantum chromodynamics, we compute dihadron fragmentation functions for a large invariant mass of the dihadron pair. The main focus is on the interference fragmentation function H(1)(∢), which plays an important role in spin physics of the nucleon. Our calculation also reveals that H(1)(∢) and the Collins fragmentation function have closely related underlying dynamics. By considering semi-inclusive deep-inelastic scattering, we further show that collinear factorization in terms of dihadron fragmentation functions and collinear factorization in terms of single-hadron fragmentation functions provide the same result in the region of intermediate invariant mass.

  15. Characterization of Lipid A Variants by Energy-Resolved Mass Spectrometry: Impact of Acyl Chains

    Science.gov (United States)

    Crittenden, Christopher M.; Akin, Lucas D.; Morrison, Lindsay J.; Trent, M. Stephen; Brodbelt, Jennifer S.

    2017-06-01

    Lipid A molecules consist of a diglucosamine sugar core with a number of appended acyl chains that vary in their length and connectivity. Because of the challenging nature of characterizing these molecules and differentiating between isomeric species, an energy-resolved MS/MS strategy was undertaken to track the fragmentation trends and map genealogies of product ions originating from consecutive cleavages of acyl chains. Generalizations were developed based on the number and locations of the primary and secondary acyl chains as well as variations in preferential cleavages arising from the location of the phosphate groups. Secondary acyl chain cleavage occurs most readily for lipid A species at the 3' position, followed by primary acyl chain fragmentation at both the 3' and 3 positions. In the instances of bisphosphorylated lipid A variants, phosphate loss occurs readily in conjunction with the most favorable primary and secondary acyl chain cleavages. [Figure not available: see fulltext.

  16. Goodness of isospin in neutron rich systems from the fission fragment distribution

    Science.gov (United States)

    Garg, Swati; Jain, Ashok Kumar

    2017-09-01

    We present the results of our calculations for the relative yields of neutron-rich fission fragments emitted in 208Pb (18O, fission) reaction by using the concept of the conservation of isospin and compare with the experimental data. We take into account a range of isospin values allowed by the isospin algebra and assume that the fission fragments are formed in isobaric analog states. We also take into account the neutron multiplicity data for various neutron-emission channels in each partition, and use them to obtain the weight factors in calculating the yields. We then calculate the relative yields of the fission fragments. Our calculated results are able to reproduce the experimental trends reasonably well. This is the first direct evidence of the isospin conservation in neutron-rich systems and may prove a very useful tool in their studies.

  17. Reframing landscape fragmentation's effects on ecosystem services.

    Science.gov (United States)

    Mitchell, Matthew G E; Suarez-Castro, Andrés F; Martinez-Harms, Maria; Maron, Martine; McAlpine, Clive; Gaston, Kevin J; Johansen, Kasper; Rhodes, Jonathan R

    2015-04-01

    Landscape structure and fragmentation have important effects on ecosystem services, with a common assumption being that fragmentation reduces service provision. This is based on fragmentation's expected effects on ecosystem service supply, but ignores how fragmentation influences the flow of services to people. Here we develop a new conceptual framework that explicitly considers the links between landscape fragmentation, the supply of services, and the flow of services to people. We argue that fragmentation's effects on ecosystem service flow can be positive or negative, and use our framework to construct testable hypotheses about the effects of fragmentation on final ecosystem service provision. Empirical efforts to apply and test this framework are critical to improving landscape management for multiple ecosystem services. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. The formation of planets by disc fragmentation

    Directory of Open Access Journals (Sweden)

    Stamatellos Dimitris

    2013-04-01

    Full Text Available I discuss the role that disc fragmentation plays in the formation of gas giant and terrestrial planets, and how this relates to the formation of brown dwarfs and low-mass stars, and ultimately to the process of star formation. Protostellar discs may fragment, if they are massive enough and can cool fast enough, but most of the objects that form by fragmentation are brown dwarfs. It may be possible that planets also form, if the mass growth of a proto-fragment is stopped (e.g. if this fragment is ejected from the disc, or suppressed and even reversed (e.g by tidal stripping. I will discuss if it is possible to distinguish whether a planet has formed by disc fragmentation or core accretion, and mention of a few examples of observed exoplanets that are suggestive of formation by disc fragmentation.

  19. Conservation biogeography: The modern scientific contribution of biogeography to the improvement of nature conservation

    Directory of Open Access Journals (Sweden)

    Đurđić Snežana

    2009-01-01

    Full Text Available In present times, there is a clear and growing need for applying theoretical biogeographic achievements in improving the state of biodiversity and conservation. Conceptual principles of conservation biogeography take the research into the relationship between fundamental biogeographic principles and the need for their appliance in nature conservation as the basic theory model, based upon biogeographic studies of isolated ranges. This paper is meant to point out the differences between spatial and functional isolation and the effects these have on the stability of populations and species. In light of this need to apply theories in biodiversity and nature conservation, it is important to research not only the processes that depend solely upon natural factors, but also those that are caused by a number of human-induced changes, e.g. habitat fragmentation, climate change or biotic homogenization.

  20. Sleep fragmentation in canine narcolepsy.

    Science.gov (United States)

    Kaitin, K I; Kilduff, T S; Dement, W C

    1986-01-01

    Genetically narcoleptic dogs were recorded continuously for 24 h to examine their sleep-wake patterns and to evaluate the extent of sleep fragmentation. Three narcoleptic and three control dogs from each of two affected breeds (Labrador retrievers and Doberman pinschers) were surgically implanted with electrodes for recording standard sleep parameters. Recordings were scored in 30-s epochs for the states of active waking, drowsiness, light sleep, deep slow wave sleep, REM sleep, and cataplexy. All affected dogs displayed marked fragmentation and disruption of the sleep-wake cycle characterized by repeated awakenings, frequent shifts in sleep stages, numerous attacks of cataplexy occurring from active waking, and a disturbance of the normal REM-NREM periodicity. This sleep disruption was reflected in significantly greater numbers of episodes of each behavioral state as well as in a 38% increase in the total number of all states. These results demonstrate a severe disturbance of the normal sleep pattern in canine narcoleptics. The possibility of a general dysfunction of circadian organization is discussed.

  1. Spatial scale and movement behaviour traits control the impacts of habitat fragmentation on individual fitness.

    Science.gov (United States)

    Cattarino, Lorenzo; McAlpine, Clive A; Rhodes, Jonathan R

    2016-01-01

    searching mortality rates. Habitat selection strongly mitigated the impact of the scale at which fragmentation occurred on individual fitness. Our findings suggest that the land use to target with conservation actions to reduce fragmentation, such as financial schemes that promote re-vegetation or retention of standing vegetation, depends on the scale at which fragmentation occurs and the movement behaviour traits of the species of conservation concern. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

  2. DNA fragmentation in chicken spermatozoa during cryopreservation.

    Science.gov (United States)

    Gliozzi, T M; Zaniboni, L; Cerolini, S

    2011-06-01

    Semen cryopreservation is fundamental both for the practice of artificial insemination, and for the conservation of genetic resources in cryobanks; nevertheless, there is still not an efficient standard freezing procedure assuring a steady and suitable level of fertility in fowl, and consequently there is no systematic use of frozen semen in the poultry industry. This study examined changes in motility (CASA), cell membrane integrity (Ethidium Bromide (EtBr) exclusion procedure and stress test) and DNA fragmentation (neutral comet assay) in fowl spermatozoa before, during and after cryopreservation and storage at -196 °C. An optimized comet assay for chicken semen was studied and applied to the analyses. Semen collected from 18 Mericanel della Brianza (local Italian breed) male chicken breeders was frozen in pellets and thawed in a water bath at 60 °C. Measurements were performed on fresh semen soon after dilution, after equilibration with 6% dimethylacetamide at 4 °C (processed semen) and after thawing. Sperm DNA damage occurred during cryopreservation of chicken semen and the proportion of spermatozoa with damaged DNA significantly increased from 6.2% in fresh and 6.4% in processed semen to 19.8% in frozen-thawed semen. The proportion of DNA in the comet tail of damaged spermatozoa was also significantly affected by cryopreservation, with an increase found from fresh (26.3%) to frozen-thawed (30.9%) sperm, whereas processed semen (30.1%) didn't show significant differences. The proportion of total membrane damaged spermatozoa (EtBr exclusion procedure) did not increase by 4 °C equilibration time, and greatly and significantly increased by cryopreservation; the values recorded in fresh, processed and frozen semen were 2.9, 5.6, and 66.7% respectively. As regards the proportion of damaged cells in the stress test, all values differed significantly (7.1% fresh semen, 11.7% processed semen, 63.7% frozen semen). Total motility was not affected by equilibration (52

  3. Conserving and Restoring the Hereford Screen

    Directory of Open Access Journals (Sweden)

    Diana Heath

    2017-04-01

    Full Text Available In this film, the Victoria and Albert Museum's Head of Metalwork Conservation, Diana Heath, describes her involvement in the intricate conservation and restoration of the Hereford Screen over a number of years. From her first encounter with the screen in 1983, as its fragments arrived in the conservation studio packed in cases stuffed with straw, to the return of the screen to its former glory when it was installed as a whole object in the Metalwork Galleries above the main entrance to the Victoria and Albert Museum, Diana Heath guides us step-by-step through the restoration process of one of the most significant pieces of nineteenth-century metalwork.

  4. Process and data fragmentation-oriented enterprise network integration with collaboration modelling and collaboration agents

    Science.gov (United States)

    Li, Qing; Wang, Ze-yuan; Cao, Zhi-chao; Du, Rui-yang; Luo, Hao

    2015-08-01

    With the process of globalisation and the development of management models and information technology, enterprise cooperation and collaboration has developed from intra-enterprise integration, outsourcing and inter-enterprise integration, and supply chain management, to virtual enterprises and enterprise networks. Some midfielder enterprises begin to serve for different supply chains. Therefore, they combine related supply chains into a complex enterprise network. The main challenges for enterprise network's integration and collaboration are business process and data fragmentation beyond organisational boundaries. This paper reviews the requirements of enterprise network's integration and collaboration, as well as the development of new information technologies. Based on service-oriented architecture (SOA), collaboration modelling and collaboration agents are introduced to solve problems of collaborative management for service convergence under the condition of process and data fragmentation. A model-driven methodology is developed to design and deploy the integrating framework. An industrial experiment is designed and implemented to illustrate the usage of developed technologies in this paper.

  5. Failures of chain systems

    CSIR Research Space (South Africa)

    James, A

    1997-03-01

    Full Text Available Chains are used for various purposes in a wide range of industries. This paper describes three case studies where a failure analysis was carried out on chains used in markedly different applications namely: a furnace health, a drilling rig for rock...

  6. Value Chain Engineering

    DEFF Research Database (Denmark)

    Wæhrens, Brian Vejrum; Slepniov, Dmitrij

    2015-01-01

    This workbook is recommended for the attention of students of and managers in Danish small and medium sized enterprises (SMEs). Danish SMEs are currently facing a number of key challenges related to their position in global value chains. This book provides an insight into value chain management...

  7. Shared Value Chain Design

    DEFF Research Database (Denmark)

    Bals, Lydia; Tate, Wendy L.

    In Sustainable Supply Chain Management (SSCM) research still the classic economic perspective is the dominating perspective, although the triple bottom line (including economic, social and ecological) is well accepted. The theoretical foundation for the paper is Stakeholder Theory. Case studies...... in local communities, fundamentally changing supply chains....

  8. Supply Chain Management

    DEFF Research Database (Denmark)

    Wieland, Andreas; Handfield, Robert B.

    Supply chain management has made great strides in becoming a discipline with a standalone body of theories. As part of this evolution, researchers have sought to embed and integrate observed supply chain management phenomena into theoretical statements. In our review, we explore where we have been...

  9. REVERSE SUPPLY CHAIN

    Directory of Open Access Journals (Sweden)

    Tomasz DOMAGAŁA

    2013-10-01

    Full Text Available The paper focuses on the presentation of the reverse supply chain, of which the role in the modern business grows along with the increasing number of environmental regulations and possibilities of reducing an operating cost. The paper also describes main problems in developing the profitable chain and possibilities to take an action in order to overcome them.

  10. Quantitative genetics in conservation biology.

    Science.gov (United States)

    Frankham, R

    1999-12-01

    Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations.

  11. Plant biodiversity of beech forests in central-northern Italy: a methodological approach for conservation purposes

    Directory of Open Access Journals (Sweden)

    Marcantonio M

    2012-07-01

    Full Text Available Forests are reckoned essentials as biodiversity reservoirs and carbon sinks. Current threats to forest ecosystems (e.g., climate changes, habitat loss and fragmentation, management changes call for monitoring their biodiversity and preserving their ecological functions. In this study, we characterized plants diversity of five beech forests located in central and north Apennines mountain chain, using results by a probabilistic sampling. In order to achieve our goals, we have considered species richness and abundance, taxonomic distinctness and species composition, using both old and new analytical approaches. Results have shown how: (1 the forest type dominated by Fagus sylvatica is characterized by high complexity, with marked compositional, structural and biodiversity differences; (2 beech forests of Pigelleto di Piancastagnaio and Valle della Corte show the highest plants diversity values. The ecological characteristics of these areas, which sustain high diversity values, are unique and of great conservation interest; (3 the use of species richness as the only diversity measure have not allowed an efficient differentiation between studied areas. Indeed, the use of different indexes and analytical methods is required to detect multiple characteristics of biological diversity, as well as to carry out efficient biodiversity surveys aimed to develop optimal conservation strategies. In the future, we plan to apply the sampling methodology and the analytical approach used in this paper to characterize plants diversity of similar forest types.

  12. Habitat fragmentation and its lasting impact on Earth’s ecosystems

    Science.gov (United States)

    Haddad, Nick M.; Brudvig, Lars A.; Clobert, Jean; Davies, Kendi F.; Gonzalez, Andrew; Holt, Robert D.; Lovejoy, Thomas E.; Sexton, Joseph O.; Austin, Mike P.; Collins, Cathy D.; Cook, William M.; Damschen, Ellen I.; Ewers, Robert M.; Foster, Bryan L.; Jenkins, Clinton N.; King, Andrew J.; Laurance, William F.; Levey, Douglas J.; Margules, Chris R.; Melbourne, Brett A.; Nicholls, A. O.; Orrock, John L.; Song, Dan-Xia; Townshend, John R.

    2015-01-01

    We conducted an analysis of global forest cover to reveal that 70% of remaining forest is within 1 km of the forest’s edge, subject to the degrading effects of fragmentation. A synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. Effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. These findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services. PMID:26601154

  13. Species-genetic diversity correlations in habitat fragmentation can be biased by small sample sizes.

    Science.gov (United States)

    Nazareno, Alison G; Jump, Alistair S

    2012-06-01

    Predicted parallel impacts of habitat fragmentation on genes and species lie at the core of conservation biology, yet tests of this rule are rare. In a recent article in Ecology Letters, Struebig et al. (2011) report that declining genetic diversity accompanies declining species diversity in tropical forest fragments. However, this study estimates diversity in many populations through extrapolation from very small sample sizes. Using the data of this recent work, we show that results estimated from the smallest sample sizes drive the species-genetic diversity correlation (SGDC), owing to a false-positive association between habitat fragmentation and loss of genetic diversity. Small sample sizes are a persistent problem in habitat fragmentation studies, the results of which often do not fit simple theoretical models. It is essential, therefore, that data assessing the proposed SGDC are sufficient in order that conclusions be robust.

  14. Entanglement Thermalization and Local Conservation Laws

    Science.gov (United States)

    Zhang, Liangsheng; Kim, Hyungwon; Huse, David

    2015-03-01

    We study the thermalization of entanglement entropy in one-dimensional spin chains under the unitary dynamics of a nonintegrable Hamiltonian or periodic driving by Floquet operators. Using full diagonalization of the Hamiltonian matrix and the Floquet operators, we analyze the time evolution of entanglement entropy starting from various initial conditions, including initial states with entanglement in excess of the thermal equilibrium value. It is found that the thermalization of entanglement entropy is coupled to local conservation laws when approaching equilibrium, and the absence of conservation laws in the Floquet system allows the entanglement entropy to thermalize more rapidly than it does in the corresponding Hamiltonian.

  15. Mitochondrial fragmentation in human macrophages attenuates palmitate-induced inflammatory responses.

    Science.gov (United States)

    Zezina, Ekaterina; Snodgrass, Ryan G; Schreiber, Yannick; Zukunft, Sven; Schürmann, Christoph; Heringdorf, Dagmar Meyer Zu; Geisslinger, Gerd; Fleming, Ingrid; Brandes, Ralf P; Brüne, Bernhard; Namgaladze, Dmitry

    2018-02-02

    Macrophages in adipose tissue contribute to inflammation and the development of insulin resistance in obesity. Exposure of macrophages to saturated fatty acids alters cell metabolism and activates pro-inflammatory signaling. How fatty acids influence macrophage mitochondrial dynamics is unclear. We investigated the mechanism of palmitate-induced mitochondrial fragmentation and its impact on inflammatory responses in primary human macrophages. Fatty acids, such as palmitate, caused mitochondrial fragmentation in human macrophages. Increased mitochondrial fragmentation was also observed in peritoneal macrophages from hyperlipidemic apolipoprotein E knockout mice. Fatty acid-induced mitochondrial fragmentation was independent of the fatty acid chain saturation and required dynamin-related protein 1 (DRP1). Mechanistically, mitochondrial fragmentation was regulated by incorporation of palmitate into mitochondrial phospholipids and their precursors. Palmitate-induced endoplasmic reticulum stress and loss of mitochondrial membrane potential did not contribute to mitochondrial fragmentation. Macrophages treated with palmitate maintained intact mitochondrial respiration and ATP levels. Pharmacological or genetic inhibition of DRP1 enhanced palmitate-induced mitochondrial ROS production, c-Jun phosphorylation, and inflammatory cytokine expression. Our results indicate that mitochondrial fragmentation is a protective mechanism attenuating inflammatory responses induced by palmitate in human macrophages. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Fragmentation in Carbon Therapy Beams

    CERN Document Server

    Charara, Y M

    2010-01-01

    The state of the art Monte Carlo code HETC-HEDS was used to simulate spallation products, secondary neutron, and secondary proton production in A-150 Tissue Equivalent Plastic phantoms to investigate fragmentation of carbon therapy beams. For a 356 MeV/Nucleon carbon ion beam, production of charged particles heavier than protons was 0.24 spallation products per incident carbon ion with atomic numbers ranging from 1 through 5 (hydrogen to boron). In addition, there were 4.73 neutrons and 2.95 protons produced per incident carbon ion. Furthermore, as the incident energy increases, the neutron production rate increases at a rate of 20% per 10 MeV/nucleon. Secondary protons were created at a rate between 2.62-2.87 per carbon ion, while spallation products were created at a rate between 0.20-0.24 per carbon ion.

  17. Fluid fragmentation from hospital toilets

    CERN Document Server

    Traverso, G; Lu, C -C; Maa, R; Langer, R; Bourouiba, L

    2013-01-01

    Hospital-acquired infections represent significant health and financial burdens to society. Clostridium difficile (C. difficile) is a particularly challenging bacteria with the potential to cause severe diarrhea and death. One mode of transmission for C. difficile, as well as other pathogens, which has received little attention is the potential air contamination by pathogen-bearing droplets emanating from toilets. In the fluid dynamics video submitted to the APS DFD Gallery of Fluid Motion 2013, we present flow visualizations via high-speed recordings showing the capture of the product of the fluid fragmentation generated by hospital toilet high-pressure flushes. Important quantities of both large and small droplets are observed. We illustrate how high-pressure flushes and cleaning products currently used in hospital toilets result in aggravating, rather than alleviating, the suspension and recirculation of tenacious airborne pathogen-bearing droplets.

  18. Building robust conservation plans.

    Science.gov (United States)

    Visconti, Piero; Joppa, Lucas

    2015-04-01

    Systematic conservation planning optimizes trade-offs between biodiversity conservation and human activities by accounting for socioeconomic costs while aiming to achieve prescribed conservation objectives. However, the most cost-efficient conservation plan can be very dissimilar to any other plan achieving the set of conservation objectives. This is problematic under conditions of implementation uncertainty (e.g., if all or part of the plan becomes unattainable). We determined through simulations of parallel implementation of conservation plans and habitat loss the conditions under which optimal plans have limited chances of implementation and where implementation attempts would fail to meet objectives. We then devised a new, flexible method for identifying conservation priorities and scheduling conservation actions. This method entails generating a number of alternative plans, calculating the similarity in site composition among all plans, and selecting the plan with the highest density of neighboring plans in similarity space. We compared our method with the classic method that maximizes cost efficiency with synthetic and real data sets. When implementation was uncertain--a common reality--our method provided higher likelihood of achieving conservation targets. We found that χ, a measure of the shortfall in objectives achieved by a conservation plan if the plan could not be implemented entirely, was the main factor determining the relative performance of a flexibility enhanced approach to conservation prioritization. Our findings should help planning authorities prioritize conservation efforts in the face of uncertainty about future condition and availability of sites. © 2014 Society for Conservation Biology.

  19. High yield DNA fragmentation using cyclical hydrodynamic shearing

    NARCIS (Netherlands)

    Shui, Lingling; Sparreboom, Wouter; Spang, Peter; Roeser, Tina; Nieto, Benjamin; Guasch, Francesc; Corbera, Antoni Homs; van den Berg, Albert; Carlen, Edwin

    2013-01-01

    We report a new DNA fragmentation technique that significantly simplifies conventional hydrodynamic shearing fragmentation by eliminating the need for sample recirculation while maintaining high fragmentation yield and low fragment length variation, and therefore, reduces instrument complexity and

  20. Understanding the supply chain

    Directory of Open Access Journals (Sweden)

    Aćimović Slobodan

    2006-01-01

    Full Text Available Supply chain management represents new business philosophy and includes strategically positioned and much wider scope of activity in comparison with its "older brother" - management of logistics. Philosophy of the concept of supply chain is directed to more coordination of key business functions of every link in distribution chain in the process of organization of the flow of both goods and information, while logistic managing instruments are focused on internal optimum of flows of goods and information within one company. Applying the concept of integrated supply chain among several companies makes the importance of operative logistics activity even greater on the level of one company, thus advancing processes of optimum and coordination within and between different companies and confirms the importance of logistics performances for the company’s profitability. Besides the fact that the borders between companies are being deleted, this concept of supply chain in one distribution channel influences increasing of importance of functional, i.e. traditional business managing approaches but instead it points out the importance of process managing approaches. Although the author is aware that "there is nothing harder, more dangerous and with uncertain success, but to find a way for introducing some novelties (Machiavelli, it would be even his additional stimulation for trying to bring closer the concept and goals of supply chain implementation that are identified in key, relevant, modern, theoretical and consulting approaches in order to achieve better understanding of the subject and faster implementation of the concept of supply chain management by domestic companies.

  1. Patch size, functional isolation, visibility and matrix permeability influences neotropical primate occurrence within highly fragmented landscapes.

    Directory of Open Access Journals (Sweden)

    Lucas Goulart da Silva

    Full Text Available Forest fragmentation and habitat loss are among the major current extinction causes. Remaining fragments are mostly small, isolated and showing poor quality. Being primarily arboreal, Neotropical primates are generally sensitive to fragmentation effects. Furthermore, primates are involved in complex ecological process. Thus, landscape changes that negatively interfere with primate population dynamic affect the structure, composition, and ultimately the viability of the whole community. We evaluated if fragment size, isolation and visibility and matrix permeability are important for explaining the occurrence of three Neotropical primate species. Employing playback, we verified the presence of Callicebus nigrifrons, Callithrix aurita and Sapajus nigritus at 45 forest fragments around the municipality of Alfenas, Brazil. We classified the landscape and evaluated the metrics through predictive models of occurrence. We selected the best models through Akaike Selection Criterion. Aiming at validating our results, we applied the plausible models to another region (20 fragments at the neighboring municipality of Poço Fundo, Brazil. Twelve models were plausible, and three were validated, two for Sapajus nigritus (Area and Area+Visibility and one for Callicebus nigrifrons (Area+Matrix. Our results reinforce the contribution of fragment size to maintain biodiversity within highly degraded habitats. At the same time, they stress the importance of including novel, biologically relevant metrics in landscape studies, such as visibility and matrix permeability, which can provide invaluable help for similar studies in the future and on conservation practices in the long run.

  2. Genetic variability of Conopophaga lineata (Conopophagidae (Wied-Neuwied, 1831 in Atlantic Forest fragments

    Directory of Open Access Journals (Sweden)

    GPM. Dantas

    Full Text Available Forest fragmentation affects bird populations in many ways, modifying the composition of communities and favouring open country species. The Atlantic Forest is considered one of the most important biomes in the world, due to its great biodiversity, accelerated rates of deforestation, and high endemism. Despite these characteristics, few studies have evaluated the effects of forest fragmentation in the genetic structure of Atlantic forest bird populations. So, this study aims to verify the effects of forest fragmentation in the genetic population structure of Conopophaga lineata, through RAPD markers. To achieve this goal, 89 C. lineata individuals were captured in nine Atlantic Forest fragments in Minas Gerais State. The RAPD data indicate that forest fragmentation has not affected the genetic variation of C. lineata populations (Mann-Whitney U = 3.50; p = 0.11. Great part of the genetic variability of this species is found within populations and it was not observed a correlation between genetic and geographic distance (Mantel test t = 0.6250; p = 073. UPGMA analyses did not show defined clades and all branches showed low statistical support. The low population differentiation observed in this species can be due to a high gene flow among populations or a recent fragmentation. Thus, the current diversity status of C. lineata populations indicates that this species is not significantly affected by fragmentation. However, more genetic studies are essential to improve conservation strategies of Brazilian Atlantic Forest birds.

  3. Patch size, functional isolation, visibility and matrix permeability influences neotropical primate occurrence within highly fragmented landscapes.

    Science.gov (United States)

    da Silva, Lucas Goulart; Ribeiro, Milton Cezar; Hasui, Érica; da Costa, Carla Aparecida; da Cunha, Rogério Grassetto Teixeira

    2015-01-01

    Forest fragmentation and habitat loss are among the major current extinction causes. Remaining fragments are mostly small, isolated and showing poor quality. Being primarily arboreal, Neotropical primates are generally sensitive to fragmentation effects. Furthermore, primates are involved in complex ecological process. Thus, landscape changes that negatively interfere with primate population dynamic affect the structure, composition, and ultimately the viability of the whole community. We evaluated if fragment size, isolation and visibility and matrix permeability are important for explaining the occurrence of three Neotropical primate species. Employing playback, we verified the presence of Callicebus nigrifrons, Callithrix aurita and Sapajus nigritus at 45 forest fragments around the municipality of Alfenas, Brazil. We classified the landscape and evaluated the metrics through predictive models of occurrence. We selected the best models through Akaike Selection Criterion. Aiming at validating our results, we applied the plausible models to another region (20 fragments at the neighboring municipality of Poço Fundo, Brazil). Twelve models were plausible, and three were validated, two for Sapajus nigritus (Area and Area+Visibility) and one for Callicebus nigrifrons (Area+Matrix). Our results reinforce the contribution of fragment size to maintain biodiversity within highly degraded habitats. At the same time, they stress the importance of including novel, biologically relevant metrics in landscape studies, such as visibility and matrix permeability, which can provide invaluable help for similar studies in the future and on conservation practices in the long run.

  4. Project Decision Chain

    DEFF Research Database (Denmark)

    Rolstadås, Asbjørn; Pinto, Jeffrey K.; Falster, Peter

    2015-01-01

    To add value to project performance and help obtain project success, a new framework for decision making in projects is defined. It introduces the project decision chain inspired by the supply chain thinking in the manufacturing sector and uses three types of decisions: authorization, selection......, and plan decision. A primitive decision element is defined where all the three decision types can be accommodated. Each task in the primitive element can in itself contain subtasks that in turn will comprise new primitive elements. The primitive elements are nested together in a project decision chain....

  5. Global Value Chain Configuration

    DEFF Research Database (Denmark)

    Hernandez, Virginia; Pedersen, Torben

    2017-01-01

    This paper reviews the literature on global value chain configuration, providing an overview of this topic. Specifically, we review the literature focusing on the concept of the global value chain and its activities, the decisions involved in its configuration, such as location, the governance...... modes chosen and the different ways of coordinating them. We also examine the outcomes of a global value chain configuration in terms of performance and upgrading. Our aim is to review the state of the art of these issues, identify research gaps and suggest new lines for future research that would...

  6. Plastic value chains

    DEFF Research Database (Denmark)

    Baxter, John; Wahlstrom, Margareta; Zu Castell-Rüdenhausen, Malin

    2014-01-01

    Optimizing plastic value chains is regarded as an important measure in order to increase recycling of plastics in an efficient way. This can also lead to improved awareness of the hazardous substances contained in plastic waste, and how to avoid that these substances are recycled. As an example......, plastics from WEEE is chosen as a Nordic case study. The project aims to propose a number of improvements for this value chain together with representatives from Nordic stakeholders. Based on the experiences made, a guide for other plastic value chains shall be developed....

  7. Agricultural extension in the facilitation of biodiversity conservation ...

    African Journals Online (AJOL)

    Biodiversity conservation, particularly on communal and rural farmlands, is still of a great concern in South Africa. This worry is further worsened with the different threats, ranging from deforestation and habitat fragmentation, encroachment, pollution, invasion of alien species, wild fires, logging, to hunting that communities ...

  8. Suiformes conservation: a study case of strategies for DNA utilization

    Indian Academy of Sciences (India)

    [Oliveira-Monteiro N., Lopes-Rodrigues V., Bastos E. and Guedes-Pinto H. 2013 Suiformes conservation: a study case of strategies for DNA utilization. J. Genet. 92, e49–e52. ... WGA technology (Barker et al. 2004; Bergen et al. 2005 ..... unprocessed food by PCR amplification of a new specific DNA fragment. J. Anim. Sci.

  9. Large landscape conservation-synthetic and real-world datasets

    Science.gov (United States)

    Bistra Dilkina; Katherine Lai; Ronan Le Bras; Yexiang Xue; Carla P. Gomes; Ashish Sabharwal; Jordan Suter; Kevin S. McKelvey; Michael K. Schwartz; Claire Montgomery

    2013-01-01

    Biodiversity underpins ecosystem goods and services and hence protecting it is key to achieving sustainability. However, the persistence of many species is threatened by habitat loss and fragmentation due to human land use and climate change. Conservation efforts are implemented under very limited economic resources, and therefore designing scalable, cost-efficient and...

  10. Conservation genetics in transition to conservation genomics

    DEFF Research Database (Denmark)

    Ouborg, N. Joop; Pertoldi, Cino; Loeschcke, Volker

    2010-01-01

    in conservation biology. This has allowed assessment of the impact of genetic drift on genetic variation, of the level of inbreeding within populations, and of the amount of gene flow between or within populations. Recent developments in genomic techniques, including next generation sequencing, whole genome scans...... and gene-expression pattern analysis, have made it possible to step up from a limited number of neutral markers to genome-wide estimates of functional genetic variation. Here, we focus on how the transition of conservation genetics to conservation genomics leads to insights into the dynamics of selectively...

  11. The actual relevance of ecological corridors in nature conservation

    Directory of Open Access Journals (Sweden)

    Ćurčić Nina B.

    2013-01-01

    Full Text Available The paper considers theoretical and applied foundations of the concept of the ecological corridors in nature conservation. Their relevance comes from recent ecological phenomenon of habitat fragmentation which is rapidly increasing during last decades. Habitat fragmentation is one of the main threats to richness and diversity of wildlife. Ecological corridors can mitigate the loss and fragmentation of habitat. Corridors perform as “bridges” between habitats for species and they provide a flow of the natural or even anthropogenic caused disturbances. In this paper we will present the meaning and significance of ecological corridors in nature conservation, as well as types of ecological corridors and their ecological benefits. Methodological and practical approaches in nature protection system in Serbia are included. [Projekat Ministarstva nauke Republike Srbije, br. 47007 i br. 176008

  12. Filter for interpretation of fragmentation during entry

    Energy Technology Data Exchange (ETDEWEB)

    Canavan, G.H.

    1997-10-01

    Objects that fragment cascade and decelerate abruptly, producing short, bright, signatures which can be used to estimate object diameter and speed. Other objects can be incorporated into a generalized fragmentation filter. This note summarizes the results of previous reports on the prediction and inversion of signatures from objects that radiate, ablate, and fragment during entry and uses them to produce models for the parameters of entering objects.

  13. Two Distantly Spaced Basic Patches in the Flexible Domain of Huntingtin-Interacting Protein 1 (HIP1 Are Essential for the Binding of Clathrin Light Chain

    Directory of Open Access Journals (Sweden)

    Joel A. Ybe

    2009-01-01

    Full Text Available The interaction between HIP family proteins (HIP1 and HIP12/1R and clathrin is fundamental to endocytosis. We used circular dichroism (CD to study the stability of an HIP1 subfragment (aa468-530 that is splayed open. CD thermal melts show HIP1 468-530 is only stable at low temperatures, but this HIP1 fragment contains a structural unit that does not melt out even at 83C∘. We then created HIP1 mutants to probe our hypothesis that a short hydrophobic path in the opened region is the binding site for clathrin light chain. We found that the binding of hub/LCb was sensitive to mutating two distantly separated basic residues (K474 and K494. The basic patches marked by K474 and K494 are conserved in HIP12/1R. The lack of conservation in sla2p (S. cerevisiae, HIP1 from D. melanogaster, and HIP1 homolog ZK370.3 from C. elegans implies the binding of HIP1 and HIP1 homologs to clathrin light chain may be different in these organisms.

  14. Interaction of three fission fragments and yields of various ternary fragments

    Science.gov (United States)

    Denisov, V. Yu.; Pilipenko, N. A.; Sedykh, I. Yu.

    2017-01-01

    The interaction potential energy of the three deformed fragments formed in fission of 252Cf is studied for various combinations of three-fragment fission. The lowest height of the potential energy ridge between three touching and separated deformed fragments is sought. The excitation energies of various three-deformed-fragment configurations, at the lowest barrier heights related to the yield of the corresponding configuration, are considered in detail. The most probable three-fragment fission configurations are discussed. The yields of various ternary fragments in fission of 250Cf agree well with available experimental data.

  15. Geotechnology and landscape ecology applied to the selection of potential forest fragments for seed harvesting.

    Science.gov (United States)

    Santos, Alexandre Rosa Dos; Antonio Alvares Soares Ribeiro, Carlos; de Oliveira Peluzio, Telma Machado; Esteves Peluzio, João Batista; de Queiroz, Vagner Tebaldi; Figueira Branco, Elvis Ricardo; Lorenzon, Alexandre Simões; Domingues, Getulio Fonseca; Marcatti, Gustavo Eduardo; de Castro, Nero Lemos Martins; Teixeira, Thaisa Ribeiro; Dos Santos, Gleissy Mary Amaral Dino Alves; Santos Mota, Pedro Henrique; Ferreira da Silva, Samuel; Vargas, Rozimelia; de Carvalho, José Romário; Macedo, Leandro Levate; da Silva Araújo, Cintia; de Almeida, Samira Luns Hatum

    2016-12-01

    The Atlantic Forest biome is recognized for its biodiversity and is one of the most threatened biomes on the planet, with forest fragmentation increasing due to uncontrolled land use, land occupation, and population growth. The most serious aspect of the forest fragmentation process is the edge effect and the loss of biodiversity. In this context, the aim of this study was to evaluate the dynamics of forest fragmentation and select potential forest fragments with a higher degree of conservation for seed harvesting in the Itapemirim river basin, Espírito Santo State, Brazil. Image classification techniques, forest landscape ecology, and multi-criteria analysis were used to evaluate the evolution of forest fragmentation to develop the landscape metric indexes, and to select potential forest fragments for seed harvesting for the years 1985 and 2013. According to the results, there was a reduction of 2.55% of the occupancy of the fragments in the basin between the years 1985 and 2013. For the years 1985 and 2013, forest fragment units 2 and 3 were spatialized with a high potential for seed harvesting, representing 6.99% and 16.01% of the total fragments, respectively. The methodology used in this study has the potential to be used to support decisions for the selection of potential fragments for seed harvesting because selecting fragments in different environments by their spatial attributes provides a greater degree of conservation, contributing to the protection and conscious management of the forests. The proposed methodology can be adapted to other areas and different biomes of the world. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Why socio-political borders and boundaries matter in conservation

    DEFF Research Database (Denmark)

    Dallimer, Martin; Strange, Niels

    2015-01-01

    on biodiversity and ecosystem conservation by fragmenting ownership, governance, and management. Where boundaries are in place, a lack of coordination on either side of a boundary affects the efficiency and efficacy of ecosystem management. We suggest four research pathways which will enhance our ability...... to address the adverse effects of socio-political borders on conservation: (i) scale-matching, (ii) quantification of the mutual economic benefits of conservation across boundaries, (iii) determining transboundary societal values, and (iv) acknowledging the importance of stakeholder behaviour and incentives....

  17. Electronic Predetermination of Ethylene Fragmentation Dynamics

    Directory of Open Access Journals (Sweden)

    Xinhua Xie

    2014-04-01

    Full Text Available We experimentally investigate the dependence of the fragmentation behavior of the ethylene dication on the intensity and duration of the laser pulses that initiate the fragmentation dynamics by strong-field double ionization. Using coincidence momentum imaging for the detection of ionic fragments, we disentangle the different contributions of ionization from lower-valence orbitals and field-driven excitation dynamics to the population of certain dissociative excited ionic states that are connected to one of several possible fragmentation pathways towards a given set of fragment ions. We find that the excitation probability to a particular excited state and therewith the outcome of the fragmentation reaction strongly depend on the parameters of the laser pulse. This, in turn, opens up new possibilities for controlling the outcome of fragmentation reactions of polyatomic molecules in that it may allow one to selectively enhance or suppress individual fragmentation channels, which was not possible in previous attempts of controlling fragmentation processes of polyatomic molecules with strong laser fields.

  18. Molecular energies from an incremental fragmentation method

    Science.gov (United States)

    Meitei, Oinam Romesh; Heßelmann, Andreas

    2016-02-01

    The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.

  19. Moldova - Value Chain Training

    Data.gov (United States)

    Millennium Challenge Corporation — The evaluation of the GHS value chain training subactivity wwas designed to measure the extent, if any, to which the training activities improved the productivity...

  20. Editorial: Supply Chain Management

    Directory of Open Access Journals (Sweden)

    Aidonis, D.

    2012-01-01

    Full Text Available This special issue has followed up the 2nd Olympus International Conference on Supply Chains held on October 5-6, 2012, in Katerini, Greece. The Conference was organized by the Department of Logistics of Alexander Technological Educational Institution (ATEI of Thessaloniki, in collaboration with the Laboratory of Quantitative Analysis, Logistics and Supply Chain Management of the Department of Mechanical Engineering, Aristotle University of Thessaloniki (AUTH. During the 2-Days Conference more than 50 research papers were presented covering the following thematic areas: (i Business Logistics, (ii Transportation, Telematics and Distribution Networks, (iii Green Logistics, (iv Information and Communication Technologies in Supply Chain Management, and (v Services and Quality. Three keynote invited speakers addressed interesting issues for the Humanitarian Logistics, Green Supply Chains of the Agrifood Sector and the Opportunities and Prospects of Greek Ports chaired Round Tables with other Greek and Foreign Scientists and Specialists.

  1. Characterizing Oregon's supply chains.

    Science.gov (United States)

    2013-03-01

    In many regions throughout the world, freight models are used to aid infrastructure investment and : policy decisions. Since freight is such an integral part of efficient supply chains, more realistic : transportation models can be of greater assista...

  2. Writing on polymer chains.

    Science.gov (United States)

    Lutz, Jean-François

    2013-11-19

    Synthetic polymer materials are currently limited by their inability to store information in their chains, unlike some well-characterized biopolymers. Nucleic acids store and transmit genetic information, and amino acids encode the complex tridimensional structures and functions within proteins. To confer similar properties on synthetic materials, researchers must develop"writing" mechanisms, facile chemical pathways that allow control over the primary structure of synthetic polymer chains. The most obvious way to control the primary structure is to connect monomer units one-by-one in a given order using iterative chemistry. Although such synthesis strategies are commonly used to produce peptides and nucleic acids, they produce limited yields and are much slower than natural polymerization mechanisms. An alternative strategy would be to use multiblock copolymers with blocks that have specified sequences. In this case, however, the basic storage element is not a single molecular unit, but a longer block composed of several repeating units. However, the synthesis of multiblock copolymers is long and tedious. Therefore, researchers will need to develop other strategies for writing information onto polymer chains. In this Account, I describe our recent progress in the development of sequence controlled polymerization methods. Although our research focuses on different strategies, we have emphasized sequence-regulation in chain-growth polymerization processes. Chain-growth polymerizations, particularly radical polymerization, are very convenient methods for synthesizing polymers. However, in most cases, such approaches do not lead to controlled monomer sequences. During the last five years, we have shown that controlled/living chain-growth polymerization mechanisms offer interesting advantages for sequence regulation. In such mechanisms, the chains form gradually over time, and therefore the primary structure can be tuned by using time-controlled monomer additions. For

  3. MASTERING SUPPLY CHAIN RISKS

    Directory of Open Access Journals (Sweden)

    Borut Jereb

    2012-11-01

    Full Text Available Risks in supply chains represent one of the major business issues today. Since every organizationstrives for success and uninterrupted operations, efficient supply chain risk management is crucial.During supply chain risk research at the Faculty of Logistics in Maribor (Slovenia some keyissues in the field were identified, the major being the lack of instruments which can make riskmanagement in an organization easier and more efficient. Consequently, a model which captures anddescribes risks in an organization and its supply chain was developed. It is in accordance with thegeneral risk management and supply chain security standards, the ISO 31000 and ISO 28000families. It also incorporates recent finding from the risk management field, especially from theviewpoint of segmenting of the public.The model described in this paper focuses on the risks itself by defining them by different keydimensions, so that risk management is simplified and can be undertaken in every supply chain andorganizations within them. Based on our mode and consequent practical research in actualorganizations, a freely accessible risk catalog has been assembled and published online from the risksthat have been identified so far. This catalog can serve as a checklist and a starting point in supplychain risk management in organizations. It also incorporates experts from the field into a community,in order to assemble an ever growing list of possible risks and to provide insight into the model andits value in practice.

  4. Innovation Across the Supply Chain

    DEFF Research Database (Denmark)

    Druehl, Cheryl; Carrillo, Janice; Hsuan, Juliana

    Innovation is an integral part of every firm’s ongoing operations. Beyond product innovation, supply chain innovations offer a unique source of competitive advantage. We synthesize recent research on innovation in the supply chain, specifically, innovative supply chain processes...

  5. The role of the matrix-edge dynamics of amphibian conservation in tropical montane fragmented landscapes La dinámica del borde-matriz en bosques mesófilos de montaña fragmentados y su papel en la conservación de los anfibios

    Directory of Open Access Journals (Sweden)

    Georgina Santos-Barrera

    2011-06-01

    Full Text Available Edge effects play a key role in forest dynamics in which the context of the anthropogenic matrix has a great influence on fragment connectivity and function. The study of the interaction between edge and matrix effects in nature is essential to understand and promote the colonization of some functional groups in managed ecosystems. We studied the dynamics of 7 species of frogs and salamanders occurring in 8 ecotones of tropical montane cloud forest (TMCF which interact with adjacent managed areas of coffee and corn plantations in Guerrero, southern Mexico. A survey effort of 196 man/hours along 72 transects detected 58 individuals of 7 amphibian species and 12 environmental and structural variables were measured. The diversity and abundance of amphibians in the forest mostly depended on the matrix context adjacent to the forest patches. The forest interior provided higher relative humidity, leaf litter cover, and canopy cover that determined the presence of some amphibian species. The use of shaded coffee plantations was preferred by the amphibians over the corn plots possibly due to the maintenance of native forest arboreal elements, low management rate and less intensity of disturbance in the coffee plantations than in the corn plots. Shaded coffee plantations reduce the edge effects in TMCF, improve the connectivity between TMCF fragments and increase habitat quality for the forest interior amphibian species. Future wildlife management research should take into account edge and matrix effects to understand species dynamics which move along anthropogenic-natural ecotones in managed ecosystems, thus prioritizing sites to buffer edge effects and increase habitat quality in remaining natural ecosystems.El efecto de borde es un evento clave en la dinámica de algunos bosques, la matriz que rodea a los fragmentos de bosque tiene una gran importancia en el funcionamiento y conectividad de estos fragmentos. El conocimiento de las interacciones entre

  6. Distribution of rock fragments and their effects on hillslope soil erosion in purple soil, China

    Science.gov (United States)

    Wang, Xiaoyan

    2017-04-01

    influence of rock fragment cover on purple soil slope erosion process were carried on, under different conditions with two kind of rock fragment positions (resting on soil surface and embedded into top soil layer), varied rock fragment coverage (Rc, 0% 40%), two kind of soils with textural porosity or structural porosity, and three kind of rainfall intensities (I, 1 mm/min, 1.5 mm/min and 2 mm/min). Simulated rainfall experiments in situ plots in the field, combined with simulated rainfall experiments in soil pans indoor, were used. The main conclusions of this dissertation are as following: 1. The spatial distribution characteristics of rock fragments in purple soil slope and its effects on the soil physical properties were clarified basically. 2. The mechanism of influence of rock fragments within top soil layer on soil erosion processes was understood and a threshold of rock fragment content on the infiltration was figured out. 3. The relationships between surface rock fragment cover and hillslope soil erosion in purple soil under different conditions with varied rock fragment positions, soil structures and rainfall intensities were obtained and the soil and water conservation function of surface rock fragment cover on reducing soil loss was affirmed.

  7. Development of procedures for the identification of human papilloma virus DNA fragments in laser plume

    Science.gov (United States)

    Woellmer, Wolfgang; Meder, Tom; Jappe, Uta; Gross, Gerd; Riethdorf, Sabine; Riethdorf, Lutz; Kuhler-Obbarius, Christina; Loening, Thomas

    1996-01-01

    For the investigation of laser plume for the existence of HPV DNA fragments, which possibly occur during laser treatment of virus infected tissue, human papillomas and condylomas were treated in vitro with the CO2-laser. For the sampling of the laser plume a new method for the trapping of the material was developed by use of water-soluble gelatine filters. These samples were analyzed with the polymerase chain reaction (PCR) technique, which was optimized in regard of the gelatine filters and the specific primers. Positive PCR results for HPV DNA fragments up to the size of a complete oncogene were obtained and are discussed regarding infectiousity.

  8. Decoupling fragmentation from habitat loss for spiders in patchy agricultural landscapes.

    Science.gov (United States)

    Gavish, Yoni; Ziv, Yaron; Rosenzweig, Michael L

    2012-02-01

    Habitat loss reduces species diversity, but the effect of habitat fragmentation on number of species is less clear because fragmentation generally accompanies loss of habitat. We compared four methods that aim to decouple the effects of fragmentation from the effects of habitat loss. Two methods are based on species-area relations, one on Fisher's alpha index of diversity, and one on plots of cumulative number of species detected against cumulative area sampled. We used these methods to analyze the species diversity of spiders in 2, 3.2 × 4 km agricultural landscapes in Southern Judea Lowlands, Israel. Spider diversity increased as fragmentation increased with all four methods, probably not because of the additive within-patch processes, such as edge effect and heterogeneity. The positive relation between fragmentation and species diversity might reflect that most species can disperse through the fields during the wheat-growing season. We suggest that if a given area was designated for the conservation of spiders in Southern Judea Lowlands, Israel, a set of several small patches may maximize species diversity over time. ©2011 Society for Conservation Biology.

  9. Effect of habitat fragmentation on ranging behavior of white-headed langurs in limestone forests in Southwest China.

    Science.gov (United States)

    Huang, Zhonghao; Yuan, Peisong; Huang, Henglian; Tang, Xiaoping; Xu, Weijian; Huang, Chengming; Zhou, Qihai

    2017-07-01

    The critically endangered white-headed langur (Trachypithecus leucocephalus) is confined to fragmented karst forests of southwest Guangxi Province, China. A lack of information on the influence of habitat fragmentation on langur behavior has prevented a comprehensive understanding of their ranging behavior and the development of effective langur conservation strategies. We collected comparative data on time budgets, daily path lengths, home range and diets of four langur groups inhabiting the lightly fragmented Fusui forest (G1, G2) and the more heavily fragmented Chongzuo forest (G3, G4). The aim was to explore the effect of this fragmentation on langur ranging behavior. Our results showed that the Fusui groups spent more time on moving and less time on feeding and playing than the Chongzuo groups. Daily path lengths were 472.4-536.1 m for the Fusui groups and 449.6-480.7 m for the Chongzuo groups, indicating no marked inter-site variation. The Fusui groups occupied much larger home ranges (23.8-33.8 ha) than the Chongzuo groups (14.5-15.8 ha). However, all groups had similar monthly home ranges. Diets significantly differed among langur groups. The Fusui groups consumed more young leaves and had much lower diet diversity compared with the Chongzuo groups. Our findings indicate that habitat fragmentation is one of the crucial determinants of white-headed langur ranging behavior because fragmentation reduces and restricts the home range. Langurs in fragmented habitat adopt an energy conservation strategy characterized by devoting more time to feeding and less time to moving, with a smaller home range and consumption of more plant species. We argue that linking fragmented forests with corridors should be considered a priority in a wider and comprehensive longer term langur population conservation and habitat management strategy.

  10. Decoupling habitat fragmentation from habitat loss: butterfly species mobility obscures fragmentation effects in a naturally fragmented landscape of lake islands.

    Science.gov (United States)

    MacDonald, Zachary G; Anderson, Iraleigh D; Acorn, John H; Nielsen, Scott E

    2018-01-01

    Since the publication of the theory of island biogeography, ecologists have postulated that fragmentation of continuous habitat presents a prominent threat to species diversity. However, negative fragmentation effects may be artifacts; the result of species diversity declining with habitat loss, and habitat loss correlating positively with degree of fragmentation. In this study, we used butterfly assemblages on islands of Lake of the Woods, Ontario, Canada to decouple habitat fragmentation from habitat loss and test two competing hypotheses: (1) the island effect hypothesis, which predicts that decreasing fragment size and increasing fragment isolation reduces species diversity beyond the effects of habitat loss, and (2) the habitat amount hypothesis, which negates fragmentation effects and predicts that only total habitat area determines the diversity of species persisting on fragmented landscapes. Using eight independent size classes of islands (ranging from 0.1 to 8.0 ha) that varied in number of islands while holding total area constant, species diversity comparisons, species accumulation curves, and species-area relationship extrapolations demonstrated that smaller insular habitats contained at least as many butterfly species as continuous habitat. However, when highly mobile species occurring on islands without their larval food plants were excluded from analyses, island effects on potentially reproducing species became apparent. Similarily, generalized linear models suggested that effects of island isolation and vascular plant richness on insular butterfly richness were confounded by species of high mobility. We conclude that inter-fragment movements of highly mobile species may obscure important fragmentation effects on potentially reproducing populations, questioning support for the habitat amount hypothesis.

  11. Incorporating agroforestry approaches into commodity value chains.

    Science.gov (United States)

    Millard, Edward

    2011-08-01

    The productivity of tropical agricultural commodities is affected by the health of the ecosystem. Shade tolerant crops such as coffee and cocoa benefit from environmental services provided by forested landscapes, enabling landscape design that meets biodiversity conservation and economic needs. What can motivate farmers to apply and maintain such landscape approaches? Rather than rely on a proliferation of externally funded projects new opportunities are emerging through the international market that buys these commodities. As part of their growing commitment to sustainable supply chains, major companies are supporting agroforestry approaches and requiring producers and traders to demonstrate that the source of their commodities complies with a set of principles that conserves forested landscapes and improves local livelihoods. The paper presents examples of international companies that are moving in this direction, analyzes why and how they are doing it and discusses the impact that has been measured in coffee and cocoa communities in Latin America and Africa. It particularly considers the role of standards and certification systems as a driver of this commitment to promote profitable operations, environmental conservation and social responsibility throughout the coffee and cocoa value chains. Such approaches are already being taken to scale and are no longer operating only in small niches of the market but the paper also considers the limitations to growth in this market-based approach.

  12. Incorporating Agroforestry Approaches into Commodity Value Chains

    Science.gov (United States)

    Millard, Edward

    2011-08-01

    The productivity of tropical agricultural commodities is affected by the health of the ecosystem. Shade tolerant crops such as coffee and cocoa benefit from environmental services provided by forested landscapes, enabling landscape design that meets biodiversity conservation and economic needs. What can motivate farmers to apply and maintain such landscape approaches? Rather than rely on a proliferation of externally funded projects new opportunities are emerging through the international market that buys these commodities. As part of their growing commitment to sustainable supply chains, major companies are supporting agroforestry approaches and requiring producers and traders to demonstrate that the source of their commodities complies with a set of principles that conserves forested landscapes and improves local livelihoods. The paper presents examples of international companies that are moving in this direction, analyzes why and how they are doing it and discusses the impact that has been measured in coffee and cocoa communities in Latin America and Africa. It particularly considers the role of standards and certification systems as a driver of this commitment to promote profitable operations, environmental conservation and social responsibility throughout the coffee and cocoa value chains. Such approaches are already being taken to scale and are no longer operating only in small niches of the market but the paper also considers the limitations to growth in this market-based approach.

  13. John Tyndall's religion: a fragment

    Science.gov (United States)

    Cantor, Geoffrey

    2015-01-01

    Both contemporaries and historians have focused on the high-profile 1874 Belfast Address in which John Tyndall was widely perceived as promulgating atheism. Although some historians have instead interpreted him as a pantheist or an agnostic, it is clear that any such labels do not accurately capture Tyndall's religious position throughout his life. By contrast, this paper seeks to chart Tyndall's religious journey from 1840 (when he was in his late teens) to the autumn of 1848 when he commenced his scientific studies at Marburg. Although he had been imbued with his father's stern conservative Irish Protestantism and opposition to Catholicism, as a youth he seems for a time to have been attracted to Methodism. Later, however, he questioned and rejected his father's religious views and was increasingly drawn to the more spiritual outlook of Ralph Waldo Emerson and Thomas Carlyle, along with a more radical attitude to politics.

  14. Small-scale experimental habitat fragmentation reduces colonization rates in species-rich grasslands.

    Science.gov (United States)

    Joshi, Jasmin; Stoll, Peter; Rusterholz, Hans-Peter; Schmid, Bernhard; Dolt, Claudine; Baur, Bruno

    2006-05-01

    Habitat fragmentation is one of the most important threats to biodiversity. Decreasing patch size may lead to a reduction in the size of populations and to an increased extinction risk of remnant populations. Furthermore, colonization rates may be reduced in isolated patches. To investigate the effects of isolation and patch size on extinction and colonization rates of plant species, calcareous grasslands at three sites in the Swiss Jura Mountains were experimentally fragmented into patches of 0.25, 2.25, and 20.25 m2 by frequent mowing of the surrounding area from 1993 to 1999. Species richness in the fragment plots and adjacent control plots of the same sizes was recorded during these 7 years. In agreement with the theory of island biogeography, colonization rate was reduced by 30% in fragments versus non-isolated controls, and extinction increased in small versus large plots. Habitat specialists, in contrast to generalists, were less likely to invade fragments. In the last 4 years of the experiment, extinction rates tended to be higher in fragment than in control plots at two of the three sites. Despite reduced colonization rates and a tendency of increased extinction rates in fragments, fragmented plots had only marginally fewer species than control plots after 7 years. Hence, rates were a more sensitive measure for community change than changes in species richness per se. From a conservation point of view, the detected reduced colonization rates are particularly problematic in small fragments, which are more likely to suffer from high extinction rates in the long run.

  15. Responses of seed-dispersing birds to amount of rainforest in the landscape around fragments.

    Science.gov (United States)

    Moran, Cath; Catterall, Carla P

    2014-04-01

    Habitat loss and fragmentation alter the composition of bird assemblages in rainforest. Because birds are major seed dispersers in rainforests, fragmentation-induced changes to frugivorous bird assemblages are also likely to alter the ecological processes of seed dispersal and forest regeneration, but the specific nature of these changes is poorly understood. We assessed the influence of fragment size and landscape forest cover on the abundance, species composition, and functional properties of the avian seed disperser community in an extensively cleared, former rainforest landscape of subtropical Australia. Bird surveys of fixed time and area in 25 rainforest fragments (1-139 ha in size across a 1800 km(2) region) provided bird assemblage data which were coupled with prior knowledge of bird species' particular roles in seed dispersal to give measurements of seven different attributes of the seed disperser assemblage. We used multimodel regression to assess how patch size and surrounding forest cover (within 200 m, 1000 m, and 5000 m radii) influenced variation in the abundance of individual bird species and of functional groups based on bird species' responses to fragmentation and their roles in seed dispersal. Surrounding forest cover, specifically rainforest cover, generally had a greater effect on frugivorous bird assemblages than fragment size. Amount of rainforest cover within 200 m of fragments was the main factor positively associated with abundances of frugivorous birds that are both fragmentation sensitive and important seed dispersers. Our results suggest a high proportion of local rainforest cover is required for the persistence of seed-dispersing birds and the maintenance of seed dispersal processes. Thus, even small rainforest fragments can function as important parts of habitat networks for seed-dispersing birds, whether or not they are physically connected by vegetation. © 2014 Society for Conservation Biology.

  16. FRAGMENTATION OF CONTINENTAL UNITES STATES FORESTS

    Science.gov (United States)

    We report a multiple-scale analysis of forest fragmentation based on 30-m land-cover maps for the conterminous United States. Each 0.09-ha unit of forest was classified according to fragmentation indices measured within the surrounding landscape, for five landscape sizes from 2....

  17. Generalized Fragmentation Functions for Fractal Jet Observables

    NARCIS (Netherlands)

    Elder, B.T.; Procura, M.; Thaler, J.; Waalewijn, W.J.; Zhou, K.

    We introduce a broad class of fractal jet observables that recursively probe the collective properties of hadrons produced in jet fragmentation. To describe these collinear-unsafe observables, we generalize the formalism of fragmentation functions, which are important objects in QCD for calculating

  18. INTERMITTENCY, A TEST FOR STRING FRAGMENTATION PROCESSES

    NARCIS (Netherlands)

    SCHOLTEN, O

    The Artru-Mennessier and the string fragmentation procedure as implemented in the code VENUS have been compared. The two fragmentation prescriptions predict a similar rapidity spectrum including its energy dependence and event multiplicities, but give rise to very different intermittency results.

  19. Fragmentation of eastern United States forest types

    Science.gov (United States)

    Kurt H. Riitters; John W. Coulston

    2013-01-01

    Fragmentation is a continuing threat to the sustainability of forests in the Eastern United States, where land use changes supporting a growing human population are the primary driver of forest fragmentation (Stein and others 2009). While once mostly forested, approximately 40 percent of the original forest area has been converted to other land uses, and most of the...

  20. Pollen and gene flow in fragmented habitats

    NARCIS (Netherlands)

    Kwak, Manja M.; Velterop, Odilia; van Andel, Jelte

    . Habitat fragmentation affects both plants and pollinators. Habitat fragmentation leads to changes in species richness, population number and size, density, and shape, thus to changes in the spatial arrangement of flowers. These changes influence the amount of food for flower-visiting insects and

  1. Long-term effects of fragmentation and fragment properties on bird species richness in Hawaiian forests

    Science.gov (United States)

    David J. Flaspohler; Christian P. Giardina; Gregory P. Asner; Patrick Hart; Jonathan Price; Cassie Ka’apu Lyons; Xeronimo. Castaneda

    2010-01-01

    Forest fragmentation is a common disturbance affecting biological diversity, yet the impacts of fragmentation on many forest processes remain poorly understood. Forest restoration is likely to be more successful when it proceeds with an understanding of how native and exotic vertebrates utilize forest patches of different size. We used a system of forest fragments...

  2. Simulation analysis of effects of single fragment size on air-blast wave and fragment propagation

    Directory of Open Access Journals (Sweden)

    ZHENG Hongwei

    2017-12-01

    Full Text Available [Objectives] This paper involves the propagation and attenuation of the velocity and energy of air-blast waves and high-velocity fragments while taking their combined effects into account.[Methods] With ANSYS/LS-DYNA software, a simulation model of a columnar TNT air blast is built with prefabricated fragments affixed to its end. When the total quality of fragments is constant, the effects of a single fragment's size on the propagation of the air-blast wave and fragments are studied by changing the size of the single fragment.[Results] The results show that fragments greatly reduce the intensity and velocity of a shockwave, and block the air-blast waves behind them. When the total quality of the fragments remains constant, the effects of single fragment size on blast shockwave propagation characteristics show little difference. The smaller the single fragment, the more kinetic energy the fragments will have and the faster that energy will dissipate.[Conclusions] As a result, more attention should be paid to the combined effects of air-blast waves and high-velocity fragments. Such research can provide reference points for the deeper study of blast loads and their interaction.

  3. An Amazonian rainforest and its fragments as a laboratory of global change.

    Science.gov (United States)

    Laurance, William F; Camargo, José L C; Fearnside, Philip M; Lovejoy, Thomas E; Williamson, G Bruce; Mesquita, Rita C G; Meyer, Christoph F J; Bobrowiec, Paulo E D; Laurance, Susan G W

    2017-05-30

    We synthesize findings from one of the world's largest and longest-running experimental investigations, the Biological Dynamics of Forest Fragments Project (BDFFP). Spanning an area of ∼1000 km(2) in central Amazonia, the BDFFP was initially designed to evaluate the effects of fragment area on rainforest biodiversity and ecological processes. However, over its 38-year history to date the project has far transcended its original mission, and now focuses more broadly on landscape dynamics, forest regeneration, regional- and global-change phenomena, and their potential interactions and implications for Amazonian forest conservation. The project has yielded a wealth of insights into the ecological and environmental changes in fragmented forests. For instance, many rainforest species are naturally rare and hence are either missing entirely from many fragments or so sparsely represented as to have little chance of long-term survival. Additionally, edge effects are a prominent driver of fragment dynamics, strongly affecting forest microclimate, tree mortality, carbon storage and a diversity of fauna. Even within our controlled study area, the landscape has been highly dynamic: for example, the matrix of vegetation surrounding fragments has changed markedly over time, succeeding from large cattle pastures or forest clearcuts to secondary regrowth forest. This, in turn, has influenced the dynamics of plant and animal communities and their trajectories of change over time. In general, fauna and flora have responded differently to fragmentation: the most locally extinction-prone animal species are those that have both large area requirements and low tolerance of the modified habitats surrounding fragments, whereas the most vulnerable plants are those that respond poorly to edge effects or chronic forest disturbances, and that rely on vulnerable animals for seed dispersal or pollination. Relative to intact forests, most fragments are hyperdynamic, with unstable or

  4. Condensation and intermittency in an open-boundary aggregation-fragmentation model.

    Science.gov (United States)

    Sachdeva, Himani; Barma, Mustansir; Rao, Madan

    2013-04-12

    We study real space condensation in aggregation-fragmentation models where the total mass is not conserved, as in phenomena such as cloud formation and intracellular trafficking. We study the scaling properties of the system with influx and outflux of mass at the boundaries using numerical simulations, supplemented by analytical results in the absence of fragmentation. The system is found to undergo a phase transition to an unusual condensate phase, characterized by strong intermittency and giant fluctuations of the total mass. A related phase transition also occurs for biased movement of large masses, but with some crucial differences which we highlight.

  5. Diquark Fragmentation Contribution in Λ b Production

    Science.gov (United States)

    Osati, T.; Movlanaei, M.

    2017-05-01

    In the framework of the quark-diquark model of baryons, Λ b can be considered as b constituent quark an ud constituent diquark. In this study, we investigate the effect ud scalar diquark fragmentation into Λ b , therefor we calculate frgmentation functions of b quark and ud diquark into Λ b baryon through the use of perturbative QCD. In the next stage, throuth the use of the obtained fragmentation functions, we calculate the total fragmentation probabilities and average fragmentation parameters for b→Λ b and u d→Λ b . Finally, the inclusive cross section of Λ b baryon in electron-positron annihilation in ALEPH experiment is calculated with regard to ud diquark fragmentation contribution.

  6. Characterizing chain-compact and chain-finite topological semilattices

    OpenAIRE

    Banakh, Taras; Bardyla, Serhii

    2017-01-01

    In the paper we present various characterizations of chain-compact and chain-finite topological semilattices. A topological semilattice $X$ is called chain-compact (resp. chain-finite) if each closed chain in $X$ is compact (finite). In particular, we prove that a (Hausdorff) $T_1$-topological semilattice $X$ is chain-finite (chain-compact) if and only if for any closed subsemilattice $Z\\subset X$ and any continuous homomorphism $h:X\\to Y$ to a (Hausdorff) $T_1$-topological semilattice $Y$ th...

  7. METRODOS: Meteorological preprocessor chain

    DEFF Research Database (Denmark)

    Astrup, P.; Mikkelsen, T.; Deme, S.

    2001-01-01

    The METRODOS meteorological preprocessor chain combines measured tower data and coarse grid numerical weather prediction (NWP) data with local scale flow models and similarity scaling to give high resolution approximations of the meteorological situation. Based on available wind velocity and dire......The METRODOS meteorological preprocessor chain combines measured tower data and coarse grid numerical weather prediction (NWP) data with local scale flow models and similarity scaling to give high resolution approximations of the meteorological situation. Based on available wind velocity...... - heat flux related measurement, e.g. a temperature gradient, are used to give local values of friction velocity and Monin-Obukhov length plus an estimate of the mixing height. The METRODOS meteorological preprocessor chain is an integral part of the RODOS - Real Time On Line Decision Support - program...

  8. Environmental Retail Supply Chains

    DEFF Research Database (Denmark)

    Kotzab, Herbert; Munch, Hilde; de Faultrier, Birgitte

    2011-01-01

    Purpose – The purpose of this paper is to develop a scale that evaluates the environmental elements in retail supply chains and to examine the environmental supply chain management initiatives of the world's largest 100 retailing companies. Design/methodology/approach – The empirical evaluation has...... been undertaken through an investigative approach applying a web-scan framework which included the analysis of web sites and publicly published documents such as annual reports and corporate social responsibility reports. Findings – The authors identified 34 environmental sustainability initiatives...... which were grouped into eight categories; they refer to “fundamental environmental attitude”, “use of energy”, “use of input material”, “product”, “packaging”, “transport”, “consumption” and “waste”. The level of environmental supply chain management can be characterised as very operational and very...

  9. Supply chain quality management

    Directory of Open Access Journals (Sweden)

    Hannan Amoozad Mahdiraji

    2012-10-01

    Full Text Available In recent years, there are several methods introduced for the improvement of operational performances. Total quality management and supply chain management are two methods recommended for this purpose. These two approaches have been studied in most researches separately, while they have objectives in common, and this makes them a strategic means, which can be used, simultaneously. Total quality management and supply chain management play significant roles to increase the organizational competitiveness power. Moreover, they have only one purpose that is customer satisfaction, and they are different only on their approaches to reach their objectives. In this research, we aim to study both approaches of quality management and supply chain, their positive increasing effects that may be generated after their integration. For this purpose, the concept and definitions of each approach is studied, independently, their similarities and differences are recognized, and finally, the advantages of their integration are introduced.

  10. Chain Mixing and Chain Recurrent Iterated Function Systems

    OpenAIRE

    Nia, Mehdi Fatehi

    2016-01-01

    This paper considers the egodicity properties in iterated function systems. First, we will introduce chain mixing and chain transitive iterated function systems then some results and examples are presented to compare with these notions in discrete dynamical systems. As our main result, using adding machine maps and topological conjugacy we show that chain mixing, chain transitive and chain recurrence properties in iterated function systems are equivalent.

  11. Exact Solutions of Fragmentation Equations with General Fragmentation Rates and Separable Particles Distribution Kernels

    Directory of Open Access Journals (Sweden)

    S. C. Oukouomi Noutchie

    2014-01-01

    Full Text Available We make use of Laplace transform techniques and the method of characteristics to solve fragmentation equations explicitly. Our result is a breakthrough in the analysis of pure fragmentation equations as this is the first instance where an exact solution is provided for the fragmentation evolution equation with general fragmentation rates. This paper is the key for resolving most of the open problems in fragmentation theory including “shattering” and the sudden appearance of infinitely many particles in some systems with initial finite particles number.

  12. Conservation: Toward firmer ground

    Science.gov (United States)

    1975-01-01

    The following aspects of energy conservation were discussed: conservation history and goals, conservation modes, conservation accounting-criteria, and a method to overcome obstacles. The conservation modes tested fall into one of the following categories: reduced energy consumption, increased efficiency of energy utilization, or substitution of one or more forms of energy for another which is in shorter supply or in some sense thought to be of more value. The conservation accounting criteria include net energy reduction, economic, and technical criteria. A method to overcome obstacles includes (approaches such as: direct personal impact (life style, income, security, aspiration), an element of crisis, large scale involvement of environmental, safety, and health issues, connections to big government, big business, big politics, involvement of known and speculative science and technology, appeal to moral and ethical standards, the transient nature of opportunities to correct the system.

  13. Life-history traits and landscape characteristics predict macro-moth responses to forest fragmentation.

    Science.gov (United States)

    Slade, Eleanor M; Merckx, Thomas; Riutta, Terhi; Bebber, Daniel P; Redhead, David; Riordan, Philip; Macdonald, David W

    2013-07-01

    How best to manage forest patches, mitigate the consequences of forest fragmentation, and enable landscape permeability are key questions facing conservation scientists and managers. Many temperate forests have become increasingly fragmented, resulting in reduced interior forest habitat, increased edge habitats, and reduced connectivity. Using a citizen science landscape-scale mark-release-recapture study on 87 macro-moth species, we investigated how both life-history traits and landscape characteristics predicted macro-moth responses to forest fragmentation. Wingspan, wing shape, adult feeding, and larval feeding guild predicted macro-moth mobility, although the predictive power of wingspan and wing shape depended on the species' affinity to the forest. Solitary trees and small fragments functioned as "stepping stones," especially when their landscape connectivity was increased, by being positioned within hedgerows or within a favorable matrix. Mobile forest specialists were most affected by forest fragmentation: despite their high intrinsic dispersal capability, these species were confined mostly to the largest of the forest patches due to their strong affinity for the forest habitat, and were also heavily dependent on forest connectivity in order to cross the agricultural matrix. Forest fragments need to be larger than five hectares and to have interior forest more than 100 m from the edge in order to sustain populations of forest specialists. Our study provides new insights into the movement patterns of a functionally important insect group, with implications for the landscape-scale management of forest patches within agricultural landscapes.

  14. Habitat fragmentation, variable edge effects, and the landscape-divergence hypothesis.

    Directory of Open Access Journals (Sweden)

    William F Laurance

    2007-10-01

    Full Text Available Edge effects are major drivers of change in many fragmented landscapes, but are often highly variable in space and time. Here we assess variability in edge effects altering Amazon forest dynamics, plant community composition, invading species, and carbon storage, in the world's largest and longest-running experimental study of habitat fragmentation. Despite detailed knowledge of local landscape conditions, spatial variability in edge effects was only partially foreseeable: relatively predictable effects were caused by the differing proximity of plots to forest edge and varying matrix vegetation, but windstorms generated much random variability. Temporal variability in edge phenomena was also only partially predictable: forest dynamics varied somewhat with fragment age, but also fluctuated markedly over time, evidently because of sporadic droughts and windstorms. Given the acute sensitivity of habitat fragments to local landscape and weather dynamics, we predict that fragments within the same landscape will tend to converge in species composition, whereas those in different landscapes will diverge in composition. This 'landscape-divergence hypothesis', if generally valid, will have key implications for biodiversity-conservation strategies and for understanding the dynamics of fragmented ecosystems.

  15. Habitat fragmentation, variable edge effects, and the landscape-divergence hypothesis.

    Science.gov (United States)

    Laurance, William F; Nascimento, Henrique E M; Laurance, Susan G; Andrade, Ana; Ewers, Robert M; Harms, Kyle E; Luizão, Regina C C; Ribeiro, José E

    2007-10-10

    Edge effects are major drivers of change in many fragmented landscapes, but are often highly variable in space and time. Here we assess variability in edge effects altering Amazon forest dynamics, plant community composition, invading species, and carbon storage, in the world's largest and longest-running experimental study of habitat fragmentation. Despite detailed knowledge of local landscape conditions, spatial variability in edge effects was only partially foreseeable: relatively predictable effects were caused by the differing proximity of plots to forest edge and varying matrix vegetation, but windstorms generated much random variability. Temporal variability in edge phenomena was also only partially predictable: forest dynamics varied somewhat with fragment age, but also fluctuated markedly over time, evidently because of sporadic droughts and windstorms. Given the acute sensitivity of habitat fragments to local landscape and weather dynamics, we predict that fragments within the same landscape will tend to converge in species composition, whereas those in different landscapes will diverge in composition. This 'landscape-divergence hypothesis', if generally valid, will have key implications for biodiversity-conservation strategies and for understanding the dynamics of fragmented ecosystems.

  16. Mapping of the antigenic and allergenic epitopes of Lol p VB using gene fragmentation.

    Science.gov (United States)

    Ong, E K; Knox, R B; Singh, M B

    1995-03-01

    The recombinant proteins of Lol p VA and Lol p VB expressed in E. coli reacted with IgE antibodies from sera of allergic patients and mAbs FMC A7 and PpV1. Cross-absorption analyses using these recombinant proteins showed that Lol p VA and Lol p VB possess both similar and unique IgE binding determinants. Gene fragmentation was utilized to localize the antigenic and allergenic determinants of Lol p VB. When full-length cDNA of Lol p VB was digested into three fragments and expressed as the fusions from the glutathione transferase of pGEX vectors, fragments Met1-Val196 and Asp197-Val339 bound IgE while fragment Met1-Pro96 did not. The data suggest that there are at least two IgE binding determinants in Lol p VB. In addition, only fragment Met1-Val196 reacted with mAb PpV1. The localization of these determinants was further resolved using random fragment expression libraries. The mAb PpV1 determinant was near the N-terminal region of Lol p VB molecule. The IgE binding determinants were distributed in the central region: region I (amino acids 111-195) and II (199-254). These IgE binding determinants are conserved in Lol p VA.

  17. The role of maternal antibodies in the emergence of severe disease as a result of fragmentation.

    Science.gov (United States)

    Fouchet, David; Marchandeau, Stéphane; Bahi-Jaber, Nargès; Pontier, Dominique

    2007-06-22

    Population fragmentation is a major problem for the conservation of mammalian species. Since the spread of an infectious disease is related to the intensity of contacts between individuals, fragmentation destabilizes the way the parasites circulate in their host population. Recently, Zinkernagel has proposed that a reduction in the frequency of infections by a parasite could lead to the emergence of severe forms of the disease, previously avoided because the disease was contracted early in life and attenuated by maternal antibodies. However, it is still unclear whether this change in disease expression increases the global mortality it induces because the disease becomes more severe and also less frequent. Here, we use a mathematical model to link population fragmentation with the hypothesis of Zinkernagel. Firstly, we show that there is a change in the severity of the disease during the fragmentation process, especially at a local scale, suggesting that host population fragmentation could be a widespread mechanism of disease emergence. Secondly, we show that the emergence of the severe form of the disease can lead to a significant increase in its induced mortality. Finally, we determine the types of interactions for which the fragmentation of the host population could be the most dangerous.

  18. Supply-Chain Optimization Template

    Science.gov (United States)

    Quiett, William F.; Sealing, Scott L.

    2009-01-01

    The Supply-Chain Optimization Template (SCOT) is an instructional guide for identifying, evaluating, and optimizing (including re-engineering) aerospace- oriented supply chains. The SCOT was derived from the Supply Chain Council s Supply-Chain Operations Reference (SCC SCOR) Model, which is more generic and more oriented toward achieving a competitive advantage in business.

  19. Essentials of supply chain management

    CERN Document Server

    Hugos, Michael H

    2011-01-01

    The latest thinking, strategies, developments, and technologies to stay current in supply chain management Presenting the core concepts and techniques of supply chain management in a clear, concise and easily readable style, the Third Edition of Essentials of Supply Chain Management outlines the most crucial tenets and concepts of supply chain management.

  20. Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker

    Energy Technology Data Exchange (ETDEWEB)

    Vernon, Robert [Hospital for Sick Children, Program in Molecular Structure and Function (Canada); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Baker, David [University of Washington, Department of Biochemistry (United States); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Department Chemie, Biomolecular NMR and Munich Center for Integrated Protein Science (Germany)

    2013-10-15

    A new fragment picker has been developed for CS-Rosetta that combines beneficial features of the original fragment picker, MFR, used with CS-Rosetta, and the fragment picker, NNMake, that was used for purely sequence based fragment selection in the context of ROSETTA de-novo structure prediction. Additionally, the new fragment picker has reduced sensitivity to outliers and other difficult to match data points rendering the protocol more robust and less likely to introduce bias towards wrong conformations in cases where data is bad, missing or inconclusive. The fragment picker protocol gives significant improvements on 6 of 23 CS-Rosetta targets. An independent benchmark on 39 protein targets, whose NMR data sets were published only after protocol optimization had been finished, also show significantly improved performance for the new fragment picker (van der Schot et al. in J Biomol NMR, 2013)

  1. Wildlife conservation on farmland

    National Research Council Canada - National Science Library

    Macdonald, David W; Feber, R. (Ruth)

    2015-01-01

    ...: Integrates more than 30 years of research by the Wildlife Conservation Research Unit at Oxford to reveal how agricultural systems and wildlife interact, presenting examples from scales varying...

  2. Continuous supply chain collaboration: Road to achieve operational excellence

    Directory of Open Access Journals (Sweden)

    N. Senthil Kumar

    2011-04-01

    Full Text Available Supply chain management (SCM is becoming critical as firms recognize that competition is shifting from company versus company to supply chain versus supply chain. In the present competitive scenario, the fierce competition has driven most companies to seek for means of enhancing performance beyond their four wall boundaries. The firm’s ability in collaborating with its upstream and downstream partners determines its success in attaining better performance with supply chain collaboration; a firm is able to serve fragmented markets in which end customers require more product varieties and availability with shorter product life cycle and, at the same time, lower supply chain costs. This paper introduces the framework of continuous supply chain collaboration (CSCC, which extends the traditional frame of reference in strategic sourcing from a supplier centric to a supply-chain-scope as continuous improvement efforts to enhance the customer satisfaction. CSCC practices are rather exceptional, yet CSCC is believed to be the single most comprehensive framework for attaining operational excellence.

  3. Dual Fragment Impact of PBX Charges

    Science.gov (United States)

    Haskins, Peter; Briggs, Richard; Leeming, David; White, Nathan; Cheese, Philip; DE&S MoD UK Team; Ordnance Test Solutions Ltd Team

    2017-06-01

    Fragment impact can pose a significant hazard to many systems containing explosives or propellants. Testing for this threat is most commonly carried out using a single fragment. However, it can be argued that an initial fragment strike (or strikes) could sensitise the energetic material to subsequent impacts, which may then lead to a more violent reaction than would have been predicted based upon single fragment studies. To explore this potential hazard we have developed the capability to launch 2 fragments from the same gun at a range of velocities, and achieve impacts on an acceptor charge with good control over the spatial and temporal separation of the strikes. In this paper we will describe in detail the experimental techniques we have used, both to achieve the dual fragment launch and observe the acceptor charge response. In addition, we will describe the results obtained against PBX filled explosive targets; discuss the mechanisms controlling the target response and their significance for vulnerability assessment. Results of these tests have clearly indicated the potential for detonation upon the second strike, at velocities well below those needed for shock initiation by a single fragment.

  4. On Disciplinary Fragmentation and Scientific Progress

    Science.gov (United States)

    Balietti, Stefano; Mäs, Michael; Helbing, Dirk

    2015-01-01

    Why are some scientific disciplines, such as sociology and psychology, more fragmented into conflicting schools of thought than other fields, such as physics and biology? Furthermore, why does high fragmentation tend to coincide with limited scientific progress? We analyzed a formal model where scientists seek to identify the correct answer to a research question. Each scientist is influenced by three forces: (i) signals received from the correct answer to the question; (ii) peer influence; and (iii) noise. We observed the emergence of different macroscopic patterns of collective exploration, and studied how the three forces affect the degree to which disciplines fall apart into divergent fragments, or so-called “schools of thought”. We conducted two simulation experiments where we tested (A) whether the three forces foster or hamper progress, and (B) whether disciplinary fragmentation causally affects scientific progress and vice versa. We found that fragmentation critically limits scientific progress. Strikingly, there is no effect in the opposite causal direction. What is more, our results shows that at the heart of the mechanisms driving scientific progress we find (i) social interactions, and (ii) peer disagreement. In fact, fragmentation is increased and progress limited if the simulated scientists are open to influence only by peers with very similar views, or when within-school diversity is lost. Finally, disciplines where the scientists received strong signals from the correct answer were less fragmented and experienced faster progress. We discuss model’s implications for the design of social institutions fostering interdisciplinarity and participation in science. PMID:25790025

  5. Identification of beef using restriction fragment length polymorphism–

    Directory of Open Access Journals (Sweden)

    R. A. Al-Sanjary

    2009-01-01

    Full Text Available To differentiate the beef from other types of meat consumed by human, DNA markers based on polymerase chain reaction restriction fragment length polymorphism technique is performed by using universal primers designed on mitochondrial cytochrome b gene to obtain amplified band 359 bp, then digested with some of restriction enzymes like Tru91, RsaI, Hinf I, Hae III, Alu I, Taq I, Mob I. The result revealed that, the Hinf I enzyme produce three bands 198, 117, 44 bp and the Hae III enzyme revealed two band 285, 74 bp, the Alu I enzyme also produced two band but the molecular weight are 190, 169 bp. The other enzymes did not reveal any digestion of the amplified bands and this result is a characteristic unique to beef compared with other types of meat when using same enzymes.

  6. Neutralisation and binding of VHS virus by monovalent antibody fragments

    DEFF Research Database (Denmark)

    Cupit, P.M.; Lorenzen, Niels; Strachan, G.

    2001-01-01

    We have previously reported the cloning and characterisation of the heavy and light chain variable domain genes encoding three monoclonal antibodies (Mabs) that bind viral haemorrhagic septicaemia virus (VHSV). Two of these antibodies, 3F1H10 and 3F1A2 both neutralised the virus though 3F1A2...... appeared to recognise a broader range of virus isolates. The variable domains of these two antibodies differ by only four residues (Lorenzen et al., 2000a. Fish Shellfish Immunol. 10, 129-142). To further study the mechanism of neutralisation, Fab fragments as well as a series of recombinant bacterial...... by BIAcore analysis and found to correlate with the capacity of each molecule to neutralise DK-F1. These investigations, together with computer assisted molecular analysis of the theoretical influence of each mutation on antigen binding, led to the identification of a single mutation at position 35a...

  7. Microsatellite analysis of the natterjack toad ( Bufo calamita ) in Denmark: populations are islands in a fragmented landscape

    DEFF Research Database (Denmark)

    Allentoft, Morten E.; Siegismund, Hans Redlef; Briggs, Lars

    2009-01-01

    The European natterjack toad (Bufo calamita) has declined rapidly in recent years, primarily due to loss of habitat, and in Denmark it is estimated that 50% of the isolated populations are lost each decade. To efficiently manage and conserve this species and its genetic diversity, knowledge...... in a highly fragmented gene pool. Future conservation management of this species is discussed in light of these results....

  8. The use of fynbos fragments by birds: Stepping-stone habitats and resource refugia

    Directory of Open Access Journals (Sweden)

    Rory N. Sandberg

    2016-03-01

    Full Text Available Fynbos habitats are threatened by fragmentation through land use and anthropogenic changes in fire regimes, leading to a loss of suitable habitat for birds. We investigated the response of fynbos-typical avifauna to fragmentation and postfire vegetation age in order to better understand the consequences of these processes for bird communities. Vegetation composition and bird inventory data were collected along wandering transects in three South Outeniqua Sandstone Fynbos habitat configurations: fragmented patches (associated with anthropogenically driven habitat loss < 150 years ago, naturally isolated fynbos islands (formed through climate-driven forest expansion in the Holocene and extensive areas of relatively pristine habitat known as ‘mainland’. The latter configurations served as references against which to investigate bird and vegetation responses to more recent habitat fragmentation. Linear regressions were used to compare the relationships of a number of bird and plant species to areas between each habitat configuration. Bird attribute frequency data were compared between habitat configurations using chi-square tests. Birds and plants showed significant species–area relationships in natural island and mainland sites, but no such relationship occurred in artificial fragments for birds, where the surrounding anthropogenic land uses are likely to have contributed generalist or colonist species. Avifaunal migratory groups were not affected by isolation distances of > 10 km in this study and their frequencies were the same across the three habitat configurations. Certain feeding guilds did, however, respond to postfire vegetation age, with nectarivore species twice as likely to occur in oldgrowth mainland fynbos. Fragmentation can alter fire disturbance regimes, which in turn alter the availability of resources in a habitat, so the impacts of fragmentation on birds are probably indirect through changes in the vegetation component.Conservation

  9. Strategic conservation planning for the Eastern North Carolina/Southeastern Virginia Strategic Habitat Conservation Team

    Science.gov (United States)

    Alexander-Vaughn, Louise B.; Collazo, Jaime A.; Drew, C. Ashton

    2014-01-01

    The Eastern North Carolina/Southeastern Virginia Strategic Habitat Conservation Team (ENCSEVA) is a partnership among local federal agencies and programs with a mission to apply Strategic Habitat Conservation to accomplish priority landscape-level conservation within its geographic region. ENCSEVA seeks to further landscape-scale conservation through collaboration with local partners. To accomplish this mission, ENCSEVA is developing a comprehensive Strategic Habitat Conservation Plan (Plan) to provide guidance for its members, partners, and collaborators by establishing mutual conservation goals, objectives, strategies, and metrics to gauge the success of conservation efforts. Identifying common goals allows the ENCSEVA team to develop strategies that leverage joint resources and are more likely to achieve desired impacts across the landscape. The Plan will also provide an approach for ENCSEVA to meet applied research needs (identify knowledge gaps), foster adaptive management principles, identify conservation priorities, prioritize threats (including potential impacts of climate change), and identify the required capacity to implement strategies to create more resilient landscapes. ENCSEVA seeks to support the overarching goals of the South Atlantic Landscape Conservation Cooperative (SALCC) and to provide scientific and technical support for conservation at landscape scales as well as inform the management of natural resources in response to shifts in climate, habitat fragmentation and loss, and other landscape-level challenges (South Atlantic LCC 2012). The ENCSEVA ecoregion encompasses the northern third of the SALCC geography and offers a unique opportunity to apply landscape conservation at multiple scales through the guidance of local conservation and natural resource management efforts and by reporting metrics that reflect the effectiveness of those efforts (Figure 1). The Environmental Decision Analysis Team, housed within the North Carolina Cooperative

  10. Protonating polymer oligomers in the gas phase to change fragmentation pathways.

    Science.gov (United States)

    Alhazmi, Abdulrahman M; Mayer, Paul M

    2009-01-01

    Ionization of polymers in mass spectrometry is usually achieved by forming metal ion adducts. The metal ion has been shown by Wesdemiotis to often play a spectator role in the collision-induced dissociation (CID) chemistry of these species, wherein they fragment according to a free-radical mechanism similar to that found in their pyrolysis. The result is a predominance of low-mass ions in the CID mass spectrum. We have changed this behavior by generating protonated oligomers in the gas phase by first forming proton-bound complexes of the oligomers with amino acids or peptides by electrospray ionization. These complexes dissociate first by loss of the amino acid/peptide to form protonated oligomers, which then undergo a unique fragmentation chemistry. In this article we discuss the results for poly(methyl methacrylate) (PMMA) and poly(butyl acrylate) (PBA). Initially, protonated PMMA and PBA lose methanol and butanol, respectively, from the side chains of the respective monomers. The resulting PMMA-derived ion then undergoes a series of neutral losses corresponding to 32 and 28 Da, methanol and carbon monoxide. This continues as collision energy increases until a final, carbon-rich backbone ion is formed, which then undergoes a classic hydrocarbon fragmentation pattern. The PBA-derived ions are proposed to fragment by the loss of butylether molecules to form anhydride rings along the oligomer chain. The number of ether molecules lost corresponded to half the number of available side chains in the oligomer. The resulting poly-anhydride ion dissociates by small molecule loss. Mechanisms have been suggested for the fragmentation chemistry of these two classes of oligomers.

  11. HETC-3STEP included fragmentation process

    Energy Technology Data Exchange (ETDEWEB)

    Shigyo, Nobuhiro; Iga, Kiminori; Ishibashi, Kenji [Kyushu Univ., Fukuoka (Japan). Faculty of Engineering

    1997-03-01

    High Energy Transport Code (HETC) based on the cascade-evaporation model is modified to calculate the fragmentation cross section. For the cascade process, nucleon-nucleon cross sections are used for collision computation; effective in-medium-corrected cross sections are adopted instead of the original free-nucleon collision. The exciton model is adopted for improvement of backward nucleon-emission cross section for low-energy nucleon-incident events. The fragmentation reaction is incorporated into the original HETC as a subroutine set by the use of the systematics of the reaction. The modified HETC (HETC-3STEP/FRG) reproduces experimental fragment yields to a reasonable degree. (author)

  12. Heart Rate Fragmentation: A Symbolic Dynamical Approach

    Directory of Open Access Journals (Sweden)

    Madalena D. Costa

    2017-11-01

    Full Text Available Background: We recently introduced the concept of heart rate fragmentation along with a set of metrics for its quantification. The term was coined to refer to an increase in the percentage of changes in heart rate acceleration sign, a dynamical marker of a type of anomalous variability. The effort was motivated by the observation that fragmentation, which is consistent with the breakdown of the neuroautonomic-electrophysiologic control system of the sino-atrial node, could confound traditional short-term analysis of heart rate variability.Objective: The objectives of this study were to: (1 introduce a symbolic dynamical approach to the problem of quantifying heart rate fragmentation; (2 evaluate how the distribution of the different dynamical patterns (“words” varied with the participants' age in a group of healthy subjects and patients with coronary artery disease (CAD; and (3 quantify the differences in the fragmentation patterns between the two sample populations.Methods: The symbolic dynamical method employed here was based on a ternary map of the increment NN interval time series and on the analysis of the relative frequency of symbolic sequences (words with a pre-defined set of features. We analyzed annotated, open-access Holter databases of healthy subjects and patients with CAD, provided by the University of Rochester Telemetric and Holter ECG Warehouse (THEW.Results: The degree of fragmentation was significantly higher in older individuals than in their younger counterparts. However, the fragmentation patterns were different in the two sample populations. In healthy subjects, older age was significantly associated with a higher percentage of transitions from acceleration/deceleration to zero acceleration and vice versa (termed “soft” inflection points. In patients with CAD, older age was also significantly associated with higher percentages of frank reversals in heart rate acceleration (transitions from acceleration to

  13. Heart Rate Fragmentation: A Symbolic Dynamical Approach.

    Science.gov (United States)

    Costa, Madalena D; Davis, Roger B; Goldberger, Ary L

    2017-01-01

    Background: We recently introduced the concept of heart rate fragmentation along with a set of metrics for its quantification. The term was coined to refer to an increase in the percentage of changes in heart rate acceleration sign, a dynamical marker of a type of anomalous variability. The effort was motivated by the observation that fragmentation, which is consistent with the breakdown of the neuroautonomic-electrophysiologic control system of the sino-atrial node, could confound traditional short-term analysis of heart rate variability. Objective: The objectives of this study were to: (1) introduce a symbolic dynamical approach to the problem of quantifying heart rate fragmentation; (2) evaluate how the distribution of the different dynamical patterns ("words") varied with the participants' age in a group of healthy subjects and patients with coronary artery disease (CAD); and (3) quantify the differences in the fragmentation patterns between the two sample populations. Methods: The symbolic dynamical method employed here was based on a ternary map of the increment NN interval time series and on the analysis of the relative frequency of symbolic sequences (words) with a pre-defined set of features. We analyzed annotated, open-access Holter databases of healthy subjects and patients with CAD, provided by the University of Rochester Telemetric and Holter ECG Warehouse (THEW). Results: The degree of fragmentation was significantly higher in older individuals than in their younger counterparts. However, the fragmentation patterns were different in the two sample populations. In healthy subjects, older age was significantly associated with a higher percentage of transitions from acceleration/deceleration to zero acceleration and vice versa (termed "soft" inflection points). In patients with CAD, older age was also significantly associated with higher percentages of frank reversals in heart rate acceleration (transitions from acceleration to deceleration and vice

  14. Composite Overwrap Fragmentation Observations, Concerns, and Recommendations

    Science.gov (United States)

    Bangham, Mike; Hovater, Mary

    2017-01-01

    A series of test activities has raised some concerns about the generation of orbital debris caused by failures of composite overwrapped pressure vessels (COPVs). These tests have indicated that a large number of composite fragments can be produced by either pressure burst failures or by high-speed impacts. A review of prior high-speed tests with COPV indicates that other tests have produced large numbers of composite fragments. As was the case with the test referenced here, the tests tended to produce a large number of small composite fragments with relatively low velocities induced by the impact and or gas expansion.

  15. Bone fragments a body can make

    Energy Technology Data Exchange (ETDEWEB)

    Stout, S.D.; Ross, L.M. Jr. (Department of Anthropology, University of Missouri, Columbia (USA))

    1991-05-01

    Data obtained from various analytical techniques applied to a number of small bone fragments recovered from a crime scene were used to provide evidence for the occurrence of a fatality. Microscopic and histomorphometric analyses confirmed that the fragments were from a human skull. X-ray microanalysis of darkened areas on the bone fragments revealed a chemical signature that matched the chemical signature of a shotgun pellet recovered at the scene of the crime. The above findings supported the deoxyribonucleic acid (DNA) fingerprint evidence which, along with other evidence, was used to convict a man for the murder of his wife, even though her body was never recovered.

  16. The late effect of grenade fragments.

    Science.gov (United States)

    Symonds, R P; Mackay, C; Morley, P

    1985-06-01

    Following the explosion of a grenade or shell, the victim may be peppered with literally hundreds of pieces of metal. Troublesome fragments which perforate a major viscus may be removed but others are often left behind, as it is felt (usually correctly) that these fragments will cause no harm. We describe a case in which a grenade fragment received 16 years previously pierced the large bowel. A psoas abscess developed which was located by ultrasound. Pus was aspirated under ultrasound control and the lesion was successfully treated by antibiotics.

  17. Extraction of 16th Century Calender Fragments

    DEFF Research Database (Denmark)

    Holck, Jakob Povl; Etheridge, Christian

    at the Cultural Heritage & Archaeometric Research Team, SDU. Upon finding medieval manuscript fragments in the university library’s special collections, scholars at the Centre for Medieval Literature are consulted. In most cases, digital pictures of the finds will circulate in the international community...... of medieval scholars. Thousands of 16th and 17th Century books are stored in the University Library of Southern Denmark. One out of five of these books is expected to contain medieval manuscript fragments or fragments of rare prints, e.g. incunabula....

  18. Global Supply Chain Management

    National Research Council Canada - National Science Library

    Mary Jo Lamberti; Mary Costello; Kenneth Getz

    2012-01-01

    ... clinical supplies will be needed. Some clinical supply managers have been using just-in-time or on-demand packaging and labeling2 or regional depots to address changes in the clinical supply chain strategy or forecasting during a trial...

  19. Exploration Supply Chain Simulation

    Science.gov (United States)

    2008-01-01

    The Exploration Supply Chain Simulation project was chartered by the NASA Exploration Systems Mission Directorate to develop a software tool, with proper data, to quantitatively analyze supply chains for future program planning. This tool is a discrete-event simulation that uses the basic supply chain concepts of planning, sourcing, making, delivering, and returning. This supply chain perspective is combined with other discrete or continuous simulation factors. Discrete resource events (such as launch or delivery reviews) are represented as organizational functional units. Continuous resources (such as civil service or contractor program functions) are defined as enabling functional units. Concepts of fixed and variable costs are included in the model to allow the discrete events to interact with cost calculations. The definition file is intrinsic to the model, but a blank start can be initiated at any time. The current definition file is an Orion Ares I crew launch vehicle. Parameters stretch from Kennedy Space Center across and into other program entities (Michaud Assembly Facility, Aliant Techsystems, Stennis Space Center, Johnson Space Center, etc.) though these will only gain detail as the file continues to evolve. The Orion Ares I file definition in the tool continues to evolve, and analysis from this tool is expected in 2008. This is the first application of such business-driven modeling to a NASA/government-- aerospace contractor endeavor.

  20. Cryochemical chain reactions

    Science.gov (United States)

    Barkalov, I. M.; Kiryukhin, D. P.

    The possibility of a chemical reaction near absolute zero has appeared doubtful since the beginning of the 1970s. The existing ideas must be revised after the radiation polymerization of formaldehyde at 4.2 K has been observed. In glassy systems, we have examined chain processes that occur under sharp (by five to six orders) changes in molecular mobility of the medium in the region of matrix devitrification. Quite unusual mechano-energetic chains of chemical conversion arise in the studied systems submerged in liquid helium. The chemical transformation initiated by local brittle fracture travels over the sample as an autowave. A series of experimental and theoretical investigations devoted to this interesting phenomenon are described. There is no generalization in this new region of chemistry up to this time. Many journal articles and reviews have been previously published only in Russian. The cycles of investigations of chain cryochemical reactions are the subject of this review. We hope that the investigation of the extraordinary peculiarities of chain cryochemical reactions should produce new ideas in chemical theory and industry.