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Sample records for bee structure molecular

  1. Protein Structure Prediction Using Bee Colony Optimization Metaheuristic

    DEFF Research Database (Denmark)

    Fonseca, Rasmus; Paluszewski, Martin; Winter, Pawel

    2010-01-01

    Predicting the native structure of proteins is one of the most challenging problems in molecular biology. The goal is to determine the three-dimensional struc- ture from the one-dimensional amino acid sequence. De novo prediction algorithms seek to do this by developing a representation of the...... proteins structure, an energy potential and some optimization algorithm that ¿nds the structure with minimal energy. Bee Colony Optimization (BCO) is a relatively new approach to solving opti- mization problems based on the foraging behaviour of bees. Several variants of BCO have been suggested in the...

  2. Social molecular pathways and the evolution of bee societies

    OpenAIRE

    Bloch, Guy; Grozinger, Christina M

    2011-01-01

    Bees provide an excellent model with which to study the neuronal and molecular modifications associated with the evolution of sociality because relatively closely related species differ profoundly in social behaviour, from solitary to highly social. The recent development of powerful genomic tools and resources has set the stage for studying the social behaviour of bees in molecular terms. We review ‘ground plan’ and ‘genetic toolkit’ models which hypothesize that discrete pathways or sets of...

  3. Population structure of honey bees in the Carpathian Basin (Hungary) confirms introgression from surrounding subspecies.

    Science.gov (United States)

    Péntek-Zakar, Erika; Oleksa, Andrzej; Borowik, Tomasz; Kusza, Szilvia

    2015-12-01

    Carniolan honey bees (Apis mellifera carnica) are considered as an indigenous subspecies in Hungary adapted to most of the ecological and climatic conditions in this area. However, during the last decades Hungarian beekeepers have recognized morphological signs of the Italian honey bee (Apis mellifera ligustica). As the natural distribution of the honey bee subspecies can be affected by the importation of honey bee queens or by natural gene flow, we aimed at determining the genetic structure and characteristics of the local honey bee population using molecular markers. All together, 48 Hungarian and 84 foreign (Italian, Polish, Spanish, Liberian) pupae and/or workers were used for mitochondrial DNA analysis. Additionally, 53 sequences corresponding to 10 subspecies and the Buckfast hybrid were downloaded from GenBank. For the nuclear analysis, 236 Hungarian and 106 foreign honey bees were genotyped using nine microsatellites. Heterozygosity values, population-specific alleles, FST values, principal coordinate analysis, assignment tests, structure analysis, and dendrograms were calculated. Haplotype and nucleotide diversity values showed moderate values. We found that one haplotype (H9) was dominant in Hungary. The presence of the black honey bee (Apis mellifera mellifera) was negligible, but a few individuals resembling other subspecies were identified. We proved that the Hungarian honey bee population is nearly homogeneous but also demonstrated introgression from the foreign subspecies. Both mitochondrial DNA and microsatellite analyses corroborated the observations of the beekeepers. Molecular analyses suggested that Carniolan honey bee in Hungary is slightly affected by Italian and black honey bee introgression. Genetic differences were detected between Polish and Hungarian Carniolan honey bee populations, suggesting the existence of at least two different gene pools within A. m. carnica. PMID:27069597

  4. Molecular biology of the honey bee

    DEFF Research Database (Denmark)

    Munk, Kathe

    While hoeneybees represent model organisms with complex social structures within populations, a comprehensive understanding of developmental regulation in relation to sexual development as well as cast determination still remains. Despite decades of research explanations on mechanistics underlyin...... functional molecular biological techniques to advance current interpretations of heneybee development...

  5. The four hexamerin genes in the honey bee: structure, molecular evolution and function deduced from expression patterns in queens, workers and drones

    Directory of Open Access Journals (Sweden)

    Martins Juliana R

    2010-03-01

    Full Text Available Abstract Background Hexamerins are hemocyanin-derived proteins that have lost the ability to bind copper ions and transport oxygen; instead, they became storage proteins. The current study aimed to broaden our knowledge on the hexamerin genes found in the honey bee genome by exploring their structural characteristics, expression profiles, evolution, and functions in the life cycle of workers, drones and queens. Results The hexamerin genes of the honey bee (hex 70a, hex 70b, hex 70c and hex 110 diverge considerably in structure, so that the overall amino acid identity shared among their deduced protein subunits varies from 30 to 42%. Bioinformatics search for motifs in the respective upstream control regions (UCRs revealed six overrepresented motifs including a potential binding site for Ultraspiracle (Usp, a target of juvenile hormone (JH. The expression of these genes was induced by topical application of JH on worker larvae. The four genes are highly transcribed by the larval fat body, although with significant differences in transcript levels, but only hex 110 and hex 70a are re-induced in the adult fat body in a caste- and sex-specific fashion, workers showing the highest expression. Transcripts for hex 110, hex 70a and hex70b were detected in developing ovaries and testes, and hex 110 was highly transcribed in the ovaries of egg-laying queens. A phylogenetic analysis revealed that HEX 110 is located at the most basal position among the holometabola hexamerins, and like HEX 70a and HEX 70c, it shares potential orthology relationship with hexamerins from other hymenopteran species. Conclusions Striking differences were found in the structure and developmental expression of the four hexamerin genes in the honey bee. The presence of a potential binding site for Usp in the respective 5' UCRs, and the results of experiments on JH level manipulation in vivo support the hypothesis of regulation by JH. Transcript levels and patterns in the fat body

  6. Structural Physics of Bee Honeycomb

    Science.gov (United States)

    Kaatz, Forrest; Bultheel, Adhemar; Egami, Takeshi

    2008-03-01

    Honeybee combs have aroused interest in the ability of honeybees to form regular hexagonal geometric constructs since ancient times. Here we use a real space technique based on the pair distribution function (PDF) and radial distribution function (RDF), and a reciprocal space method utilizing the Debye-Waller Factor (DWF) to quantify the order for a range of honeycombs made by Apis mellifera. The PDFs and RDFs are fit with a series of Gaussian curves. We characterize the order in the honeycomb using a real space order parameter, OP3, to describe the order in the combs and a two-dimensional Fourier transform from which a Debye-Waller order parameter, u, is derived. Both OP3 and u take values from [0, 1] where the value one represents perfect order. The analyzed combs have values of OP3 from 0.33 to 0.60 and values of u from 0.83 to 0.98. RDF fits of honeycomb histograms show that naturally made comb can be crystalline in a 2D ordered structural sense, yet is more `liquid-like' than cells made on `foundation' wax. We show that with the assistance of man-made foundation wax, honeybees can manufacture highly ordered arrays of hexagonal cells.

  7. Molecular Effects of Neonicotinoids in Honey Bees (Apis mellifera).

    Science.gov (United States)

    Christen, Verena; Mittner, Fabian; Fent, Karl

    2016-04-01

    Neonicotinoids are implicated in the decline of bee populations. As agonists of nicotinic acetylcholine receptors, they disturb acetylcholine receptor signaling leading to neurotoxicity. Several behavioral studies showed the link between neonicotinoid exposure and adverse effects on foraging activity and reproduction. However, molecular effects underlying these effects are poorly understood. Here we elucidated molecular effects at environmental realistic levels of three neonicotinoids and nicotine, and compared laboratory studies to field exposures with acetamiprid. We assessed transcriptional alterations of eight selected genes in caged honey bees exposed to different concentrations of the neonicotinoids acetamiprid, clothianidin, imidacloporid, and thiamethoxam, as well as nicotine. We determined transcripts of several targets, including nicotinic acetylcholine receptor α 1 and α 2 subunit, the multifunctional gene vitellogenin, immune system genes apidaecin and defensin-1, stress-related gene catalase and two genes linked to memory formation, pka and creb. Vitellogenin showed a strong increase upon neonicotinoid exposures in the laboratory and field, while creb and pka transcripts were down-regulated. The induction of vitellogenin suggests adverse effects on foraging activity, whereas creb and pka down-regulation may be implicated in decreased long-term memory formation. Transcriptional alterations occurred at environmental concentrations and provide an explanation for the molecular basis of observed adverse effects of neonicotinoids to bees. PMID:26990785

  8. Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

    Directory of Open Access Journals (Sweden)

    Flávio de Oliveira Francisco

    2013-01-01

    Full Text Available Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.

  9. Molecular diagnosis and characterization of honey bee pathogens

    OpenAIRE

    Forsgren, Eva

    2009-01-01

    Bees are crucial for maintaining biodiversity by pollination of numerous plant species. The European honey bee, Apis mellifera, is of great importance not only for the honey they produce, but also as vital pollinators of agricultural and horticultural crops. The economical value of pollination has been estimated to be several billion dollars, and pollinator declines are a global biodiversity threat. Hence, honey bee health has great impact on the economy, food production and biodiversity worl...

  10. Molecular identification of Amazonian stingless bees using polymerase chain reaction single-strand conformation polymorphism.

    Science.gov (United States)

    Souza, M T; Carvalho-Zilse, G A

    2014-01-01

    In countries containing a mega diversity of wildlife, such as Brazil, identifying and characterizing biological diversity is a continuous process for the scientific community, even in face of technological and scientific advances. This activity demands initiatives for the taxonomic identification of highly diverse groups, such as stingless bees, including molecular analysis strategies. This type of bee is distributed in all of the Brazilian states, with the highest species diversity being found in the State of Amazônia. However, the estimated number of species diverges among taxonomists. These bees are considered the main pollinators in the Amazon rainforest, in which they obtain food and shelter; however, their persistence is constantly threatened by deforestation pressure. Hence, it is important to classify the number and abundance of bee specie, to measure their decline and implement meaningful, priority conservation strategies. This study aims to maximize the implementation of more direct, economic and successful techniques for the taxonomic identification of stingless bees. Specifically, the genes 16S rRNA and COI from mitochondrial DNA were used as molecular markers to differentiate 9 species of Amazonian stingless bees based on DNA polymorphism, using the polymerase chain reaction-single-strand conformation polymorphism technique. We registered different, exclusive SSCP haplotypes for both genes in all species analyzed. These results demonstrate that SSCP is a simple and cost-effective technique that is applicable to the molecular identification of stingless bee species. PMID:25117306

  11. Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations.

    Science.gov (United States)

    Schiffmann, Christoph; Sebastiani, Daniel

    2011-05-10

    We present an algorithmic extension of a numerical optimization scheme for analytic capping potentials for use in mixed quantum-classical (quantum mechanical/molecular mechanical, QM/MM) ab initio calculations. Our goal is to minimize bond-cleavage-induced perturbations in the electronic structure, measured by means of a suitable penalty functional. The optimization algorithm-a variant of the artificial bee colony (ABC) algorithm, which relies on swarm intelligence-couples deterministic (downhill gradient) and stochastic elements to avoid local minimum trapping. The ABC algorithm outperforms the conventional downhill gradient approach, if the penalty hypersurface exhibits wiggles that prevent a straight minimization pathway. We characterize the optimized capping potentials by computing NMR chemical shifts. This approach will increase the accuracy of QM/MM calculations of complex biomolecules. PMID:26610125

  12. Molecular and phylogenetic characterization of honey bee viruses, Nosema microsporidia, protozoan parasites, and parasitic mites in China

    OpenAIRE

    YANG, BU; Peng, Guangda; Li, Tianbang; Kadowaki, Tatsuhiko

    2013-01-01

    China has the largest number of managed honey bee colonies, which produce the highest quantity of honey and royal jelly in the world; however, the presence of honey bee pathogens and parasites has never been rigorously identified in Chinese apiaries. We thus conducted a molecular survey of honey bee RNA viruses, Nosema microsporidia, protozoan parasites, and tracheal mites associated with nonnative Apis mellifera ligustica and native Apis cerana cerana colonies in China. We found the presence...

  13. Molecular Biological Study of Anti-cancer Effects of Bee Venom Aqua-acupuncture

    Directory of Open Access Journals (Sweden)

    Park Chan-Yol

    2000-07-01

    Full Text Available To study anti-cancer effect and molecular biological mechanism of bee venom for aqua-acupuncture, the effects of bee venom on cell viability and apoptosis were analyzed using MTT assay, tryphan blue assay, [3H]thymidine release assay, flow cytometric analysis, and activity of caspase-3 protease activity assay. To explore whether anti-cancer effects of bee venom are associated with the transcriptional control of gene expression, quantitative RT-PCR analysis of apoptosis-related genes was performed. The obtained results are summarized as follows: 1. The MTT assay demonstrated that cell viability was decreased by bee venom in a dose-dependant manner. 2. Significant induction of apoptosis was identified using tryphan blue assay, [3H]thymidine release assay, and flow cytometric analysis of sub G1 fraction. 3. In analysis of caspase-3 protease activity, the activity had increased significantly, in a dose-dependant manner. 4. Quantitative RT-PCR analysis of the apoptosis-related genes showed that Bcl-2 and Bcl-XL were down-regulated whereas Bax was up-regulated by bee venom treatment.

  14. Polyphenols from Bee Pollen: Structure, Absorption, Metabolism and Biological Activity

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    Anna Rzepecka-Stojko

    2015-12-01

    Full Text Available Bee pollen constitutes a natural source of antioxidants such as phenolic acids and flavonoids, which are responsible for its biological activity. Research has indicated the correlation between dietary polyphenols and cardioprotective, hepatoprotective, anti-inflammatory, antibacterial, anticancerogenic, immunostimulating, antianaemic effects, as well as their beneficial influence on osseous tissue. The beneficial effects of bee pollen on health result from the presence of phenolic acids and flavonoids which possess anti-inflammatory properties, phytosterol and linolenic acid which play an anticancerogenic role, and polysaccharides which stimulate immunological activity. Polyphenols are absorbed in the alimentary tract, metabolised by CYP450 enzymes, and excreted with urine and faeces. Flavonoids and phenolic acids are characterised by high antioxidative potential, which is closely related to their chemical structure. The high antioxidant potential of phenolic acids is due to the presence and location of hydroxyl groups, a carboxyl group in the immediate vicinity of ortho-diphenolic substituents, and the ethylene group between the phenyl ring and the carboxyl group. As regards flavonoids, essential structural elements are hydroxyl groups at the C5 and C7 positions in the A ring, and at the C3′ and C4′ positions in the B ring, and a hydroxyl group at the C3 position in the C ring. Furthermore, both, the double bond between C2 and C3, and a ketone group at the C4 position in the C ring enhance the antioxidative potential of these compounds. Polyphenols have an ideal chemical structure for scavenging free radicals and for creating chelates with metal ions, which makes them effective antioxidants in vivo.

  15. Molecular genetic analysis of Varroa destructor mites in brood, fallen injured mites and worker bee longevity in honey bees

    Science.gov (United States)

    Two important traits that contribute to honey bee (Apis mellifera) colony survival are resistance to Varroa destructor and longevity of worker bees. We investigated the relationship between a panel of single nucleotide polymorphism (SNP) markers and three phenotypic measurements of colonies: a) perc...

  16. Handling sticky resin by Stingless Bees: adhesive properties of surface structures.

    Science.gov (United States)

    Gastauer, Markus; Campos, Lucio A O; Wittmann, Dieter

    2013-09-01

    Many Stingless Bees (Hymenoptera: Meliponini) like Tetragonisca angustula collect resin to defend their nests against intruders like ants or Robber Bees. Small portions of resin are attached to intruders bodies and extremities causing their immobilization. It has been observed that resin is removed easily from the bee's mandible but adheres strongly to the intruder's cuticle. We tested the hypothesis that resin sticks lesser to the mandibles of Stingless Bees than to the surface of intruders due to special surface structures or adhesive properties of these structures. The surface structures of the mandible of T. angustula and the trochanter of Camponotus sericeiventris were studied by scanning electron microscopy. To measure adhesion properties, selected surfaces were fixed on a fine glass pin and withdrawn from a glass tip covered with resin. The deformation of the glass pin indicates adhesion forces operating between the resin and the selective surface. The absolute value of the forces is computed from the glass pin's stiffness. It has been shown that resin sticks more to the smooth mandible of the bee than to the structured trochanter of the ant. A new hypothesis to be tested says that the bees might lubricate their mandibles with nectar or honey to reduce the resin's adhesion temporarily. PMID:24068098

  17. Species diversity and community structure in trap-nesting bees in Southern Brazil

    OpenAIRE

    Luisa Tunes Buschini, Maria

    2006-01-01

    International audience The species diversity and community structure of trap-nesting bees in the Parque Municipal das Araucárias in Southern Brazil was studied during 2 years. Three different habitats (Araucaria forest, swamp and grassland) were investigated in terms of abundance, richness, diversity and similarity of bee communicites. A total of 120 nests of 11 species were collected. The largest abundance of individuals and species richness was found for the family Megachilidae. The most...

  18. Molecular and phylogenetic characterization of honey bee viruses, Nosema microsporidia, protozoan parasites, and parasitic mites in China.

    Science.gov (United States)

    Yang, Bu; Peng, Guangda; Li, Tianbang; Kadowaki, Tatsuhiko

    2013-02-01

    China has the largest number of managed honey bee colonies, which produce the highest quantity of honey and royal jelly in the world; however, the presence of honey bee pathogens and parasites has never been rigorously identified in Chinese apiaries. We thus conducted a molecular survey of honey bee RNA viruses, Nosema microsporidia, protozoan parasites, and tracheal mites associated with nonnative Apis mellifera ligustica and native Apis cerana cerana colonies in China. We found the presence of black queen cell virus (BQCV), chronic bee paralysis virus (CBPV), deformed wing virus (DWV), Israeli acute paralysis virus (IAPV), and sacbrood virus (SBV), but not that of acute bee paralysis virus (ABPV) or Kashmir bee virus (KBV). DWV was the most prevalent in the tested samples. Phylogenies of Chinese viral isolates demonstrated that genetically heterogeneous populations of BQCV, CBPV, DWV, and A. cerana-infecting SBV, and relatively homogenous populations of IAPV and A. meliifera-infecting new strain of SBV with single origins, are spread in Chinese apiaries. Similar to previous observations in many countries, Nosema ceranae, but not Nosema apis, was prevalent in the tested samples. Crithidia mellificae, but not Apicystis bombi was found in five samples, including one A. c. cerana colony, demonstrating that C. mellificae is capable of infecting multiple honey bee species. Based on kinetoplast-encoded cytochrome b sequences, the C. mellificae isolate from A. c. cerana represents a novel haplotype with 19 nucleotide differences from the Chinese and Japanese isolates from A. m. ligustica. This suggests that A. c. cerana is the native host for this specific haplotype. The tracheal mite, Acarapis woodi, was detected in one A. m. ligustica colony. Our results demonstrate that honey bee RNA viruses, N. ceranae, C. mellificae, and tracheal mites are present in Chinese apiaries, and some might be originated from native Asian honey bees. PMID:23467539

  19. Valency and molecular structure

    CERN Document Server

    Cartmell, E

    1977-01-01

    Valency and Molecular Structure, Fourth Edition provides a comprehensive historical background and experimental foundations of theories and methods relating to valency and molecular structures. In this edition, the chapter on Bohr theory has been removed while some sections, such as structures of crystalline solids, have been expanded. Details of structures have also been revised and extended using the best available values for bond lengths and bond angles. Recent developments are mostly noted in the chapter on complex compounds, while a new chapter has been added to serve as an introduction t

  20. A molecular phylogeny of the stingless bee genus Melipona (Hymenoptera: Apidae).

    Science.gov (United States)

    Ramírez, Santiago R; Nieh, James C; Quental, Tiago B; Roubik, David W; Imperatriz-Fonseca, Vera L; Pierce, Naomi E

    2010-08-01

    Stingless bees (Meliponini) constitute a diverse group of highly eusocial insects that occur throughout tropical regions around the world. The meliponine genus Melipona is restricted to the New World tropics and has over 50 described species. Melipona, like Apis, possesses the remarkable ability to use representational communication to indicate the location of foraging patches. Although Melipona has been the subject of numerous behavioral, ecological, and genetic studies, the evolutionary history of this genus remains largely unexplored. Here, we implement a multigene phylogenetic approach based on nuclear, mitochondrial, and ribosomal loci, coupled with molecular clock methods, to elucidate the phylogenetic relationships and antiquity of subgenera and species of Melipona. Our phylogenetic analysis resolves the relationship among subgenera and tends to agree with morphology-based classification hypotheses. Our molecular clock analysis indicates that the genus Melipona shared a most recent common ancestor at least approximately 14-17 million years (My) ago. These results provide the groundwork for future comparative analyses aimed at understanding the evolution of complex communication mechanisms in eusocial Apidae. PMID:20433931

  1. Bee poison

    Science.gov (United States)

    Bee poisoning is caused by a sting from a bee, wasp , or yellow jacket. This article is for ... Bee, wasp, and yellow jacket stings contain a substance called venom. Africanized bee colonies are very sensitive ...

  2. Molecular genetic analysis of tracheal mite resistance of colonies and individual honey bees

    Science.gov (United States)

    Honey bee resistance to the potentially damaging parasitic tracheal mite is known to be mediated by autogrooming. During autogrooming bees use their midlegs to remove migrating foundress mites, thereby reducing infestation rates in their trachea. We investigated the relationship between markers iden...

  3. First molecular detection of Chronic Bee Paralysis Virus (CBPV in Iran

    Directory of Open Access Journals (Sweden)

    Modirrousta, H.

    2015-12-01

    Full Text Available Among the viruses infecting honey bees, chronic bee paralysis virus (CBPV is known to induce significant losses in honey bee colonies. CBPV is an unclassified polymorphic single stranded RNA virus. Using RT-PCR, the virus infections in honey bees can be detected in a rapid and accurate manner. Bee samples were collected from 23 provinces of Iran, between July-September 2011 and 2012. A total of 160 apiaries were sampled and submitted for virus screening. RNA extraction and RT-PCR were performed with QIAGEN kits. The primers lead to a fragment of 315 bp. The PCR products were electrophoresed in a 1.2 % agarose gel. Following the RT-PCR reaction with the specific primers, out of the 160 apiaries examined, 12 (7.5 % were infected with CBPV. This is the first study of CBPV detection in Iranian apiaries. We identified CBPV in the collected samples from different geographic regions of Iran.

  4. Microsatellites for the inference of population structures in the Red Mason bee Osmia rufa (Hymenoptera, Megachilidae)

    OpenAIRE

    Neumann, Karsten; Seidelmann, Karsten

    2006-01-01

    Microsatellite loci were isolated from the solitary Red Mason bee (Osmia rufa) by an enrichment protocol for partial genomic libraries. Six polymorphic microsatellite loci were used for a first population structure survey including 9 continental European and one island population. Observed levels of genetic variability and heterozygosity proved to be moderate. There was no significant differentiation among continental O. rufa populations. Only the island population from Cyprus was clearly sep...

  5. Molecular Identification of Chronic Bee Paralysis Virus Infection in Apis mellifera Colonies in Japan

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    Tomomi Morimoto

    2012-06-01

    Full Text Available Chronic bee paralysis virus (CBPV infection causes chronic paralysis and loss of workers in honey bee colonies around the world. Although CBPV shows a worldwide distribution, it had not been molecularly detected in Japan. Our investigation of Apis mellifera and Apis cerana japonica colonies with RT-PCR has revealed CBPV infection in A. mellifera but not A. c. japonica colonies in Japan. The prevalence of CBPV is low compared with that of other viruses: deformed wing virus (DWV, black queen cell virus (BQCV, Israel acute paralysis virus (IAPV, and sac brood virus (SBV, previously reported in Japan. Because of its low prevalence (5.6% in A. mellifera colonies, the incidence of colony losses by CBPV infection must be sporadic in Japan. The presence of the (− strand RNA in dying workers suggests that CBPV infection and replication may contribute to their symptoms. Phylogenetic analysis demonstrates a geographic separation of Japanese isolates from European, Uruguayan, and mainland US isolates. The lack of major exchange of honey bees between Europe/mainland US and Japan for the recent 26 years (1985–2010 may have resulted in the geographic separation of Japanese CBPV isolates.

  6. The Antiquity and Evolutionary History of Social Behavior in Bees

    OpenAIRE

    Cardinal, Sophie; Danforth, Bryan N.

    2011-01-01

    A long-standing controversy in bee social evolution concerns whether highly eusocial behavior has evolved once or twice within the corbiculate Apidae. Corbiculate bees include the highly eusocial honey bees and stingless bees, the primitively eusocial bumble bees, and the predominantly solitary or communal orchid bees. Here we use a model-based approach to reconstruct the evolutionary history of eusociality and date the antiquity of eusocial behavior in apid bees, using a recent molecular phy...

  7. Genetic structure of the gentle Africanized honey bee population (gAHB) in Puerto Rico

    OpenAIRE

    Galindo-Cardona, Alberto; Acevedo-Gonzalez, Jenny P; Rivera-Marchand, Bert; Giray, Tugrul

    2013-01-01

    Background The Africanized honey bee is one of the most spectacular invasions in the Americas. African bees escaped from apiaries in Brazil in 1956, spread over Americas and by 1994 they were reported in Puerto Rico. In contrast to other places, the oceanic island conditions in Puerto Rico may mean a single introduction and different dynamics of the resident European and new-coming Africanized bees. To examine the genetic variation of honey bee feral populations and colonies from different lo...

  8. Effect of bee venom or proplis on molecular and parasitological aspects of Schistosoma mansoni infected mice.

    Science.gov (United States)

    Mohamed, Azza H; Hassab El-Nabi, Sobhy E; Bayomi, Asmaa E; Abdelaal, Ahmed A

    2016-06-01

    The present study was performed to elucidate the efficacy of Apis mellifera L bee venom (BV) or proplis (200 mg/kg orally for three consecutive days) on Schistosoma mansoni infected mice. The results recorded reduction in the total worm burden, numbers of immature eggs and the ova count in hepatic tissue in BV (sting or injection) or proplis treated groups as compared to the infected group. Histological examination illustrated a significant increase (P ≤ 0.05) in the diameter of hepatic granuloma in BV treated groups (272.78 and 266.9, respectively) and a significant decrease in proplis treated mice (229.35) compared with the infected group (260.67). Electrophoretic pattern of RNA showed a decrease in mean of maximal optical density in liver and intestine of S. mansoni infected mice treated with bee venom (sting or injection) as compared with infected group. Flow cytometry analyses of RNA or apoptotic percentage of worms recovered from BV sting (19 and 49 % respectively); BV injected (20.5 and 51.17 %, respectively) and proplis (35 and 23.93 %, respectively) groups were compared with S. mansoni infected group (37.87 and 39.21 %, respectively). It can be concluded that administration of bee venom or proplis are effective in case of S. mansoni infection. Although bee venom cause increase of granuloma diameter and this might be due to venom concentration and further studies are required to avoid such harmful effect. PMID:27413311

  9. Predicting honey bee sensitivity based on the conservation of the pesticide molecular initiating event

    Science.gov (United States)

    Concern surrounding the potential adverse impacts of pesticides to honey bee colonies has led to the need for rapid/cost efficient methods for aiding decision making relative to the protection of this important pollinator species. Neonicotinoids represent a class of pesticides th...

  10. Molecular Prevalence of Acarapis Mite Infestations in Honey Bees in Korea.

    Science.gov (United States)

    Ahn, Ah-Jin; Ahn, Kyu-Sung; Noh, Jin-Hyeong; Kim, Young-Ha; Yoo, Mi-Sun; Kang, Seung-Won; Yu, Do-Hyeon; Shin, Sung Shik

    2015-06-01

    Acarapis mites, including Acarapis woodi, Acarapis externus, and Acarapis dorsalis, are parasites of bees which can cause severe damage to the bee industry by destroying colonies and decreasing honey production. All 3 species are prevalent throughout many countries including UK, USA, Iran, Turkey, China, and Japan. Based on previous reports of Acarapis mites occurring in northeast Asia, including China and Japan, we investigated a survey of Acarapis mite infestations in honey bees in Korean apiaries. A total of 99 colonies of Apis mellifera were sampled from 5 provinces. The head and thorax of 20 bees from each colony were removed for DNA extraction. PCR assays were performed with 3 primer sets, including T, A, and K primers. Results indicated that 42.4% (42/99) of samples were Acarapis-positive by PCR assay which were sequenced to identify species. Each sequence showed 92.6-99.3% homology with reference sequences. Based on the homology, the number of colonies infected with A. dorsalis was 32 which showed the highest infection rate among the 3 species, while the number of colonies infected with A. externus and A. woodi was 9 and 1, respectively. However, none of the Acarapis mites were morphologically detected. This result could be explained that all apiaries in the survey used acaricides against bee mites such as Varroa destructor and Tropilaelaps clareae which also affect against Acarapis mites. Based on this study, it is highly probable that Acarapis mites as well as Varroa and Tropilaelaps could be prevalent in Korean apiaries. PMID:26174825

  11. [Effect of landscape change on the structure of the sting-less bee community (Hymenoptera: Apidae) in Meta, Colombia].

    Science.gov (United States)

    Nates-Parra, Guiomar; Palacios, Eliana; Parra-H, Alejandro

    2008-09-01

    Stingless bees represent one of the most diversified components of the natural Apoidea fauna of pollinators in the tropics. They use diverse kinds of substrates and inhabit varied habitats. Some species are typical for some natural either artificial place. The landscape alteration were this group of bees nests, has and important impact on the natural composition of its community structure, fact which is reflected in the nest density. We analyzed the structure composition of the stingless bees' community in three environments in the Colombian Ilanos piedmont, an important region that represents the transition between Andean ecosystems and a savannah that is seriously threatened by cattle practices. We made systematic samples in secondary forest, agro-ecosystems and urban areas, recording the presence of 204 nests from 11 genera (24 species). The nest density per landscape was heterogeneous and never higher than 16 nests/Ha. We observed two nesting patterns and an effect of sampling criterion on the measured biodiversity. PMID:19419046

  12. Paenilamicin: structure and biosynthesis of a hybrid nonribosomal peptide/polyketide antibiotic from the bee pathogen Paenibacillus larvae.

    Science.gov (United States)

    Müller, Sebastian; Garcia-Gonzalez, Eva; Mainz, Andi; Hertlein, Gillian; Heid, Nina C; Mösker, Eva; van den Elst, Hans; Overkleeft, Herman S; Genersch, Elke; Süssmuth, Roderich D

    2014-09-26

    The spore-forming bacterium Paenibacillus larvae is the causative agent of American Foulbrood (AFB), a fatal disease of honey bees that occurs worldwide. Previously, we identified a complex hybrid nonribosomal peptide/polyketide synthesis (NRPS/PKS) gene cluster in the genome of P. larvae. Herein, we present the isolation and structure elucidation of the antibacterial and antifungal products of this gene cluster, termed paenilamicins. The unique structures of the paenilamicins give deep insight into the underlying complex hybrid NRPS/PKS biosynthetic machinery. Bee larval co-infection assays reveal that the paenilamicins are employed by P. larvae in fighting ecological niche competitors and are not directly involved in killing the bee larvae. Their antibacterial and antifungal activities qualify the paenilamicins as attractive candidates for drug development. PMID:25080172

  13. Simulating a base population in honey bee for molecular genetic studies

    Directory of Open Access Journals (Sweden)

    Gupta Pooja

    2012-06-01

    Full Text Available Abstract Background Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding value estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has a distinct genetic and reproductive biology. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee. Results Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1 the position of markers on each chromosome, (2 allele frequency, (3 χ2 statistics for Hardy-Weinberg equilibrium, (4 a sorted list of markers with a minor allele frequency less than or equal to the input value, (5 average r2 values of linkage disequilibrium between all simulated marker loci pair for all generations and (6 average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. Conclusion We developed a software program that takes into account the genetic and reproductive biology specific to the honey bee

  14. Structural Examination of the Dufour's Gland of the Cavity-nesting Bees Osmia lignaria Say and Megachile rotundata (Fabricius) (Hymenoptera: Megachilidae)

    Science.gov (United States)

    The Dufour’s gland of two solitary cavity-nesting bees, Osmia lignaria and Megachile rotundata (Hymenoptera: Megachilidae), were examined with microscopy to determine the structure and arrangement of the gland as part of the sting apparatus. The Dufour’s glands of these two bee species are similar ...

  15. Dynamics and Communication Structures of Nectar Foraging in Honey Bees (Apis mellifera)

    OpenAIRE

    Thom, Corinna

    2002-01-01

    In this thesis, I examined honey bee nectar foraging with emphasis on the communication system. To document how a honey bee colony adjusts its daily nectar foraging effort, I observed a random sample of individually marked workers during the entire day, and then estimated the number and activity of all nectar foragers in the colony. The total number of active nectar foragers in a colony changed frequently between days. Foraging activity did not usually change between days. A honey bee colony ...

  16. Atomic and molecular structure

    International Nuclear Information System (INIS)

    This book is a textbook for an introductory course of atomic physics for students of chemistry. After an introduction to the mathematical and physical foundations the quantum mechanical theory of atoms is described starting from simple examples of quantum mechanics. Then the atomic structure and the chemical bending are extensively discussed. This book is also suited for physicists who are especially interested in the atomic structure and the theory of chemical reactions. (HSI)

  17. Molecular electronic-structure theory

    CERN Document Server

    Helgaker, Trygve; Olsen, Jeppe

    2014-01-01

    Ab initio quantum chemistry has emerged as an important tool in chemical research and is appliced to a wide variety of problems in chemistry and molecular physics. Recent developments of computational methods have enabled previously intractable chemical problems to be solved using rigorous quantum-mechanical methods. This is the first comprehensive, up-to-date and technical work to cover all the important aspects of modern molecular electronic-structure theory. Topics covered in the book include: * Second quantization with spin adaptation * Gaussian basis sets and molecular-integral evaluati

  18. Effect of linkage disequilibrium on inferences of population structure and introgression of iberian and black honey bees

    OpenAIRE

    Chavez-Galarza, Julio; Henriques, Dora; Kryger, Per; De La Rúa, Pilar; Johnston, J. Spencer; Rufino, José; Pinto, M. Alice

    2012-01-01

    Identification of population structure, a primary goal in population genetics, is easily performed because there is a number of methods available, implemented by user-friendly software packages. However, the user must be cautious when inferring population structure because spurious results may be obtained when there is strong linkage disequilibrium. With recent development of high-density SNPs we have now more power to interrogate the honey bee genome. However, the greater the number of loci ...

  19. Prediction of molecular crystal structures

    CERN Document Server

    Beyer, T

    2001-01-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of parac...

  20. Ordered structures of molecular bottlebrushes

    NARCIS (Netherlands)

    ten Brinke, G.; Ikkala, O.

    1997-01-01

    In this review 'molecular bottlebrushes' are flexible polymers densely loaded with equally flexible side chains. Interest in these structures arises from the possibility of lyotropic behaviour in dilute solution in a good solvent, as well as the possibility, of highly, ordered microphase-separated s

  1. Ordered Structures of Molecular Bottlebrushes

    NARCIS (Netherlands)

    Brinke, Gerrit ten; Ikkala, Olli

    1997-01-01

    In this review 'molecular bottlebrushes' are flexible polymers densely loaded with equally flexible side chains. Interest in these structures arises from the possibility of lyotropic behaviour in dilute solution in a good solvent, as well as the possibility of highly ordered microphase-separated sta

  2. Prediction of molecular crystal structures

    International Nuclear Information System (INIS)

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol-1 of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy structures

  3. Prediction of molecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Theresa

    2001-07-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  4. Characterisation of Structural Proteins from Chronic Bee Paralysis Virus (CBPV Using Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Aurore Chevin

    2015-06-01

    Full Text Available Chronic bee paralysis virus (CBPV is the etiological agent of chronic paralysis, an infectious and contagious disease in adult honeybees. CBPV is a positive single-stranded RNA virus which contains two major viral RNA fragments. RNA 1 (3674 nt and RNA 2 (2305 nt encode three and four putative open reading frames (ORFs, respectively. RNA 1 is thought to encode the viral RNA-dependent RNA polymerase (RdRp since the amino acid sequence derived from ORF 3 shares similarities with the RdRP of families Nodaviridae and Tombusviridae. The genomic organization of CBPV and in silico analyses have suggested that RNA 1 encodes non-structural proteins, while RNA 2 encodes structural proteins, which are probably encoded by ORFs 2 and 3. In this study, purified CBPV particles were used to characterize virion proteins by mass spectrometry. Several polypeptides corresponding to proteins encoded by ORF 2 and 3 on RNA 2 were detected. Their role in the formation of the viral capsid is discussed.

  5. Prediction of social structure and genetic relatedness in colonies of the facultative polygynous stingless bee Melipona bicolor (Hymenoptera, Apidae

    Directory of Open Access Journals (Sweden)

    Evelyze Pinheiro dos Reis

    2011-01-01

    Full Text Available Stingless bee colonies typically consist of one single-mated mother queen and her worker offspring. The stingless bee Melipona bicolor (Hymenoptera: Apidae shows facultative polygyny, which makes this species particularly suitable for testing theoretical expectations concerning social behavior. In this study, we investigated the social structure and genetic relatedness among workers from eight natural and six manipulated colonies of M. bicolor over a period of one year. The populations of M. bicolor contained monogynous and polygynous colonies. The estimated genetic relatedness among workers from monogynous and polygynous colonies was 0.75 ± 0.12 and 0.53 ± 0.16 (mean ± SEM, respectively. Although the parental genotypes had significant effects on genetic relatedness in monogynous and polygynous colonies, polygyny markedly decreased the relatedness among nestmate workers. Our findings also demonstrate that polygyny in M. bicolor may arise from the adoption of related or unrelated queens.

  6. Interactive Modelling of Molecular Structures

    Science.gov (United States)

    Rustad, J. R.; Kreylos, O.; Hamann, B.

    2004-12-01

    The "Nanotech Construction Kit" (NCK) [1] is a new project aimed at improving the understanding of molecular structures at a nanometer-scale level by visualization and interactive manipulation. Our very first prototype is a virtual-reality program allowing the construction of silica and carbon structures from scratch by assembling them one atom at a time. In silica crystals or glasses, the basic building block is an SiO4 unit, with the four oxygen atoms arranged around the central silicon atom in the shape of a regular tetrahedron. Two silicate units can connect to each other by their silicon atoms covalently bonding to one shared oxygen atom. Geometrically, this means that two tetrahedra can link at their vertices. Our program is based on geometric representations and uses simple force fields to simulate the interaction of building blocks, such as forming/breaking of bonds and repulsion. Together with stereoscopic visualization and direct manipulation of building blocks using wands or data gloves, this enables users to create realistic and complex molecular models in short amounts of time. The NCK can either be used as a standalone tool, to analyze or experiment with molecular structures, or it can be used in combination with "traditional" molecular dynamics (MD) simulations. In a first step, the NCK can create initial configurations for subsequent MD simulation. In a more evolved setup, the NCK can serve as a visual front-end for an ongoing MD simulation, visualizing changes in simulation state in real time. Additionally, the NCK can be used to change simulation state on-the-fly, to experiment with different simulation conditions, or force certain events, e.g., the forming of a bond, and observe the simulation's reaction. [1] http://graphics.cs.ucdavis.edu/~okreylos/ResDev/NanoTech

  7. Molecular approaches to the analysis of deformed wing virus replication and pathogenesis in the honey bee, Apis mellifera

    Directory of Open Access Journals (Sweden)

    Pettis Jeffery S

    2009-12-01

    Full Text Available Abstract Background For years, the understanding of the pathogenetic mechanisms that underlie honey bee viral diseases has been severely hindered because of the lack of a cell culture system for virus propagation. As a result, it is very imperative to develop new methods that would permit the in vitro pathogenesis study of honey bee viruses. The identification of virus replication is an important step towards the understanding of the pathogenesis process of viruses in their respective hosts. In the present study, we developed a strand-specific RT-PCR-based method for analysis of Deformed Wing Virus (DWV replication in honey bees and in honey bee parasitic mites, Varroa Destructor. Results The results shows that the method developed in our study allows reliable identification of the virus replication and solves the problem of falsely-primed cDNA amplifications that commonly exists in the current system. Using TaqMan real-time quantitative RT-PCR incorporated with biotinylated primers and magnetic beads purification step, we characterized the replication and tissue tropism of DWV infection in honey bees. We provide evidence for DWV replication in the tissues of wings, head, thorax, legs, hemolymph, and gut of honey bees and also in Varroa mites. Conclusion The strategy reported in the present study forms a model system for studying bee virus replication, pathogenesis and immunity. This study should be a significant contribution to the goal of achieving a better understanding of virus pathogenesis in honey bees and to the design of appropriate control measures for bee populations at risk to virus infections.

  8. Outbreeding and lack of temporal genetic structure in a drone congregation of the neotropical stingless bee Scaptotrigona mexicana.

    Science.gov (United States)

    Mueller, Matthias Y; Moritz, Robin Fa; Kraus, F Bernhard

    2012-06-01

    Drone aggregations are a widespread phenomenon in many stingless bee species (Meliponini), but the ultimate and proximate causes for their formation are still not well understood. One adaptive explanation for this phenomenon is the avoidance of inbreeding, which is especially detrimental for stingless bees due to the combined effects of the complementary sex-determining system and the small effective population size caused by eusociality and monandry. We analyzed the temporal genetic dynamics of a drone aggregation of the stingless bee Scaptotrigona mexicana with microsatellite markers over a time window of four weeks. We estimated the drones of the aggregation to originate from a total of 55 colonies using sibship re-construction. There was no detectable temporal genetic differentiation or sub-structuring in the aggregation. Most important, we could exclude all colonies in close proximity of the aggregation as origin of the drones in the aggregation, implicating that they originate from more distant colonies. We conclude that the diverse genetic composition and the distant origin of the drones of the S. mexicana drone congregation provides an effective mechanism to avoid mating among close relatives. PMID:22833802

  9. Nest suitability, fine-scale population structure and male-mediated dispersal of a solitary ground nesting bee in an urban landscape.

    Directory of Open Access Journals (Sweden)

    Margarita M López-Uribe

    Full Text Available Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of gene flow and effective population sizes, increasing potential for inbreeding depression in wild bee populations. In this study, we investigated the fine-scale population structure of the solitary bee Colletes inaequalis in an urbanized landscape. First, we developed a predictive spatial model to detect suitable nesting habitat for this ground nesting bee and to inform our field search for nests. We genotyped 18 microsatellites in 548 female individuals collected from nest aggregations throughout the study area. Genetic relatedness estimates revealed that genetic similarity among individuals was slightly greater within nest aggregations than among randomly chosen individuals. However, genetic structure among nest aggregations was low (Nei's GST = 0.011. Reconstruction of parental genotypes revealed greater genetic relatedness among females than among males within nest aggregations, suggesting male-mediated dispersal as a potentially important mechanism of population connectivity and inbreeding avoidance. Size of nesting patch was positively correlated with effective population size, but not with other estimators of genetic diversity. We detected a positive trend between geographic distance and genetic differentiation between nest aggregations. Our landscape genetic models suggest that increased urbanization is likely associated with higher levels of inbreeding. Overall, these findings emphasize the importance of density and distribution of suitable nesting

  10. Nest suitability, fine-scale population structure and male-mediated dispersal of a solitary ground nesting bee in an urban landscape.

    Science.gov (United States)

    López-Uribe, Margarita M; Morreale, Stephen J; Santiago, Christine K; Danforth, Bryan N

    2015-01-01

    Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of gene flow and effective population sizes, increasing potential for inbreeding depression in wild bee populations. In this study, we investigated the fine-scale population structure of the solitary bee Colletes inaequalis in an urbanized landscape. First, we developed a predictive spatial model to detect suitable nesting habitat for this ground nesting bee and to inform our field search for nests. We genotyped 18 microsatellites in 548 female individuals collected from nest aggregations throughout the study area. Genetic relatedness estimates revealed that genetic similarity among individuals was slightly greater within nest aggregations than among randomly chosen individuals. However, genetic structure among nest aggregations was low (Nei's GST = 0.011). Reconstruction of parental genotypes revealed greater genetic relatedness among females than among males within nest aggregations, suggesting male-mediated dispersal as a potentially important mechanism of population connectivity and inbreeding avoidance. Size of nesting patch was positively correlated with effective population size, but not with other estimators of genetic diversity. We detected a positive trend between geographic distance and genetic differentiation between nest aggregations. Our landscape genetic models suggest that increased urbanization is likely associated with higher levels of inbreeding. Overall, these findings emphasize the importance of density and distribution of suitable nesting patches for enhancing

  11. Rotational spectra and molecular structure

    CERN Document Server

    Wollrab, James E

    1967-01-01

    Physical Chemistry, A Series of Monographs: Rotational Spectra and Molecular Structure covers the energy levels and rotational transitions. This book is divided into nine chapters that evaluate the rigid asymmetric top molecules and the nuclear spin statistics for asymmetric tops. Some of the topics covered in the book are the asymmetric rotor functions; rotational transition intensities; classes of molecules; nuclear spin statistics for linear molecules and symmetric tops; and classical appearance of centrifugal and coriolis forces. Other chapters deal with the energy levels and effects of ce

  12. CSMB | Center For Structural Molecular Biology

    Data.gov (United States)

    Federal Laboratory Consortium — The Center for Structural Molecular Biologyat ORNL is dedicated to developing instrumentation and methods for determining the 3-dimensional structures of proteins,...

  13. Molecular phylogeny of the stingless bees (Apidae, Apinae, Meliponini) inferred from mitochondrial 16S rDNA sequences

    OpenAIRE

    Costa, Marco; Marco A. Del Lama,; Melo,Gabriel; Sheppard, Walter

    2003-01-01

    Sequence data from the mitochondrial 16S rDNA of 34 species from 22 genera of stingless bees plus outgroup sequences from 11 species of other corbiculate bees were used to investigate the phylogenetic relationships among the Meliponini. Equally weighted parsimony and maximum likelihood analyses were performed. Four main clades were recognized in the parsimony consensus tree: (A) Hypotrigona, (B) Austroplebeia, (C) remaining African genera (Plebeina, Meliplebeia, and Axestotrigona) plus the tw...

  14. Bee health

    DEFF Research Database (Denmark)

    Lecocq, Antoine

    with a queen bee, based on their health status. Some of the methodological novelty, set-backs and preliminary results are discussed. In the fourth part, the thesis concludes by zooming out of the confines of the inner hive in order to address recent concerns regarding the potential spill-over of honey bee...

  15. Ontological Status of Molecular Structure

    Directory of Open Access Journals (Sweden)

    Giuseppe Del Re

    1998-11-01

    Full Text Available Molecular structure (MS has been treated as a convention or an epiphenomenon by physicists and quantum chemists interpreting the mathematical formalism of quantum mechanics as the essential reality criterion in the submicroscopic world (R2 world. This paper argues that, (a even in the R2 world there is a class of entities which are real per se, even though they cannot be separated from their material support, and MS may belong to that class; (b MS actualizes a particular molecule from the many potentialities of a given set of nuclei and electrons, all present in the same Schroedinger equation; (c MS is a fact established in the XIXth century, albeit as a result of circumstantial evidence (because of its belonging to the R2 world; (d the fact that MS is known, as all objects of the atomic world, in terms of analogies with macroscopic models, is not valid grounds for questioning its reality; (e MS is a set of topological as well as geometrical relations. All along the discussion, observability according to Bohr, Heisenberg, Feynman is taken as the essential criterion of reality in the R2 world. On its basis, quantum mechanics is by no means in conflict with the reality of molecular structure and shape. On the other hand, the question of the minimum lifetime required for a MS proper to exist should be left open, pending a detailed analysis of measurement techniques.

  16. To bee or not to bee—comments on “Discrete optimum design of truss structures using artificial bee colony algorithm”

    DEFF Research Database (Denmark)

    Stolpe, Mathias

    2011-01-01

    An Artificial Bee Colony algorithm was presented by Sonmez (StructMultidisc Optim 43:85–97, 2011) for solving discrete truss design problems. It was numerically tested on four benchmark examples and concluded to be robust and efficient. We compare the Artificial Bee Colony algorithm numerically to...... three alternative heuristics on the same benchmark examples. The most advanced heuristics presented herein find equally good, or better, designs compared to those presented in Sonmez (Struct Multidisc Optim 43:85–97, 2011). However, for the largest benchmark example, we use four orders of magnitude...

  17. Electron spectroscopy and molecular structure

    International Nuclear Information System (INIS)

    Electron spectroscopy can now be applied to solids, liquids and gases. Some fields of research require ultrahigh vacuum conditions, in particular those directly concerned with surface phenomena on the monolayer level. Liquids have just recently been subject to studies and several improvements and extensions of this technique can be done. Much advance has lately been achieved in the case of gases, where the pressure range presently is 10-5-1 torr. Signal-to-background ratios for core lines can be approximately 1000:1 and the resolution has been increased to the extent that vibrational fine structures of 1s levels in some small molecules have been observed. These improvements are based on the monochromatization of the exciting AlKα radiation. Under such conditions the background is furthermore so much reduced that shake-up structures are more generally accessible for closer studies. ESCA shifts are also much easier to resolve and to measure with higher precision, around 0.02 eV. The photoionization dynamics including atomic and molecular relaxations has been investigated, both experimentally and theoretically. In the valence electron region improvements in energy resolution and in the application of the intensity model based on the MO-LCAO approximation greatly facilitate the assignments of the valence orbitals. Accumulation of empirical evidences gathered from series of similar chemical species and also better methods of calculation, both ab initio and semiempirical, have gradually resulted in a much better understanding of the molecular orbital description. The experience of the latest ESCA instrument with monochromatization has motivated an attempt to design an optimized apparatus according to the general principles of this prototype. A considerable gain in intensity can be made at an improved resolution set by the inherent diffraction pattern of the focussing spherical quartz crystals. (author)

  18. A balance-evolution artificial bee colony algorithm for protein structure optimization based on a three-dimensional AB off-lattice model.

    Science.gov (United States)

    Li, Bai; Chiong, Raymond; Lin, Mu

    2015-02-01

    Protein structure prediction is a fundamental issue in the field of computational molecular biology. In this paper, the AB off-lattice model is adopted to transform the original protein structure prediction scheme into a numerical optimization problem. We present a balance-evolution artificial bee colony (BE-ABC) algorithm to address the problem, with the aim of finding the structure for a given protein sequence with the minimal free-energy value. This is achieved through the use of convergence information during the optimization process to adaptively manipulate the search intensity. Besides that, an overall degradation procedure is introduced as part of the BE-ABC algorithm to prevent premature convergence. Comprehensive simulation experiments based on the well-known artificial Fibonacci sequence set and several real sequences from the database of Protein Data Bank have been carried out to compare the performance of BE-ABC against other algorithms. Our numerical results show that the BE-ABC algorithm is able to outperform many state-of-the-art approaches and can be effectively employed for protein structure optimization. PMID:25463349

  19. Bee Pollen

    Science.gov (United States)

    ... Pollen Extract, Buckwheat Pollen, Extrait de Pollen d’Abeille, Honeybee Pollen, Honey Bee Pollen, Maize Pollen, Pine Pollen, Polen de Abeja, Pollen, Pollen d'Abeille, Pollen d’Abeille de Miel, Pollen de Sarrasin.

  20. Floral and nesting resources, habitat structure, and fire influence bee distribution across an open-forest gradient

    Science.gov (United States)

    Grundel, R.; Jean, R.P.; Frohnapple, K.J.; Glowacki, G.A.; Scott, P.E.; Pavlovic, N.B.

    2010-01-01

    Given bees' central effect on vegetation communities, it is important to understand how and why bee distributions vary across ecological gradients. We examined how plant community composition, plant diversity, nesting suitability, canopy cover, land use, and fire history affected bee distribution across an open-forest gradient in northwest Indiana, USA, a gradient similar to the historic Midwest United States landscape mosaic. When considered with the other predictors, plant community composition was not a significant predictor of bee community composition. Bee abundance was negatively related to canopy cover and positively to recent fire frequency, bee richness was positively related to plant richness and abundance of potential nesting resources, and bee community composition was significantly related to plant richness, soil characteristics potentially related to nesting suitability, and canopy cover. Thus, bee abundance was predicted by a different set of environmental characteristics than was bee species richness, and bee community composition was predicted, in large part, by a combination of the significant predictors of bee abundance and richness. Differences in bee community composition along the woody vegetation gradient were correlated with relative abundance of oligolectic, or diet specialist, bees. Because oligoleges were rarer than diet generalists and were associated with open habitats, their populations may be especially affected by degradation of open habitats. More habitat-specialist bees were documented for open and forest/scrub habitats than for savanna/woodland habitats, consistent with bees responding to habitats of intermediate woody vegetation density, such as savannas, as ecotones rather than as distinct habitat types. Similarity of bee community composition, similarity of bee abundance, and similarity of bee richness between sites were not significantly related to proximity of sites to each other. Nestedness analysis indicated that species

  1. Cocaine Tolerance in Honey Bees

    OpenAIRE

    Eirik Søvik; Jennifer L. Cornish; Barron, Andrew B.

    2013-01-01

    Increasingly invertebrates are being used to investigate the molecular and cellular effects of drugs of abuse to explore basic mechanisms of addiction. However, in mammals the principle factors contributing to addiction are long-term adaptive responses to repeated drug use. Here we examined whether adaptive responses to cocaine are also seen in invertebrates using the honey bee model system. Repeated topical treatment with a low dose of cocaine rendered bees resistant to the deleterious motor...

  2. Mitochondrial structure and dynamics as critical factors in honey bee (Apis mellifera L.) caste development.

    Science.gov (United States)

    Santos, Douglas Elias; Alberici, Luciane Carla; Hartfelder, Klaus

    2016-06-01

    The relationship between nutrition and phenotype is an especially challenging question in cases of facultative polyphenism, like the castes of social insects. In the honey bee, Apis mellifera, unexpected modifications in conserved signaling pathways revealed the hypoxia response as a possible mechanism underlying the regulation of body size and organ growth. Hence, the current study was designed to investigate possible causes of why the three hypoxia core genes are overexpressed in worker larvae. Parting from the hypothesis that this has an endogenous cause and is not due to differences in external oxygen levels we investigated mitochondrial numbers and distribution, as well as mitochondrial oxygen consumption rates in fat body cells of queen and worker larvae during the caste fate-critical larval stages. By immunofluorescence and electron microscopy we found higher densities of mitochondria in queen larval fat body, a finding further confirmed by a citrate synthase assay quantifying mitochondrial functional units. Oxygen consumption measurements by high-resolution respirometry revealed that queen larvae have higher maximum capacities of ATP production at lower physiological demand. Finally, the expression analysis of mitogenesis-related factors showed that the honey bee TFB1 and TFB2 homologs, and a nutritional regulator, ERR, are overexpressed in queen larvae. These results are strong evidence that the differential nutrition of queen and worker larvae by nurse bees affects mitochondrial dynamics and functionality in the fat body of these larvae, hence explaining their differential hypoxia response. PMID:27058771

  3. Native bees and plant pollination

    Science.gov (United States)

    Ginsberg, H.S.

    2004-01-01

    Bees are important pollinators, but evidence suggests that numbers of some species are declining. Decreases have been documented in the honey bee, Apis mellifera (which was introduced to North America), but there are no monitoring programs for the vast majority of native species, so we cannot be sure about the extent of this problem. Recent efforts to develop standardized protocols for bee sampling will help us collect the data needed to assess trends in bee populations. Unfortunately, diversity of bee life cycles and phenologies, and the large number of rare species, make it difficult to assess trends in bee faunas. Changes in bee populations can affect plant reproduction, which can influence plant population density and cover, thus potentially modifying horizontal and vertical structure of a community, microclimate near the ground, patterns of nitrogen deposition, etc. These potential effects of changes in pollination patterns have not been assessed in natural communities. Effects of management actions on bees and other pollinators should be considered in conservation planning.

  4. ANALYSIS OF STRUCTURAL PLASTICITY IN THE HONEY BEE BRAIN USING THE CAVALIERI ESTIMATOR OF VOLUME AND THE DISECTOR METHOD

    Directory of Open Access Journals (Sweden)

    Sheena M Brown

    2011-05-01

    Full Text Available The antennal lobe of the worker honey bee has been used as a model system to address the origins of structural plasticity in the central nervous system. A combination of light and electron microscopy was used to determine total synapse number within an easily identifiable sub-unit of the antennal lobe neuropil, the T4-2(1 glomerulus. The Cavalieri method was applied at the light microscope level to determine a reference volume (Vref of this glomerulus. Using transmission electron microscopy, the physical disector was used to determine synaptic density (Nv within the T4-2(1 glomerulus. An estimate of the total synapse number N(syn was determined by; N(syn = V(ref Nv. Newly emerged, 4-day old,10-day old and forager-aged bees were analysed. Results showed that despite a significant increase in T4-2(1 volume with age, the total number of synapses in this glomerulus did not show a corresponding increase. Disturbingly, it is possible that huge variances within age groups, due to one or two outlying data points, could be masking the true trend of synapse number. This variance, the heterogeneous distribution of synapses within this glomerulus and the problems associated with reproducibility of synapse counts are discussed.

  5. Molecular characterization of Turkish honey bee populations (Apis mellifera) inferred from mitochondrial DNA RFLP and sequence results*

    OpenAIRE

    Özdil, Fulya; Yildiz, Mehmet Ali; Hall, H. Glenn

    2009-01-01

    International audience To identify the evolutionary lineage of honey bee colonies in Turkey, the mtDNA of 244 colonies from 20 locations was analyzed. Several polymorphic restriction sites showed that they belonged to the Mediterranean C lineage. DraI digestion of the CoxI-CoxII intergenic region produced four fragment patterns, one first seen in this study. From 37 colonies from 16 different locations in Turkey and two colonies from Iran, the intergenic region was sequenced. Previously, f...

  6. Molecular characterization of Turkish honey bee populations (Apis mellifera) inferred from mitochondrial DNA RFLP and sequence results

    OpenAIRE

    Özdil, Fulya; Yildiz, Mehmet Ali; Hall, H. Glenn

    2009-01-01

    International audience To identify the evolutionary lineage of honey bee colonies in Turkey, the mtDNA of 244 colonies from 20 locations was analyzed. Several polymorphic restriction sites showed that they belonged to the Mediterranean C lineage. DraI digestion of the CoxI-CoxII intergenic region produced four fragment patterns, one first seen in this study. From 37 colonies from 16 different locations in Turkey and two colonies from Iran, the intergenic region was sequenced. Previously, f...

  7. Bee Stings & Their Consequences.

    Science.gov (United States)

    Rupp, Robert M.

    1991-01-01

    Relevant information concerning bee stings is provided. Possible reactions to a bee sting and their symptoms, components of bee venom, diagnosis of hypersensitivity, and bee sting prevention and treatment are topics of discussion. The possibility of bee stings occurring during field trips and the required precautions are discussed. (KR)

  8. Structure parameters in molecular tunneling ionization theory

    Science.gov (United States)

    Wang, Jun-Ping; Li, Wei; Zhao, Song-Feng

    2014-04-01

    We extracted the accurate structure parameters in molecular tunneling ionization theory (so called MO-ADK theory) for 22 selected linear molecules including some inner orbitals. The molecular wave functions with the correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials numerically constructed using the modified Leeuwen-Baerends (LBα) model.

  9. Structure parameters in molecular tunneling ionization theory

    International Nuclear Information System (INIS)

    We extracted the accurate structure parameters in molecular tunneling ionization theory (so called MO-ADK theory) for 22 selected linear molecules including some inner orbitals. The molecular wave functions with the correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials numerically constructed using the modified Leeuwen-Baerends (LBα) model.

  10. Molecular modeling of nucleic acid structure

    OpenAIRE

    Galindo-Murillo, Rodrigo; Bergonzo, Christina; Cheatham, Thomas E

    2001-01-01

    This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. This unit provides an overview of computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, generation of an initial model, and characterization of the overall three-dimensional structure.

  11. Cocaine tolerance in honey bees.

    Directory of Open Access Journals (Sweden)

    Eirik Søvik

    Full Text Available Increasingly invertebrates are being used to investigate the molecular and cellular effects of drugs of abuse to explore basic mechanisms of addiction. However, in mammals the principle factors contributing to addiction are long-term adaptive responses to repeated drug use. Here we examined whether adaptive responses to cocaine are also seen in invertebrates using the honey bee model system. Repeated topical treatment with a low dose of cocaine rendered bees resistant to the deleterious motor effects of a higher cocaine dose, indicating the development of physiological tolerance to cocaine in bees. Cocaine inhibits biogenic amine reuptake transporters, but neither acute nor repeated cocaine treatments caused measurable changes in levels of biogenic amines measured in whole bee brains. Our data show clear short and long-term behavioural responses of bees to cocaine administration, but caution that, despite the small size of the bee brain, measures of biogenic amines conducted at the whole-brain level may not reveal neurochemical effects of the drug.

  12. The Molecular Structure of Penicillin

    Science.gov (United States)

    Bentley, Ronald

    2004-01-01

    Overviews of the observations that constitute a structure proof for penicillin, specifically aimed at the general student population, are presented. Melting points and boiling points were criteria of purity and a crucial tool was microanalysis leading to empirical formulas.

  13. Molecular structure by Coulomb explosion imaging of stored molecular ions

    International Nuclear Information System (INIS)

    An experimental scheme, which combines Coulomb explosion imaging (CEI) with storage of fast molecular ions, has been introduced recently at the TSR heavy ion storage ring facility in Heidelberg. CEI is an experimental technique that provides direct observation of the nuclear conformations within small molecules. The combination of CEI with the storage ring technique enables the control of the internal excitation of the measured molecules, which is an essential condition to the interpretation of CEI results in terms of ''structure'' assigned to specific molecular states. This structure is measured as a function of storage time, thus enabling one to study processes of slow intramolecular dynamics such as isomerization, metastable states, etc. Moreover in this scheme, CEI can be used as a diagnostic tool for the intramolecular excitation, while other molecular interactions (e.g. with electrons or photons) are investigated. In this report, the CEI principle and the new experimental setup are described with an emphasis on the new prospects for studies in molecular physics. CEI measurements of stored CH2+ and NH2+ molecular ions are presented. The study of the angular distribution in these molecules as a function of their vibrational relaxation to the ground state, reveals unexpected behavior near the linear conformation which is inconsistent with the current adiabatic theories

  14. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    International Nuclear Information System (INIS)

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory 13CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  15. Quantum mechanics of molecular structures

    CERN Document Server

    Yamanouchi, Kaoru

    2012-01-01

    At a level accessible to advanced undergraduates, this textbook explains the fundamental role of quantum mechanics in determining the structure, dynamics, and other properties of molecules. Readers will come to understand the quantum-mechanical basis for harmonic oscillators, angular momenta and scattering processes. Exercises are provided to help readers deepen their grasp of the essential phenomena.

  16. Modeling Honey Bee Populations.

    Directory of Open Access Journals (Sweden)

    David J Torres

    Full Text Available Eusocial honey bee populations (Apis mellifera employ an age stratification organization of egg, larvae, pupae, hive bees and foraging bees. Understanding the recent decline in honey bee colonies hinges on understanding the factors that impact each of these different age castes. We first perform an analysis of steady state bee populations given mortality rates within each bee caste and find that the honey bee colony is highly susceptible to hive and pupae mortality rates. Subsequently, we study transient bee population dynamics by building upon the modeling foundation established by Schmickl and Crailsheim and Khoury et al. Our transient model based on differential equations accounts for the effects of pheromones in slowing the maturation of hive bees to foraging bees, the increased mortality of larvae in the absence of sufficient hive bees, and the effects of food scarcity. We also conduct sensitivity studies and show the effects of parameter variations on the colony population.

  17. Structured Molecular Gas Reveals Galactic Spiral Arms

    CERN Document Server

    Sawada, Tsuyoshi; Koda, Jin

    2012-01-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function (BDF) and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory 13CO J=1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formati...

  18. Phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) and a predicted structural protein (pSP) of the Chronic bee paralysis virus (CBPV) isolated from various geographic regions.

    OpenAIRE

    Blanchard, Philippe; Schurr, Frank; Olivier, Violaine; Celle, Olivier; Antùnez, Karina; Bakonyi, Tamàs; Berthoud, Hélène; Haubruge, Eric; Higes, Mariano; Kasprzak, Sylwia; Koeglberger, Hemma; Kryger, Per; Thiéry, Richard; Ribière, Magali

    2009-01-01

    Chronic bee paralysis virus (CBPV) is responsible for chronic paralysis, an infectious and contagious disease of adult honey bees (Apis mellifera L.). The full-length nucleotide sequences of the two major RNAs of CBPV have previously been characterized. The Orf3 of RNA1 has shown significant similarities to the RNA-dependent RNA polymerase (RdRp) of positive single-stranded RNA viruses, whereas the Orf3 of RNA2 encodes a putative structural protein (pSP). In the present study, honey bees orig...

  19. Exploring RNA structure by integrative molecular modelling

    DEFF Research Database (Denmark)

    Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

    2010-01-01

    RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...... in three dimensions (3D) and used as building blocks assembled manually during a bioinformatic interactive process. Comparing the models to the corresponding crystal structures has validated the method as being powerful to predict the RNA topology and architecture while being less accurate regarding...

  20. Rotational structure in molecular infrared spectra

    CERN Document Server

    di Lauro, Carlo

    2013-01-01

    Recent advances in infrared molecular spectroscopy have resulted in sophisticated theoretical and laboratory methods that are difficult to grasp without a solid understanding of the basic principles and underlying theory of vibration-rotation absorption spectroscopy. Rotational Structure in Molecular Infrared Spectra fills the gap between these recent, complex topics and the most elementary methods in the field of rotational structure in the infrared spectra of gaseous molecules. There is an increasing need for people with the skills and knowledge to interpret vibration-rotation spectra in ma

  1. Study on Molecular Structure of TATFIW

    Institute of Scientific and Technical Information of China (English)

    LI Li-jie; LI Yan-yue; LU Lin; CHEN Shu-sen; CHEN Hua-xiong; JIN Shao-hua; ZHAO Xin-qi

    2008-01-01

    The molecular structure of triacetyltriformylhexaazaisowurtzitane (TATFIW) is optimized by using Gaussian98 software package at the level of B3LYP/6-31G. Theoretically analyzed the TATFIW molecular structure, namely bond length, bond angle, dihedral angle and the charge distribution, it was found that hydrogen bond exists in TATFIW, and acetyl is easily taken off than formyl in the nitrolysis with nitric-sulfuric mixed acid. These results mentioned above agree with experiments. The comparison of calculated vibration frequency and intensity with the experiment values are also given.

  2. Anatomy of molecular structures in $^{20}$Ne

    CERN Document Server

    Zhou, E F; Li, Z P; Meng, J; Ring, P

    2015-01-01

    We present a beyond mean-field study of clusters and molecular structures in low-spin states of $^{20}$Ne with a multireference relativistic energy density functional, where the dynamical correlation effects of symmetry restoration and quadrupole-octupole shapes fluctuation are taken into account with projections on parity, particle number and angular momentum in the framework of the generator coordinate method. Both the energy spectrum and the electric multipole transition strengths for low-lying parity-doublet bands are better reproduced after taking into account the dynamical octupole vibration effect. Consistent with the finding in previous antisymmetrized molecular dynamics studies, a rotation-induced dissolution of the $\\alpha+^{16}$O molecular structure in $^{20}$Ne is predicted and this peculiar phenomenon is partially attributed to the special deformation-dependent moment of inertia.

  3. Molecular cloning and characterization of juvenile hormone acid methyltransferase in the honey bee, Apis mellifera, and its differential expression during caste differentiation.

    Science.gov (United States)

    Li, Wenfeng; Huang, Zachary Y; Liu, Fang; Li, Zhiguo; Yan, Limin; Zhang, Shaowu; Chen, Shenglu; Zhong, Boxiong; Su, Songkun

    2013-01-01

    Juvenile hormone acid methyltransferase (JHAMT) is an enzyme involved in one of the final steps of juvenile hormone biosynthesis in insects. It transfers a methyl group from S-adenosyl-L-methionine (SAM) to the carboxyl group of either farnesoic acid (FA) or JH acid (JHA). Several genes coding for JHAMT have been cloned and characterized from insects from different orders, and they have been shown to play critical roles in metamorphosis and reproduction. However, the significance of JHAMT in Hymenopteran insects is unknown. We used RACE amplification method to clone JHAMT cDNA from the honey bee, Apis mellifera (AmJHAMT). The full length cDNA of AmJHAMT that we cloned is 1253bp long and encodes a 278-aa protein that shares 32-36% identity with known JHAMTs. A SAM-binding motif, conserved in the SAM-dependent methyltransferase (SAM-MT) superfamily, is present in AmJHAMT. Its secondary structure also contains a typical SAM-MT fold. Most of the active sites bound with SAM and substrates (JHA or FA) are conserved in AmJHAMT as in other JHAMT orthologs. Phylogenetic analysis clustered AmJHAMT with the other orthologs from Hymenoptera to form a major clade in the phylogenetic tree. Purified recombinant AmJHAMT protein expressed in E. coli was used to produce polyclonal antibodies and to verify the identity of AmJHAMT by immunoblotting and mass spectrometry. Quantitative RT-PCR and immunoblotting analyses revealed that queen larvae contained significantly higher levels of AmJHAMT mRNA and protein than worker larvae during the periods of caste development. The temporal profiles of both AmJHAMT mRNA and protein in queens and workers showed a similar pattern as the JH biosynthesis. These results suggest that the gene that we cloned codes for a functional JHAMT that catalyzes the final reactions of JH biosynthesis in honey bees. In addition, AmJHAMT may play an important role in honey bee caste differentiation. PMID:23874662

  4. Molecular cloning and characterization of juvenile hormone acid methyltransferase in the honey bee, Apis mellifera, and its differential expression during caste differentiation.

    Directory of Open Access Journals (Sweden)

    Wenfeng Li

    Full Text Available Juvenile hormone acid methyltransferase (JHAMT is an enzyme involved in one of the final steps of juvenile hormone biosynthesis in insects. It transfers a methyl group from S-adenosyl-L-methionine (SAM to the carboxyl group of either farnesoic acid (FA or JH acid (JHA. Several genes coding for JHAMT have been cloned and characterized from insects from different orders, and they have been shown to play critical roles in metamorphosis and reproduction. However, the significance of JHAMT in Hymenopteran insects is unknown. We used RACE amplification method to clone JHAMT cDNA from the honey bee, Apis mellifera (AmJHAMT. The full length cDNA of AmJHAMT that we cloned is 1253bp long and encodes a 278-aa protein that shares 32-36% identity with known JHAMTs. A SAM-binding motif, conserved in the SAM-dependent methyltransferase (SAM-MT superfamily, is present in AmJHAMT. Its secondary structure also contains a typical SAM-MT fold. Most of the active sites bound with SAM and substrates (JHA or FA are conserved in AmJHAMT as in other JHAMT orthologs. Phylogenetic analysis clustered AmJHAMT with the other orthologs from Hymenoptera to form a major clade in the phylogenetic tree. Purified recombinant AmJHAMT protein expressed in E. coli was used to produce polyclonal antibodies and to verify the identity of AmJHAMT by immunoblotting and mass spectrometry. Quantitative RT-PCR and immunoblotting analyses revealed that queen larvae contained significantly higher levels of AmJHAMT mRNA and protein than worker larvae during the periods of caste development. The temporal profiles of both AmJHAMT mRNA and protein in queens and workers showed a similar pattern as the JH biosynthesis. These results suggest that the gene that we cloned codes for a functional JHAMT that catalyzes the final reactions of JH biosynthesis in honey bees. In addition, AmJHAMT may play an important role in honey bee caste differentiation.

  5. Molecular Association and Structure of Hydrogen Peroxide.

    Science.gov (United States)

    Giguere, Paul A.

    1983-01-01

    The statement is sometimes made in textbooks that liquid hydrogen peroxide is more strongly associated than water, evidenced by its higher boiling point and greater heat of vaporization. Discusses these and an additional factor (the nearly double molecular mass of the peroxide), focusing on hydrogen bonds and structure of the molecule. (JN)

  6. Foraging on the potential energy surface: A swarm intelligence-based optimizer for molecular geometry

    Science.gov (United States)

    Wehmeyer, Christoph; Falk von Rudorff, Guido; Wolf, Sebastian; Kabbe, Gabriel; Schärf, Daniel; Kühne, Thomas D.; Sebastiani, Daniel

    2012-11-01

    We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials.

  7. Non-bee insects are important contributors to global crop pollination.

    Science.gov (United States)

    Rader, Romina; Bartomeus, Ignasi; Garibaldi, Lucas A; Garratt, Michael P D; Howlett, Brad G; Winfree, Rachael; Cunningham, Saul A; Mayfield, Margaret M; Arthur, Anthony D; Andersson, Georg K S; Bommarco, Riccardo; Brittain, Claire; Carvalheiro, Luísa G; Chacoff, Natacha P; Entling, Martin H; Foully, Benjamin; Freitas, Breno M; Gemmill-Herren, Barbara; Ghazoul, Jaboury; Griffin, Sean R; Gross, Caroline L; Herbertsson, Lina; Herzog, Felix; Hipólito, Juliana; Jaggar, Sue; Jauker, Frank; Klein, Alexandra-Maria; Kleijn, David; Krishnan, Smitha; Lemos, Camila Q; Lindström, Sandra A M; Mandelik, Yael; Monteiro, Victor M; Nelson, Warrick; Nilsson, Lovisa; Pattemore, David E; Pereira, Natália de O; Pisanty, Gideon; Potts, Simon G; Reemer, Menno; Rundlöf, Maj; Sheffield, Cory S; Scheper, Jeroen; Schüepp, Christof; Smith, Henrik G; Stanley, Dara A; Stout, Jane C; Szentgyörgyi, Hajnalka; Taki, Hisatomo; Vergara, Carlos H; Viana, Blandina F; Woyciechowski, Michal

    2016-01-01

    Wild and managed bees are well documented as effective pollinators of global crops of economic importance. However, the contributions by pollinators other than bees have been little explored despite their potential to contribute to crop production and stability in the face of environmental change. Non-bee pollinators include flies, beetles, moths, butterflies, wasps, ants, birds, and bats, among others. Here we focus on non-bee insects and synthesize 39 field studies from five continents that directly measured the crop pollination services provided by non-bees, honey bees, and other bees to compare the relative contributions of these taxa. Non-bees performed 25-50% of the total number of flower visits. Although non-bees were less effective pollinators than bees per flower visit, they made more visits; thus these two factors compensated for each other, resulting in pollination services rendered by non-bees that were similar to those provided by bees. In the subset of studies that measured fruit set, fruit set increased with non-bee insect visits independently of bee visitation rates, indicating that non-bee insects provide a unique benefit that is not provided by bees. We also show that non-bee insects are not as reliant as bees on the presence of remnant natural or seminatural habitat in the surrounding landscape. These results strongly suggest that non-bee insect pollinators play a significant role in global crop production and respond differently than bees to landscape structure, probably making their crop pollination services more robust to changes in land use. Non-bee insects provide a valuable service and provide potential insurance against bee population declines. PMID:26621730

  8. Bee-Wild about Pollinators!

    Science.gov (United States)

    Johnson, Bonnie; Kil, Jenny; Evans, Elaine; Koomen, Michele Hollingsworth

    2014-01-01

    With their sunny stripes and fuzzy bodies, bees are beloved--but unfortunately, they are in trouble. Bee decline, of both wild bees as well as managed bees like honey bees, has been in the news for the last several years. Habitat loss, diseases, pests, and pesticides have made it difficult for bees to survive in many parts of our world (Walsh…

  9. Metatranscriptomic analyses of honey bee colonies.

    Science.gov (United States)

    Tozkar, Cansu Ö; Kence, Meral; Kence, Aykut; Huang, Qiang; Evans, Jay D

    2015-01-01

    Honey bees face numerous biotic threats from viruses to bacteria, fungi, protists, and mites. Here we describe a thorough analysis of microbes harbored by worker honey bees collected from field colonies in geographically distinct regions of Turkey. Turkey is one of the World's most important centers of apiculture, harboring five subspecies of Apis mellifera L., approximately 20% of the honey bee subspecies in the world. We use deep ILLUMINA-based RNA sequencing to capture RNA species for the honey bee and a sampling of all non-endogenous species carried by bees. After trimming and mapping these reads to the honey bee genome, approximately 10% of the sequences (9-10 million reads per library) remained. These were then mapped to a curated set of public sequences containing ca. Sixty megabase-pairs of sequence representing known microbial species associated with honey bees. Levels of key honey bee pathogens were confirmed using quantitative PCR screens. We contrast microbial matches across different sites in Turkey, showing new country recordings of Lake Sinai virus, two Spiroplasma bacterium species, symbionts Candidatus Schmidhempelia bombi, Frischella perrara, Snodgrassella alvi, Gilliamella apicola, Lactobacillus spp.), neogregarines, and a trypanosome species. By using metagenomic analysis, this study also reveals deep molecular evidence for the presence of bacterial pathogens (Melissococcus plutonius, Paenibacillus larvae), Varroa destructor-1 virus, Sacbrood virus, and fungi. Despite this effort we did not detect KBV, SBPV, Tobacco ringspot virus, VdMLV (Varroa Macula like virus), Acarapis spp., Tropilaeleps spp. and Apocephalus (phorid fly). We discuss possible impacts of management practices and honey bee subspecies on microbial retinues. The described workflow and curated microbial database will be generally useful for microbial surveys of healthy and declining honey bees. PMID:25852743

  10. Metatranscriptomic analyses of honey bee colonies

    Directory of Open Access Journals (Sweden)

    Cansu Ozge Tozkar

    2015-03-01

    Full Text Available Honey bees face numerous biotic threats from viruses to bacteria, fungi, protists, and mites. Here we describe a thorough analysis of microbes harbored by worker honey bees collected from field colonies in geographically distinct regions of Turkey. Turkey is one of the World’s most important centers of apiculture, harboring 5 subspecies of Apis mellifera L., approximately 20% of the honey bee subspecies in the world. We use deep ILLUMINA-based RNA sequencing to capture RNA species for the honey bee and a sampling of all non-endogenous species carried by bees. After trimming and mapping these reads to the honey bee genome, approximately 10% of the sequences (9-10 million reads per library remained. These were then mapped to a curated set of public sequences containing ca. 60 megabase-pairs of sequence representing known microbial species associated with honey bees. Levels of key honey bee pathogens were confirmed using quantitative PCR screens. We contrast microbial matches across different sites in Turkey, showing new country recordings of Lake Sinai virus, two Spiroplasma bacterium species, symbionts Candidatus Schmidhempelia bombi, Frischella perrara, Snodgrassella alvi, Gilliamella apicola, Lactobacillus spp., neogregarines, and a trypanosome species. By using metagenomic analysis, this study also reveals deep molecular evidence for the presence of bacterial pathogens (Melissococcus plutonius, Paenibacillus larvae, Varroa destructor-1 virus, Sacbrood virus, Apis filamentous virus and fungi. Despite this effort we did not detect KBV, SBPV, Tobacco ringspot virus, VdMLV (Varroa Macula like virus, Acarapis spp., Tropilaeleps spp. and Apocephalus (phorid fly. We discuss possible impacts of management practices and honey bee subspecies on microbial retinues. The described workflow and curated microbial database will be generally useful for microbial surveys of healthy and declining honey bees.

  11. Nutrigenomics in honey bees: digital gene expression analysis of pollen's nutritive effects on healthy and varroa-parasitized bees

    Directory of Open Access Journals (Sweden)

    Parrinello Hughes

    2011-10-01

    Full Text Available Abstract Background Malnutrition is a major factor affecting animal health, resistance to disease and survival. In honey bees (Apis mellifera, pollen, which is the main dietary source of proteins, amino acids and lipids, is essential to adult bee physiological development while reducing their susceptibility to parasites and pathogens. However, the molecular mechanisms underlying pollen's nutritive impact on honey bee health remained to be determined. For that purpose, we investigated the influence of pollen nutrients on the transcriptome of worker bees parasitized by the mite Varroa destructor, known for suppressing immunity and decreasing lifespan. The 4 experimental groups (control bees without a pollen diet, control bees fed with pollen, varroa-parasitized bees without a pollen diet and varroa-parasitized bees fed with pollen were analyzed by performing a digital gene expression (DGE analysis on bee abdomens. Results Around 36, 000 unique tags were generated per DGE-tag library, which matched about 8, 000 genes (60% of the genes in the honey bee genome. Comparing the transcriptome of bees fed with pollen and sugar and bees restricted to a sugar diet, we found that pollen activates nutrient-sensing and metabolic pathways. In addition, those nutrients had a positive influence on genes affecting longevity and the production of some antimicrobial peptides. However, varroa parasitism caused the development of viral populations and a decrease in metabolism, specifically by inhibiting protein metabolism essential to bee health. This harmful effect was not reversed by pollen intake. Conclusions The DGE-tag profiling methods used in this study proved to be a powerful means for analyzing transcriptome variation related to nutrient intake in honey bees. Ultimately, with such an approach, applying genomics tools to nutrition research, nutrigenomics promises to offer a better understanding of how nutrition influences body homeostasis and may help reduce

  12. Structural identification by mass spectrometry of a novel antimicrobial peptide from the venom of the solitary bee Osmia rufa (Hymenoptera: Megachilidae).

    Science.gov (United States)

    Stöcklin, Reto; Favreau, Philippe; Thai, Robert; Pflugfelder, Jochen; Bulet, Philippe; Mebs, Dietrich

    2010-01-01

    The venom from the solitary bee Osmia rufa (Hymenoptera: Megachilidae) was analyzed using mass spectrometry (MS)-based techniques. Sensitive proteomic methods such as on-line LC-ESI-MS and nanoESI-MS analyses revealed more than 50 different compounds with molecular masses ranging from 400 to 4000Da. The major component has a monoisotopic molecular mass of 1924.20Da and its amino acid sequence was elucidated by de novo sequencing using tandem mass spectrometry and Edman degradation. This 17-residue cysteine-free peptide, named osmin, shows some similarities with the mast cell degranulation (MCD) peptide family. Free acid and C-terminally amidated osmins were chemically synthesized and tested for antimicrobial and haemolytic activities. The synthetic C-amidated peptide (native osmin) was found to be about three times more haemolytic than its free acid counterpart, but both peptides are much less lytic than melittin from social bee venom. Preliminary antimicrobial and antifungal tests indicate that both peptides are able to inhibit bacterial and fungal growth at micromolar concentrations. PMID:19109988

  13. Turbulent Velocity Structure in Molecular Clouds

    CERN Document Server

    Ossenkopf, V; Ossenkopf, Volker; Low, Mordecai-Mark Mac

    2002-01-01

    We compare velocity structure observed in the Polaris Flare molecular cloud at scales ranging from 0.015 pc to 20 pc to the velocity structure of a suite of simulations of supersonic hydrodynamic and MHD turbulence computed with the ZEUS MHD code. We examine different methods of characterising the structure, including a scanning-beam size-linewidth relation, structure functions, velocity and velocity difference probability distribution functions (PDFs), and the Delta-variance wavelet transform, and use them to compare models and observations. The Delta-variance is most sensitive in detecting characteristic scales and varying scaling laws, but is limited in the observational application by its lack of intensity weighting. We compare the true velocity PDF in our models to simulated observations of velocity centroids and average line profiles in optically thin lines, and find that the line profiles reflect the true PDF better. The observed velocity structure is consistent with supersonic turbulence showing a com...

  14. Molecular structure and interfacial behaviour of polymers.

    OpenAIRE

    Lent, van, J.

    1989-01-01

    The aim of this study was to investigate the influence of the molecular structure on the interfacial behaviour of polymers. Theoretical models were developed for three different systems. All these models are based on the self-consistent field theory of Scheutjens and Fleer for the adsorption of homopolymers.This self-consistent field theory is a lattice model. All possible polymer conformations on the lattice are taken into account. The potential of a conformation is sum of the local potentia...

  15. The Structure of Cold Molecular Cloud Cores

    OpenAIRE

    Ward-Thompson, D.; D. J. Nutter; Kirk, J M; Andre, P.

    2003-01-01

    A brief summary is presented of our current knowledge of the structure of cold molecular cloud cores that do not contain protostars, sometimes known as starless cores. The most centrally condensed starless cores are known as pre-stellar cores. These cores probably represent observationally the initial conditions for protostellar collapse that must be input into all models of star formation. The current debate over the nature of core density profiles is summarised. A cautionary note is sounded...

  16. The molecular structure of future fuels

    OpenAIRE

    Hellier, P. R.

    2013-01-01

    Future fuels will be developed from a variety of biomass and fossil sources, and must seek to address the adverse environmental impacts of current fossil fuel usage. To this end, understanding how the molecular structure of a fuel impacts on the processes of combustion and emissions production is critical in selecting suitable feed-stocks and conversion methods. This work presents experimental studies carried out on a compression ignition engine equipped with a novel low volume fuel system. T...

  17. 2004 Reversible Associations in Structure & Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  18. Structure-activity study of macropin, a novel antimicrobial peptide from the venom of solitary bee Macropis fulvipes (Hymenoptera: Melittidae)

    Czech Academy of Sciences Publication Activity Database

    Monincová, Lenka; Veverka, Václav; Slaninová, Jiřina; Buděšínský, Miloš; Fučík, Vladimír; Bednárová, Lucie; Straka, J.; Čeřovský, Václav

    2014-01-01

    Roč. 20, č. 6 (2014), s. 375-384. ISSN 1075-2617 R&D Projects: GA ČR GA203/08/0536 Institutional support: RVO:61388963 Keywords : antimicrobial peptide * analog * wild bee venom * NMR spectroscopy * CD spectroscopy Subject RIV: CE - Biochemistry Impact factor: 1.546, year: 2014

  19. Generalist Bee Species on Brazilian Bee-Plant Interaction Networks

    OpenAIRE

    Astrid de Matos Peixoto Kleinert; Tereza Cristina Giannini

    2012-01-01

    Determining bee and plant interactions has an important role on understanding general biology of bee species as well as the potential pollinating relationship between them. Bee surveys have been conducted in Brazil since the end of the 1960s. Most of them applied standardized methods and had identified the plant species where the bees were collected. To analyze the most generalist bees on Brazilian surveys, we built a matrix of bee-plant interactions. We estimated the most generalist bees det...

  20. Nutrigenomics in honey bees: digital gene expression analysis of pollen's nutritive effects on healthy and varroa-parasitized bees.

    OpenAIRE

    Parrinello Hughes; Dantec Christelle; Alaux Cédric; Le Conte Yves

    2011-01-01

    Abstract Background Malnutrition is a major factor affecting animal health, resistance to disease and survival. In honey bees (Apis mellifera), pollen, which is the main dietary source of proteins, amino acids and lipids, is essential to adult bee physiological development while reducing their susceptibility to parasites and pathogens. However, the molecular mechanisms underlying pollen's nutritive impact on honey bee health remained to be determined. For that purpose, we investigated the inf...

  1. New molecular evidence for fragmentation between two distant populations of the threatened stingless bee Melipona subnitida Ducke (Hymenoptera, Apidae, Meliponini

    Directory of Open Access Journals (Sweden)

    Geice R. Silva

    2014-06-01

    Full Text Available For a snapshot assessment of the genetic diversity present within Melipona subnitida, an endemic stingless bee distributed in the semi-arid region of northeastern Brazil, populations separated by over 1,000 km distance were analyzed by ISSR genotyping. This is a prerequisite for the establishment of efficient management and conservation practices. From 21 ISSR primers tested, only nine revealed consistent and polymorphic bands (loci. PCR reactions resulted in 165 loci, of which 92 were polymorphic (57.5%. Both ΦST (ARLEQUIN and θB (HICKORY presented high values of similar magnitude (0.34, p<0.0001 and 0.33, p<0.0001, respectively, showing that these two groups were highly structured. The dendrogram obtained by the cluster analysis and the scatter-plot of the PCoA corroborate with the data presented by the AMOVA and θB tests. Clear evidence of subdivision among sampling sites was also observed by the Bayesian grouping model analysis (STRUCTURE of the ISSR data. It is clear from this study that conservation strategies should take into account the heterogeneity of these two separate populations, and address actions towards their sustainability by integrating our findings with ecological tools.

  2. Nest Suitability, Fine-Scale Population Structure and Male-Mediated Dispersal of a Solitary Ground Nesting Bee in an Urban Landscape

    OpenAIRE

    López-Uribe, Margarita M.; Morreale, Stephen J.; Santiago, Christine K.; Danforth, bryan N.

    2015-01-01

    Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of g...

  3. Molecular Models of Genetic and Organismic Structures

    CERN Document Server

    Baianu, I C

    2004-01-01

    In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

  4. Molecular Modeling of the Chain Structures of Polybenzoxazines

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The structures and properties of benzoxazines were investigated by virtue of molecular modeling at a molecular level. By means of Cerius software(version 4.0) supplied by Molecular Simulations Inc., the molecular mechanics and the molecular dynamics were performed under a PCFF force field. Five kinds of the polymeric chains of benzoxazines were created by using polymer builder and energy minimization. The relaxation process was conducted with both energy minimization and molecular dynamics.

  5. Effects of gamma radiation on bee venom: preliminary studies

    International Nuclear Information System (INIS)

    Africanized honeybees are very common insects in Brazil and frequently cause accidents followed by important immunological reactions and even deaths. Their venoms are composed of a complex mixture of substances of general biological actions. several works utilizing ionizing radiation showed that it is able to modify protein structures, and successfully detoxify snake venoms toxins, although maintaining its immunological properties. The main objective of this paper was to study the effects of gamma radiation on bee venom, regarding some biochemical and toxicological aspects. Africanized Apis melllifera whole venom (2 mg/ml) in 0.15 M Na Cl solution was irradiated with 2 kGy in a 60 Co source. Preliminary studies has been carried out in order to identify some biochemical changes after irradiation. Concerning this, irradiated and native venom were submitted to a molecular exclusion chromatography (Sephadex G-100), UV absorption spectrum and protein concentration analysis. It could be seen that irradiated bee venom spectrum presented differences when compared to native bee venom, suggesting that some structural alterations has occurred. Protein concentration and chromatography profiles were not changes after irradiation. In order to evaluate the toxicity a lethality assay (L D50) has been performed with both venoms, and irradiated venom showed to be less toxic than native one. (author)

  6. Molecular structure of actinides in biochemistry

    International Nuclear Information System (INIS)

    In case of internal contamination, drugs used for decorporation are scarce and do not act very specifically. For instance the sole de-corporating drug recommended for plutonium decontamination is a water-soluble ligand named DTPA (Diethylene-Triamino-Pentaacetate). The transport of DTPA to its organ-target and its bio-availability on the spot are not satisfactorily understood. The conventional method to develop new ligands is based on molecular approaches but it is not sufficient. A new method that combines methods from structural biochemistry with methods of bio-inorganic chemistry and with methods from physico-chemistry (particularly X-ray absorption spectroscopy) is so far the best way to understand molecular speciation and to detail the local arrangement of atoms around a cation for instance, which are valuable information to understand the behaviour of a ligand. EXAFS (Extended X-ray Absorption Fine structure Spectroscopy) measurements suggest that during the formation of a complex involving an actinide (An) and a ligand, the inter-atomic distance An-O decreases when the atomic number of the cation increases while it is the reverse in the case of An-N

  7. Widespread occurrence of honey bee pathogens in solitary bees.

    Science.gov (United States)

    Ravoet, Jorgen; De Smet, Lina; Meeus, Ivan; Smagghe, Guy; Wenseleers, Tom; de Graaf, Dirk C

    2014-10-01

    Solitary bees and honey bees from a neighbouring apiary were screened for a broad set of putative pathogens including protists, fungi, spiroplasmas and viruses. Most sampled bees appeared to be infected with multiple parasites. Interestingly, viruses exclusively known from honey bees such as Apis mellifera Filamentous Virus and Varroa destructor Macula-like Virus were also discovered in solitary bees. A microsporidium found in Andrena vaga showed most resemblance to Nosema thomsoni. Our results suggest that bee hives represent a putative source of pathogens for other pollinators. Similarly, solitary bees may act as a reservoir of honey bee pathogens. PMID:25196470

  8. Morphological, molecular, and phylogenetic characterization of Nosema cerana, a microsporidian parasite isolated from the European honey bee, Apis mellifera

    Science.gov (United States)

    Nosema ceranae, a microsporidian parasite originally described from Apis cerana, has been found to infect Apis melllifera and is highly pathogenic to its new host. In the present study, data on N. ceranae ultrastructure, host tissue tropism, secondary structures of ribosomal RNA, and phylogenetic ...

  9. Plant sex chromosomes: molecular structure and function.

    Science.gov (United States)

    Jamilena, M; Mariotti, B; Manzano, S

    2008-01-01

    Recent molecular and genomic studies carried out in a number of model dioecious plant species, including Asparagus officinalis, Carica papaya, Silene latifolia, Rumex acetosa and Marchantia polymorpha, have shed light on the molecular structure of both homomorphic and heteromorphic sex chromosomes, and also on the gene functions they have maintained since their evolution from a pair of autosomes. The molecular structure of sex chromosomes in species from different plant families represents the evolutionary pathway followed by sex chromosomes during their evolution. The degree of Y chromosome degeneration that accompanies the suppression of recombination between the Xs and Ys differs among species. The primitive Ys of A. officinalis and C. papaya have only diverged from their homomorphic Xs in a short male-specific and non-recombining region (MSY), while the heteromorphic Ys of S. latifolia, R. acetosa and M. polymorpha have diverged from their respective Xs. As in the Y chromosomes of mammals and Drosophila, the accumulation of repetitive DNA, including both transposable elements and satellite DNA, has played an important role in the divergence and size enlargement of plant Ys, and consequently in reducing gene density. Nevertheless, the degeneration process in plants does not appear to have reached the Y-linked genes. Although a low gene density has been found in the sequenced Y chromosome of M. polymorpha, most of its genes are essential and are expressed in the vegetative and reproductive organs in both male and females. Similarly, most of the Y-linked genes that have been isolated and characterized up to now in S. latifolia are housekeeping genes that have X-linked homologues, and are therefore expressed in both males and females. Only one of them seems to be degenerate with respect to its homologous region in the X. Sequence analysis of larger regions in the homomorphic X and Y chromosomes of papaya and asparagus, and also in the heteromorphic sex chromosomes

  10. Molecular Component Structures Mediated Formation of Self-assemblies

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Molecular recognition directed self-assemblies from complementary molecular components, melamine and barbituric acid derivatives were studied by means of NMR, fluorescence, and TEM. It was found that both the process of the self-assembly and the morphologies of the result ed self-assemblies could be mediated by modifying the structures of the molecular components used. The effect of the structures of the molecular components on the formation of the self-as semblies was discussed in terms of intermolecular interactions.

  11. Molecular structure input on the web

    Directory of Open Access Journals (Sweden)

    Ertl Peter

    2010-02-01

    Full Text Available Abstract A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential. The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

  12. Collective thermoregulation in bee clusters

    OpenAIRE

    Ocko, Samuel A; Mahadevan, L.

    2014-01-01

    Swarming is an essential part of honeybee behaviour, wherein thousands of bees cling onto each other to form a dense cluster that may be exposed to the environment for several days. This cluster has the ability to maintain its core temperature actively without a central controller, and raises the question of how this is achieved. We suggest that the swarm cluster is akin to an active porous structure whose functional requirement is to adjust to outside conditions by varying its porosity to co...

  13. Filamentary structure in the Orion molecular cloud

    International Nuclear Information System (INIS)

    A large scale 13CO map (containing 33,000 spectra) of the giant molecular cloud located in the southern part of Orion is presented which contains the Orion Nebula, NGC1977, and the LI641 dark cloud complex. The overall structure of the cloud is filamentary, with individual features having a length up to 40 times their width. This morphology may result from the effects of star formation in the region or embedded magnetic fields in the cloud. We suggest a simple picture for the evolution of the Orion-A cloud and the formation of the major filament. A rotating proto-cloud (counter rotating with respect to the galaxy) contians a b-field aligned with the galaxtic plane. The northern protion of this cloud collapsed first, perhaps triggered by the pressure of the Ori I OB association. The magnetic field combined with the anisotropic pressure produced by the OB-association breaks the symmetry of the pancake instability, a filament rather than a disc is produced. The growth of instabilities in the filament formed sub-condensations which are recent sites of star formation

  14. The Determination of Molecular Structure from Rotational Spectra

    Science.gov (United States)

    Laurie, V. W.; Herschbach, D. R.

    1962-07-01

    An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

  15. One World: Service Bees

    Science.gov (United States)

    Thomason, Rhonda

    2009-01-01

    Bees are a vital part of the ecology. People of conscience are a vital part of society. In Nina Frenkel's "One World" poster, the bee is also a metaphor for the role of the individual in a diverse society. This article presents a lesson that uses Frenkel's poster to help early-grades students connect these ideas and explore both the importance of…

  16. Wild bees and pollination

    OpenAIRE

    Pfiffner, Lukas; Müller, Andreas

    2016-01-01

    The fact sheet summarizes the current state of academic knowledge on the importance of wild bees in the pollination of wild and cultivated plants. It mentions the known causes for the decline of wild bees, describes the effects of organic farming and lists necessary measures for promotion and protection of the pollinators.

  17. No apparent correlation between honey bee forager gut microbiota and honey production

    OpenAIRE

    Horton, Melissa A.; Oliver, Randy; Irene L. Newton

    2015-01-01

    One of the best indicators of colony health for the European honey bee (Apis mellifera) is its performance in the production of honey. Recent research into the microbial communities naturally populating the bee gut raise the question as to whether there is a correlation between microbial community structure and colony productivity. In this work, we used 16S rRNA amplicon sequencing to explore the microbial composition associated with forager bees from honey bee colonies producing large amount...

  18. Widespread occurrence of honey bee pathogens in solitary bees

    OpenAIRE

    Ravoet, J.; De Smet, L.; Meeus, I; Smagghe, G.; Wenseleers, Tom; de Graaf, D C

    2014-01-01

    Solitary bees and honey bees from a neighbouring apiary were screened for a broad set of putative pathogens including protists, fungi, spiroplasmas and viruses. Most sampled bees appeared to be infected with multiple parasites. Interestingly, viruses exclusively known from honey bees such as Apis mellifera Filamentous Virus and Varroa destructor Macula-like Virus were also discovered in solitary bees. A microsporidium found in Andrena vaga showed most resemblance to Nosema thomsoni. Our resul...

  19. Molecular structure and motion in zero field magnetic resonance

    International Nuclear Information System (INIS)

    Zero field magnetic resonance is well suited for the determination of molecular structure and the study of motion in disordered materials. Experiments performed in zero applied magnetic field avoid the anisotropic broadening in high field nuclear magnetic resonance (NMR) experiments. As a result, molecular structure and subtle effects of motion are more readily observed

  20. New molecular evidence for fragmentation between two distant populations of the threatened stingless bee Melipona subnitida Ducke (Hymenoptera, Apidae, Meliponini)

    OpenAIRE

    Silva,Geice R.; Bruno A. Souza; Pereira,Fabia M.; Lopes,Maria T.R.; Sergio Emílio Valente; Fabio Diniz

    2014-01-01

    For a snapshot assessment of the genetic diversity present within Melipona subnitida, an endemic stingless bee distributed in the semi-arid region of northeastern Brazil, populations separated by over 1,000 km distance were analyzed by ISSR genotyping. This is a prerequisite for the establishment of efficient management and conservation practices. From 21 ISSR primers tested, only nine revealed consistent and polymorphic bands (loci). PCR reactions resulted in 165 loci, of which 92 were polym...

  1. Bee bread

    DEFF Research Database (Denmark)

    Evans, Joshua David

    2015-01-01

    Honeybees (Apis mellifera) have mastered feats of chemical engineering as various as they are alchemical. Their most well-known substances are of course honey, their concentrated, stable, hive-warming energy source, and wax, their pliable, moisture-proof structural material. Yet there are other s...... of raw nuts or avocado....

  2. Ancient Duplications Have Led to Functional Divergence of Vitellogenin-Like Genes Potentially Involved in Inflammation and Oxidative Stress in Honey Bees.

    Science.gov (United States)

    Salmela, Heli; Stark, Taina; Stucki, Dimitri; Fuchs, Siiri; Freitak, Dalial; Dey, Alivia; Kent, Clement F; Zayed, Amro; Dhaygude, Kishor; Hokkanen, Heikki; Sundström, Liselotte

    2016-03-01

    Protection against inflammation and oxidative stress is key in slowing down aging processes. The honey bee (Apis mellifera) shows flexible aging patterns linked to the social role of individual bees. One molecular factor associated with honey bee aging regulation is vitellogenin, a lipoglycophosphoprotein with anti-inflammatory and antioxidant properties. Recently, we identified three genes in Hymenopteran genomes arisen from ancient insect vitellogenin duplications, named vg-like-A, -B, and -C. The function of these vitellogenin homologs is unclear. We hypothesize that some of them might share gene- and protein-level similarities and a longevity-supporting role with vitellogenin. Here, we show how the structure and modifications of the vg-like genes and proteins have diverged from vitellogenin. Furthermore, all three vg-like genes show signs of positive selection, but the spatial location of the selected protein sites differ from those found in vitellogenin. We show that all these genes are expressed in both long-lived winter worker bees and in summer nurse bees with intermediate life expectancy, yet only vg-like-A shows elevated expression in winter bees as found in vitellogenin. Finally, we show that vg-like-A responds more strongly than vitellogenin to inflammatory and oxidative conditions in summer nurse bees, and that also vg-like-B responds to oxidative stress. We associate vg-like-A and, to lesser extent, vg-like-B to the antiaging roles of vitellogenin, but that vg-like-C probably is involved in some other function. Our analysis indicates that an ancient duplication event facilitated the adaptive and functional divergence of vitellogenin and its paralogs in the honey bee. PMID:26961250

  3. Ancient Duplications Have Led to Functional Divergence of Vitellogenin-Like Genes Potentially Involved in Inflammation and Oxidative Stress in Honey Bees

    Science.gov (United States)

    Salmela, Heli; Stark, Taina; Stucki, Dimitri; Fuchs, Siiri; Freitak, Dalial; Dey, Alivia; Kent, Clement F.; Zayed, Amro; Dhaygude, Kishor; Hokkanen, Heikki; Sundström, Liselotte

    2016-01-01

    Protection against inflammation and oxidative stress is key in slowing down aging processes. The honey bee (Apis mellifera) shows flexible aging patterns linked to the social role of individual bees. One molecular factor associated with honey bee aging regulation is vitellogenin, a lipoglycophosphoprotein with anti-inflammatory and antioxidant properties. Recently, we identified three genes in Hymenopteran genomes arisen from ancient insect vitellogenin duplications, named vg-like-A, -B, and -C. The function of these vitellogenin homologs is unclear. We hypothesize that some of them might share gene- and protein-level similarities and a longevity-supporting role with vitellogenin. Here, we show how the structure and modifications of the vg-like genes and proteins have diverged from vitellogenin. Furthermore, all three vg-like genes show signs of positive selection, but the spatial location of the selected protein sites differ from those found in vitellogenin. We show that all these genes are expressed in both long-lived winter worker bees and in summer nurse bees with intermediate life expectancy, yet only vg-like-A shows elevated expression in winter bees as found in vitellogenin. Finally, we show that vg-like-A responds more strongly than vitellogenin to inflammatory and oxidative conditions in summer nurse bees, and that also vg-like-B responds to oxidative stress. We associate vg-like-A and, to lesser extent, vg-like-B to the antiaging roles of vitellogenin, but that vg-like-C probably is involved in some other function. Our analysis indicates that an ancient duplication event facilitated the adaptive and functional divergence of vitellogenin and its paralogs in the honey bee. PMID:26961250

  4. Topological Indices Study of Molecular Structure in Anticancer Drugs

    OpenAIRE

    Wei Gao; Weifan Wang; Mohammad Reza Farahani

    2016-01-01

    Numerous studies indicate that there is strong inherent relationship between the chemical characteristics of chemical compounds and drugs (e.g., boiling point and melting point) and their molecular structures. Topological indices defined on these chemical molecular structures can help researchers better understand the physical features, chemical reactivity, and biological activity. Thus, the study of the topological indices on chemical structure of chemical materials and drugs can make up for...

  5. Ecological adaptation of diverse honey bee (Apis mellifera populations.

    Directory of Open Access Journals (Sweden)

    Robert Parker

    Full Text Available BACKGROUND: Honey bees are complex eusocial insects that provide a critical contribution to human agricultural food production. Their natural migration has selected for traits that increase fitness within geographical areas, but in parallel their domestication has selected for traits that enhance productivity and survival under local conditions. Elucidating the biochemical mechanisms of these local adaptive processes is a key goal of evolutionary biology. Proteomics provides tools unique among the major 'omics disciplines for identifying the mechanisms employed by an organism in adapting to environmental challenges. RESULTS: Through proteome profiling of adult honey bee midgut from geographically dispersed, domesticated populations combined with multiple parallel statistical treatments, the data presented here suggest some of the major cellular processes involved in adapting to different climates. These findings provide insight into the molecular underpinnings that may confer an advantage to honey bee populations. Significantly, the major energy-producing pathways of the mitochondria, the organelle most closely involved in heat production, were consistently higher in bees that had adapted to colder climates. In opposition, up-regulation of protein metabolism capacity, from biosynthesis to degradation, had been selected for in bees from warmer climates. CONCLUSIONS: Overall, our results present a proteomic interpretation of expression polymorphisms between honey bee ecotypes and provide insight into molecular aspects of local adaptation or selection with consequences for honey bee management and breeding. The implications of our findings extend beyond apiculture as they underscore the need to consider the interdependence of animal populations and their agro-ecological context.

  6. The corbiculate bees arose from New World oil-collecting bees: implications for the origin of pollen baskets.

    Science.gov (United States)

    Martins, Aline C; Melo, Gabriel A R; Renner, Susanne S

    2014-11-01

    The economically most important group of bees is the "corbiculates", or pollen basket bees, some 890 species of honeybees (Apis), bumblebees (Bombus), stingless bees (Meliponini), and orchid bees (Euglossini). Molecular studies have indicated that the corbiculates are closest to the New World genera Centris, with 230 species, and Epicharis, with 35, albeit without resolving the precise relationships. Instead of concave baskets, these bees have hairy hind legs on which they transport pollen mixed with floral oil, collected with setae on the anterior and middle legs. We sampled two-thirds of all Epicharis, a third of all Centris, and representatives of the four lineages of corbiculates for four nuclear gene regions, obtaining a well-supported phylogeny that has the corbiculate bees nested inside the Centris/Epicharis clade. Fossil-calibrated molecular clocks, combined with a biogeographic reconstruction incorporating insights from the fossil record, indicate that the corbiculate clade arose in the New World and diverged from Centris 84 (72-95)mya. The ancestral state preceding corbiculae thus was a hairy hind leg, perhaps adapted for oil transport as in Epicharis and Centris bees. Its replacement by glabrous, concave baskets represents a key innovation, allowing efficient transport of plant resins and large pollen/nectar loads and freeing the corbiculate clade from dependence on oil-offering flowers. The transformation could have involved a novel function of Ubx, the gene known to change hairy into smooth pollen baskets in Apis and Bombus. PMID:25034728

  7. [Poisoning by bee sting].

    Science.gov (United States)

    de Roodt, Adolfo R; Salomón, Oscar D; Orduna, Tomás A; Robles Ortiz, Luis E; Paniagua Solís, Jorge F; Alagón Cano, Alejandro

    2005-01-01

    Among the human pathologies produced by venomous animals, bee stings constitute the largest number of accidents in several countries, exceeding the mortality rate caused by other venomous animals such as snakes, spiders or scorpions. The clinical picture after the bee sting may include anaphylaxis or poisoning. The latter is produced by massive attacks and is a serious problem that may put the patient's life at risk. People that are poisoned display hemolysis, rhabdomiolysis and acute renal failure that together with other systemic failures can bring about death. The knowledge of the physiopathological mechanisms involved in the massive attack of bees is crucial for health care professionals as to date we do not have antivenoms with proven clinical efficacy. In this review we include the bee's biological aspects, venom composition and its relation with the occurrence and severity of accidents as well as epidemiological data that can be useful for this type of accidents. PMID:16025987

  8. A Study on Major Components of Bee Venom Using Electrophoresis

    Directory of Open Access Journals (Sweden)

    Lee, Jin-Seon

    2000-12-01

    Full Text Available This study was designed to study on major components of various Bee Venom(Bee Venom by electrical stimulation in Korea; K-BV I, Bee Venom by Microwave stimulation in Korea; K -BV II, 0.5rng/ml, Fu Yu Pharmaceutical Factory, China; C-BV, 1mg /ml, Monmouth Pain Institute, Inc., U.S.A.; A-BV using Electrophoresis. The results were summarized as follows: 1. In 1:4000 Bee Venom solution rate, the band was not displayed distinctly usmg Electrophoresis. But in 1: 1000, the band showed clearly. 2. The results of Electrophoresis at solution rate 1:1000, K-BV I and K-BVII showed similar band. 3. The molecular weight of Phospholipase A2 was known as 19,000 but its band was seen at 17,000 in Electrophoresis. 4. Protein concentration of Bee Venom by Lowry method was different at solution rate 1:4000 ; C-BV was 250μg/ml, K-BV I was 190μg/ml, K-BV Ⅱ was 160μg/ml and C-BV was 45μg/ml. 5. Electrophoresis method was unuseful for analysis of Bee Venom when solution rate is above 1:4000 but Protein concentration of Bee Venom by Lowry method was possible. These data from the study can be applied to establish the standard measurement of Bee Venom and prevent pure bee venom from mixing of another components. I think it is desirable to study more about safety of Bee Venom as time goes by.

  9. Wild bees and agroecosystems

    OpenAIRE

    Morandin, Lora

    2005-01-01

    Research in agriculture often focuses on development of new technologies rather than on potential environmental impacts. Pollinators, primarily bees, are essential to agriculture, providing significant yield benefit in over 66% of crop species. Currently, dramatic losses of managed honey bee pollinators in North America along with suspected world-wide losses of wild pollinators are focusing research attention on an impending but still poorly documented pollination crisis. Essential questions ...

  10. Molecular structural order and anomalies in liquid silica

    OpenAIRE

    Shell, M. S.; Debenedetti, P. G.; Panagiotopoulos, A. Z.

    2002-01-01

    The present investigation examines the relationship between structural order, diffusivity anomalies, and density anomalies in liquid silica by means of molecular dynamics simulations. We use previously defined orientational and translational order parameters to quantify local structural order in atomic configurations. Extensive simulations are performed at different state points to measure structural order, diffusivity, and thermodynamic properties. It is found that silica shares many trends ...

  11. Bees (Hymenoptera, Apoidea, Apiformes in the Agricultural Landscape of Bulgaria: Species Diversity

    Directory of Open Access Journals (Sweden)

    Banaszak Józef

    2014-06-01

    Full Text Available Wild bees (Apiformes were studied in 4 crop fields and 8 refuge habitats for 2 - 5 years in agricultural landscapes in the Pleven and Plovdiv regions of Bulgaria. In total, 233 bee species were recorded. Bee forage plants visited by the honey bee and wild Apiformes are listed for each refuge habitat. Species composition is given for individual habitats, including fields of alfalfa (Medicago sativa, oilseed rape (Brassica napus, sunflower (Helianthus annuus, and radish (Raphanus sativus. Species richness and dominance structure of bee communities in the 2 regions are compared, and species responsible for significant differences are identified.

  12. Antimicrobial Peptide from the Wild Bee Hylaeus signatus Venom and Its Analogues: Structure-Activity Study and Synergistic Effect with Antibiotics.

    Science.gov (United States)

    Nešuta, Ondřej; Hexnerová, Rozálie; Buděšínský, Miloš; Slaninová, Jiřina; Bednárová, Lucie; Hadravová, Romana; Straka, Jakub; Veverka, Václav; Čeřovský, Václav

    2016-04-22

    Venoms of hymenopteran insects have attracted considerable interest as a source of cationic antimicrobial peptides (AMPs). In the venom of the solitary bee Hylaeus signatus (Hymenoptera: Colletidae), we identified a new hexadecapeptide of sequence Gly-Ile-Met-Ser-Ser-Leu-Met-Lys-Lys-Leu-Ala-Ala-His-Ile-Ala-Lys-NH2. Named HYL, it belongs to the category of α-helical amphipathic AMPs. HYL exhibited weak antimicrobial activity against several strains of pathogenic bacteria and moderate activity against Candida albicans, but its hemolytic activity against human red blood cells was low. We prepared a set of HYL analogues to evaluate the effects of structural modifications on its biological activity and to increase its potency against pathogenic bacteria. This produced several analogues exhibiting significantly greater activity compared to HYL against strains of both Staphylococcus aureus and Pseudomonas aeruginosa even as their hemolytic activity remained low. Studying synergism of HYL peptides and conventional antibiotics showed the peptides act synergistically and preferentially in combination with rifampicin. Fluorescent dye propidium iodide uptake showed the tested peptides were able to facilitate entrance of antibiotics into the cytoplasm by permeabilization of the outer and inner bacterial cell membrane of P. aeruginosa. Transmission electron microscopy revealed that treatment of P. aeruginosa with one of the HYL analogues caused total disintegration of bacterial cells. NMR spectroscopy was used to elucidate the structure-activity relationship for the effect of amino acid residue substitution in HYL. PMID:26998557

  13. Molecular and Crystal Structures of Three Berberine Derivatives

    OpenAIRE

    Jiří Dostál; Zdirad Žák; Marek NeÄÂas; Milan PotáÄÂek; Stanislav Man

    2001-01-01

    Berberine azide, berberine thiocyanate, and 8-cyano-8H-berberine were prepared from berberine chloride, a quaternary protoberberine alkaloid. The molecular and crystal structures of all compounds are reported and discussed.

  14. Molecular and Crystal Structures of Three Berberine Derivatives

    Directory of Open Access Journals (Sweden)

    Jiří Dostál

    2001-04-01

    Full Text Available Berberine azide, berberine thiocyanate, and 8-cyano-8H-berberine were prepared from berberine chloride, a quaternary protoberberine alkaloid. The molecular and crystal structures of all compounds are reported and discussed.

  15. Modeling Polymorphic Molecular Crystals with Electronic Structure Theory.

    Science.gov (United States)

    Beran, Gregory J O

    2016-05-11

    Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed. PMID:27008426

  16. Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees.

    Science.gov (United States)

    Tamarit, Daniel; Ellegaard, Kirsten M; Wikander, Johan; Olofsson, Tobias; Vásquez, Alejandra; Andersson, Siv G E

    2015-06-01

    Lactobacillus kunkeei is the most abundant bacterial species in the honey crop and food products of honeybees. The 16 S rRNA genes of strains isolated from different bee species are nearly identical in sequence and therefore inadequate as markers for studies of coevolutionary patterns. Here, we have compared the 1.5 Mb genomes of ten L. kunkeei strains isolated from all recognized Apis species and another two strains from Meliponini species. A gene flux analysis, including previously sequenced Lactobacillus species as outgroups, indicated the influence of reductive evolution. The genome architecture is unique in that vertically inherited core genes are located near the terminus of replication, whereas genes for secreted proteins and putative host-adaptive traits are located near the origin of replication. We suggest that these features have resulted from a genome-wide loss of genes, with integrations of novel genes mostly occurring in regions flanking the origin of replication. The phylogenetic analyses showed that the bacterial topology was incongruent with the host topology, and that strains of the same microcluster have recombined frequently across the host species barriers, arguing against codiversification. Multiple genotypes were recovered in the individual hosts and transfers of mobile elements could be demonstrated for strains isolated from the same host species. Unlike other bacteria with small genomes, short generation times and multiple rRNA operons suggest that L. kunkeei evolves under selection for rapid growth in its natural growth habitat. The results provide an extended framework for reductive genome evolution and functional genome organization in bacteria. PMID:25953738

  17. Gut Pathology and Responses to the Microsporidium Nosema ceranae in the Honey Bee Apis mellifera

    OpenAIRE

    Claudia Dussaubat; Jean-Luc Brunet; Mariano Higes; Colbourne, John K.; Jacqueline Lopez; Jeong-Hyeon Choi; Raquel Martín-Hernández; Cristina Botías; Marianne Cousin; Cynthia McDonnell; Marc Bonnet; Luc P Belzunces; Moritz, Robin F.A.; Yves Le Conte; Cédric Alaux

    2012-01-01

    The microsporidium Nosema ceranae is a newly prevalent parasite of the European honey bee (Apis mellifera). Although this parasite is presently spreading across the world into its novel host, the mechanisms by it which affects the bees and how bees respond are not well understood. We therefore performed an extensive characterization of the parasite effects at the molecular level by using genetic and biochemical tools. The transcriptome modifications at the midgut level were characterized seve...

  18. Magnetic effect on dancing bees

    Science.gov (United States)

    Lindauer, M.; Martin, H.

    1972-01-01

    Bee sensitivity to the earth's magnetic field is studied. Data cover sensitivity range and the use of magnetoreception for orientation purposes. Experimental results indicate bee orientation is aided by gravity fields when the magnetic field is compensated.

  19. Insemination of Honey Bee Queens

    OpenAIRE

    SOJKOVÁ, Lada

    2013-01-01

    Instrumental insemination honey bee queen is in Czech Republic only possibility, how make controlled mating bees. Main significance lies in expanding desirable feature in the bee colony. Instrumental inseminations are thus obtained the required feature, that are the mildness of bees, sitting on the comb, or resistance to disease. Insemination must precede controlled breeding drones and controlled breeding queens. That drones were sexually mature at the time of insemination must be breeding dr...

  20. Paenilarvins: Iturin family lipopeptides from the honey bee pathogen Paenibacillus larvae.

    Science.gov (United States)

    Sood, Sakshi; Steinmetz, Heinrich; Beims, Hannes; Mohr, Kathrin I; Stadler, Marc; Djukic, Marvin; von der Ohe, Werner; Steinert, Michael; Daniel, Rolf; Müller, Rolf

    2014-09-01

    The bacterium Paenibacillus larvae has been extensively studied as it is an appalling honey bee pathogen. In the present work, we screened crude extracts derived from fermentations of P. larvae genotypes ERIC I and II for antimicrobial activity, following the detection of four putative secondary metabolite gene clusters that show high sequence homology to known biosynthetic gene clusters for the biosynthesis of antibiotics. Low molecular weight metabolites produced by P. larvae have recently been shown to have toxic effects on honey bee larvae. Moreover, a novel tripeptide, sevadicin, was recently characterized from laboratory cultures of P. larvae. In this study, paenilarvins, which are iturinic lipopeptides exhibiting strong antifungal activities, were obtained by bioassay-guided fractionation from cultures of P. larvae, genotype ERIC II. Their molecular structures were determined by extensive 2D NMR spectroscopy, high resolution mass spectrometry, and other methods. Paenilarvins are the first antifungal secondary metabolites to be identified from P. larvae. In preliminary experiments, these lipopeptides also affected honey bee larvae and might thus play a role in P. larvae survival and pathogenesis. However, further studies are needed to investigate their function. PMID:25069424

  1. Biochemical characterization, molecular cloning and localization of a putative odorant-binding protein in the honey bee Apis mellifera L. (Hymenoptera : Apidea).

    Science.gov (United States)

    Danty, E; Michard-Vanhée, C; Huet, J C; Genecque, E; Pernollet, J C; Masson, C

    1997-09-15

    A honey bee antennal water-soluble protein, APS2, was purified and characterized as the first Hymenoptera putative odorant-binding protein. Comparison of its measured Mr (13695.2+/-1.6) to that of the corresponding cDNA clone shows it does not undergo any post-translational modification other than a 19-residue signal peptide cleavage and formation of three disulfide bridges. These biochemical features are close to those of Lepidoptera odorant-binding proteins. In situ hybridization experiments demonstrated its specific expression in olfactory areas. Based on its higher expression in the worker than in the drone, ASP2 might be more involved in general odorant than in sex pheromone detection. PMID:9323043

  2. Adsorbed films containing tetrazole on steel surface. 1. Molecular structure

    International Nuclear Information System (INIS)

    By the method of IR- and X-ray electron spectroscopy the molecular structure of the compound formed on steel during exposure to aqueous corrosion - active solution containing tetrazole (tet) is investigated. Most possibility tet act as bridging bidentate ligand form surface complex [Fe(tet)2(H2O)]m which is network polymeric structure. 29 refs.; 4 figs

  3. Euglossine bee communities in small forest fragments of the Atlantic Forest, Rio de Janeiro state, southeastern Brazil (Hymenoptera, Apidae)

    OpenAIRE

    Willian Moura Aguiar; Maria Cristina Gaglianone

    2012-01-01

    Euglossine bee communities in small forest fragments of the Atlantic Forest, Rio de Janeiro state, southeastern Brazil (Hymenoptera, Apidae). Euglossine bees are important pollinators in forests and agricultural areas. Although the structure of their communities is critically affected by anthropogenic disturbances, little is known about these bees in small forest fragments. The objectives of this study were to analyze the composition, abundance, and diversity of euglossine bee species in nine...

  4. Effects of queen importation on the genetic diversity of Macaronesian island honey bee populations (Apis mellifera Linneaus 1758)

    OpenAIRE

    Muñoz, Irene; Pinto, M. Alice; De La Rúa, Pilar

    2014-01-01

    Beekeeping practices such as the importation of non-native honey bee queens may interact with the conservation of honey bee biodiversity. Island honey bee populations are particularly appropriate to test the impact of the introduction of foreign subspecies into their genetic diversity and structure. Here we have used microsatellite markers to evaluate the temporal genetic variation over the last decade in Macaronesian honey bee populations, which have been exposed to different beekeeping stra...

  5. In-vitro infection of pupae with Israeli Acute Paralysis Virus suggests variation for susceptibility and disturbance of transcriptional homeostasis in honey bees (Apis mellifera)

    Science.gov (United States)

    The ongoing decline of honey bee health worldwide is a serious economic and ecological concern. One major contributor to the decline are pathogens, including several honey bee viruses. However, information is limited on the biology of bee viruses and molecular interactions with their hosts. An exper...

  6. Modelling molecular flexibility for crystal structure prediction

    OpenAIRE

    Uzoh, O. G.

    2015-01-01

    In the crystal packing of molecules wherein a single bond links aromatic groups, a change in the torsion angle can optimise close packing of the molecule. The improved intermolecular interactions, Uinter, outweigh the conformational energy penalty, ΔEintra, to give a more stable lattice energy, Elatt = Uinter + ΔEintra. This thesis uses this lattice energy model hierarchically in a new Crystal Structure Prediction (CSP) algorithm, CrystalPredictor version 1.6, which varies the low-barrier tor...

  7. Crystal and molecular structure of paclitaxel (taxol).

    OpenAIRE

    Mastropaolo, D; Camerman, A; Luo, Y.; Brayer, G. D.; Camerman, N

    1995-01-01

    Paclitaxel (formerly called taxol), an important anticancer drug, inhibits cell replication by binding to and stabilizing microtubule polymers. As drug-receptor interactions are governed by the three-dimensional stereochemistries of both participants, we have determined the crystal structure of paclitaxel to identify its conformational preferences that may be related to biological activity. The monoclinic crystals contain two independent paclitaxel molecules in the asymmetric unit plus severa...

  8. Molecular Eigensolution Symmetry Analysis and Fine Structure

    Directory of Open Access Journals (Sweden)

    William G. Harter

    2013-01-01

    Full Text Available Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES. Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES used in Born-Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v, then applied to families of Oh clusters in SF6 spectra and to extreme clusters.

  9. Modelling of Spectroscopic and Structural Properties using Molecular Dynamics

    OpenAIRE

    Francesco Muniz Miranda

    2013-01-01

    The following dissertation is about the study that I performed at the Chemistry Department of the University of Florence and at the European Laboratory for Non- Linear Spectroscopy (LENS) to recover and elucidate structural, dynamical, and spectroscopic molecular features adopting computer simulations. In particular, here ab initio molecular dynamics simulations and time-frequency analysis are the most employed “tools”, in order to have a better understanding of the origins ...

  10. Ionization probes of molecular structure and chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, P.M. [State Univ. of New York, Stony Brook (United States)

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  11. Linking numerical simulations of molecular cloud structure with observations.

    Science.gov (United States)

    Kainulainen, Jouni

    2015-08-01

    Understanding the physical processes that control the life-cycle of the cold interstellar medium (ISM) is one of the key themes in the astrophysics of galaxies today. This importance derives from the role of the cold ISM as the birthplace of new stars, and consequently, as an indivisible constituent of galaxy evolution. In the current paradigm of turbulence-regulated ISM, star formation is controlled by the internal structure of individual molecular clouds, which in turn is set by a complex interplay of turbulence, gravity, and magnetic fields in the clouds. It is in the very focus of the field to determine how these processes give rise to the observed structure of molecular clouds. In this talk, I will review our current efforts to confront this paradigm with the goal of observationally constraining how different processes regulate molecular cloud structure and star formation. At the heart of these efforts lies the use of numerical simulations of gravo-turbulent media to A) define physically meaningful characteristics that are sensitive to the different cloud-shaping processes, and B) determine if and how such characteristics can be recovered by observations. I will show in my talk how this approach has recently led to new constraints for some fundamental measures of the molecular cloud structure. Such constraints allow us to assess the roles of turbulence and gravity in controlling the ISM structure and star formation. I will also highlight specific recent results, focusing on the nature of filamentary structures within molecular clouds. These results may provide a novel set of observational constraints with which to challenge the turbulence-regulated ISM paradigm. Finally, I will discuss the current challenges and open questions in understanding the link between molecular cloud structure and star formation, and speculate on key directions to aim the near-future studies.

  12. The mitochondrial genome of the stingless bee Melipona bicolor (Hymenoptera, Apidae, Meliponini): sequence, gene organization and a unique tRNA translocation event conserved across the tribe Meliponini

    OpenAIRE

    Daniela Silvestre; Mark Dowton; Maria Cristina Arias

    2008-01-01

    At present a complete mtDNA sequence has been reported for only two hymenopterans, the Old World honey bee, Apis mellifera and the sawfly Perga condei. Among the bee group, the tribe Meliponini (stingless bees) has some distinction due to its Pantropical distribution, great number of species and large importance as main pollinators in several ecosystems, including the Brazilian rain forest. However few molecular studies have been conducted on this group of bees and few sequence data from mito...

  13. Watching coherent molecular structural dynamics during photoreaction: beyond kinetic description

    CERN Document Server

    Lemke, Henrik T; Hartsock, Robert; van Driel, Tim Brandt; Chollet, Matthieu; Glownia, J M; Song, Sanghoon; Zhu, Diling; Pace, Elisabetta; Nielsen, Martin M; Benfatto, Maurizio; Gaffney, Kelly J; Collet, Eric; Cammarata, Marco

    2015-01-01

    A deep understanding of molecular photo-transformations occurring is challenging because of the complex interaction between electronic and nuclear structure. The initially excited electronic energy dissipates into electronic and structural reconfigurations often in less than a billionth of a second. Molecular dynamics induced by photoexcitation have been very successfully studied with femtosecond optical spectroscopies, but electronic and nuclear dynamics are often very difficult to disentangle. X-ray based spectroscopies can reduce the ambiguity between theoretical models and experimental data, but it is only with the recent development of bright ultrafast X-ray sources, that key information during transient molecular processes can be obtained on their intrinsic timescale. We use Free Electron Laser (FEL) based time-resolved X-ray Absorption Near Edge Structure (XANES) measurements around the Iron K-edge of a spin crossover prototypical compound. We reveal its transformation from the ligand-located electroni...

  14. Differential gene expression of two extreme honey bee (Apis mellifera) colonies showing varroa tolerance and susceptibility.

    Science.gov (United States)

    Jiang, S; Robertson, T; Mostajeran, M; Robertson, A J; Qiu, X

    2016-06-01

    Varroa destructor, an ectoparasitic mite of honey bees (Apis mellifera), is the most serious pest threatening the apiculture industry. In our honey bee breeding programme, two honey bee colonies showing extreme phenotypes for varroa tolerance/resistance (S88) and susceptibility (G4) were identified by natural selection from a large gene pool over a 6-year period. To investigate potential defence mechanisms for honey bee tolerance to varroa infestation, we employed DNA microarray and real time quantitative (PCR) analyses to identify differentially expressed genes in the tolerant and susceptible colonies at pupa and adult stages. Our results showed that more differentially expressed genes were identified in the tolerant bees than in bees from the susceptible colony, indicating that the tolerant colony showed an increased genetic capacity to respond to varroa mite infestation. In both colonies, there were more differentially expressed genes identified at the pupa stage than at the adult stage, indicating that pupa bees are more responsive to varroa infestation than adult bees. Genes showing differential expression in the colony phenotypes were categorized into several groups based on their molecular functions, such as olfactory signalling, detoxification processes, exoskeleton formation, protein degradation and long-chain fatty acid metabolism, suggesting that these biological processes play roles in conferring varroa tolerance to naturally selected colonies. Identification of differentially expressed genes between the two colony phenotypes provides potential molecular markers for selecting and breeding varroa-tolerant honey bees. PMID:26919127

  15. Phylogenetic analysis of honey bee behavioral evolution.

    Science.gov (United States)

    Raffiudin, Rika; Crozier, Ross H

    2007-05-01

    DNA sequences from three mitochondrial (rrnL, cox2, nad2) and one nuclear gene (itpr) from all 9 known honey bee species (Apis), a 10th possible species, Apis dorsata binghami, and three outgroup species (Bombus terrestris, Melipona bicolor and Trigona fimbriata) were used to infer Apis phylogenetic relationships using Bayesian analysis. The dwarf honey bees were confirmed as basal, and the giant and cavity-nesting species to be monophyletic. All nodes were strongly supported except that grouping Apis cerana with A. nigrocincta. Two thousand post-burnin trees from the phylogenetic analysis were used in a Bayesian comparative analysis to explore the evolution of dance type, nest structure, comb structure and dance sound within Apis. The ancestral honey bee species was inferred with high support to have nested in the open, and to have more likely than not had a silent vertical waggle dance and a single comb. The common ancestor of the giant and cavity-dwelling bees is strongly inferred to have had a buzzing vertical directional dance. All pairwise combinations of characters showed strong association, but the multiple comparisons problem reduces the ability to infer associations between states between characters. Nevertheless, a buzzing dance is significantly associated with cavity-nesting, several vertical combs, and dancing vertically, a horizontal dance is significantly associated with a nest with a single comb wrapped around the support, and open nesting with a single pendant comb and a silent waggle dance. PMID:17123837

  16. Genetic variability in captive populations of the stingless bee Tetragonisca angustula.

    Science.gov (United States)

    Santiago, Leandro R; Francisco, Flávio O; Jaffé, Rodolfo; Arias, Maria C

    2016-08-01

    Low genetic variability has normally been considered a consequence of animal husbandry and a major contributing factor to declining bee populations. Here, we performed a molecular analysis of captive and wild populations of the stingless bee Tetragonisca angustula, one of the most commonly kept species across South America. Microsatellite analyses showed similar genetic variability between wild and captive populations However, captive populations showed lower mitochondrial genetic variability. Male-mediated gene flow, transport and division of nests are suggested as the most probable explanations for the observed patterns of genetic structure. We conclude that increasing the number of colonies kept through nest divisions does not negatively affect nuclear genetic variability, which seems to be maintained by small-scale male dispersal and human-mediated nest transport. However, the transport of nests from distant localities should be practiced with caution given the high genetic differentiation observed between samples from western and eastern areas. The high genetic structure verified is the result of a long-term evolutionary process, and bees from distant localities may represent unique evolutionary lineages. PMID:27305916

  17. Behavior genetics: Bees as model

    International Nuclear Information System (INIS)

    The honeybee Apis mellifera (Apidae) is a model widely used in behavior because of its elaborate social life requiring coordinate actions among the members of the society. Within a colony, division of labor, the performance of tasks by different individuals, follows genetically determined physiological changes that go along with aging. Modern advances in tools of molecular biology and genomics, as well as the sequentiation of A. mellifera genome, have enabled a better understanding of honeybee behavior, in particular social behavior. Numerous studies show that aspects of worker behavior are genetically determined, including defensive, hygienic, reproductive and foraging behavior. For example, genetic diversity is associated with specialization to collect water, nectar and pollen. Also, control of worker reproduction is associated with genetic differences. In this paper, I review the methods and the main results from the study of the genetic and genomic basis of some behaviors in bees.

  18. Contrasting responses of hoverflies and wild bees to habitat structure and land use change in a tropical landscape (southern Yunnan, SW China)

    Institute of Scientific and Technical Information of China (English)

    Ling-Zeng Meng; Konrad Martin; Jing-Xin Liu; Frank Burger; Jin Chen

    2012-01-01

    The response of insects to monoculture plantations has mainly proceeded at the expense of natural forest areas,and is an outstanding and important issue in ecology and conservation biology,with pollination services declined around the world.In this study,species richness and distribution of hoverfly and wild bee communities were investigated in a changing tropical landscape in southern Yunnan,south-west China by Malaise traps periodically from 2008 to 2009.Species were recorded from the traditional land use types (natural forest,grassland,shrubland and rice field fallows),and from recently established rubber plantations of different ages.Hoverflies (total 53 species) were most common in young successional stages of vegetation,including rice field fallow and shrubland.Species richness was highest in rice field fallows and lowest in forests and showed a highly significant relationship with the number of forb species and ground vegetation cover.In contrast,the highest richness of wild bees (total 44 species) was recorded from the natural forest sites,which showed a discrete bee community composition compared to the remaining habitat types.There was no significant relationship between the bee species richness and the environmental variables,including the numbers of different plant life forms,coverage of canopy and ground vegetation,successional age of vegetation and land use type.At the landscape scale,open land use systems,including young rubber plantations,are assumed to increase the species richness ofhoverflies; however,this might decrease wild bee diversity.The present land use change by rubber cultivation can be expected to have negative impacts on the native wild bee communities.

  19. On the structure of molecular clouds

    CERN Document Server

    Ballesteros-Paredes,; D'Alessio,; P.,; Hartmann,; W., L

    2012-01-01

    We show that the inter-cloud Larson scaling relation between mean volume density and size $\\rho\\propto R^{-1}$, which in turn implies that mass $M\\propto R^2$, or that the column density $N$ is constant, is an artifact of the observational methods used. Specifically, setting the column density threshold near or above the peak of the column density probability distribution function Npdf ($N\\sim 10^{21}$ cm\\alamenos 2) produces the Larson scaling as long as the Npdf decreases rapidly at higher column densities. We argue that the physical reasons behind local clouds to have this behavior are that (1) this peak column density is near the value required to shield CO from photodissociation in the solar neighborhood, and (2) gas at higher column densities is rare because it is susceptible to gravitational collapse into much smaller structures in specific small regions of the cloud. Similarly, we also use previous results to show that if instead a threshold is set for the volume density, the density will appear to be...

  20. Crystal and molecular structure of aflatrem

    Directory of Open Access Journals (Sweden)

    Bruno N. Lenta

    2015-11-01

    Full Text Available The crystal structure of the title compound, C32H39NO4, confirms the absolute configuration of the seven chiral centres in the molecule. The molecule has a 1,1-dimethylprop-2-enyl substituent on the indole nucleus and this nucleus shares one edge with the five-membered ring which is, in turn, connected to a sequence of three edge-shared fused rings. The skeleton is completed by the 7,7-trimethyl-6,8-dioxabicyclo[3.2.1]oct-3-en-2-one group connected to the terminal cyclohexene ring. The two cyclohexane rings adopt chair and half-chair conformations, while in the dioxabicyclo[3.2.1]oct-3-en-2-one unit, the six-membered ring has a half-chair conformation. The indole system of the molecule exhibits a tilt of 2.02 (1° between its two rings. In the crystal, O—H...O hydrogen bonds connect molecules into chains along [010]. Weak N—H...π interactions connect these chains, forming sheets parallel to (10-1.

  1. Differential diagnosis of the honey bee trypanosomatids Crithidia mellificae and Lotmaria passim.

    Science.gov (United States)

    Ravoet, Jorgen; Schwarz, Ryan S; Descamps, Tine; Yañez, Orlando; Tozkar, Cansu Ozge; Martin-Hernandez, Raquel; Bartolomé, Carolina; De Smet, Lina; Higes, Mariano; Wenseleers, Tom; Schmid-Hempel, Regula; Neumann, Peter; Kadowaki, Tatsuhiko; Evans, Jay D; de Graaf, Dirk C

    2015-09-01

    Trypanosomatids infecting honey bees have been poorly studied with molecular methods until recently. After the description of Crithidia mellificae (Langridge and McGhee, 1967) it took about forty years until molecular data for honey bee trypanosomatids became available and were used to identify and describe a new trypanosomatid species from honey bees, Lotmaria passim (Evans and Schwarz, 2014). However, an easy method to distinguish them without sequencing is not yet available. Research on the related bumble bee parasites Crithidia bombi and Crithidia expoeki revealed a fragment length polymorphism in the internal transcribed spacer 1 (ITS1), which enabled species discrimination. In search of fragment length polymorphisms for differential diagnostics in honey bee trypanosomatids, we studied honey bee trypanosomatid cell cultures of C. mellificae and L. passim. This research resulted in the identification of fragment length polymorphisms in ITS1 and ITS1-2 markers, which enabled us to develop a diagnostic method to differentiate both honey bee trypanosomatid species without the need for sequencing. However, the amplification success of the ITS1 marker depends probably on the trypanosomatid infection level. Further investigation confirmed that L. passim is the dominant species in Belgium, Japan and Switzerland. We found C. mellificae only rarely in Belgian honey bee samples, but not in honey bee samples from other countries. C. mellificae was also detected in mason bees (Osmia bicornis and Osmia cornuta) besides in honey bees. Further, the characterization and comparison of additional markers from L. passim strain SF (published as C. mellificae strain SF) and a Belgian honey bee sample revealed very low divergence in the 18S rRNA, ITS1-2, 28S rRNA and cytochrome b sequences. Nevertheless, a variable stretch was observed in the gp63 virulence factor. PMID:26146231

  2. Floral nectar guide patterns discourage nectar robbing by bumble bees.

    Directory of Open Access Journals (Sweden)

    Anne S Leonard

    Full Text Available Floral displays are under selection to both attract pollinators and deter antagonists. Here we show that a common floral trait, a nectar guide pattern, alters the behavior of bees that can act opportunistically as both pollinators and as antagonists. Generally, bees access nectar via the floral limb, transporting pollen through contact with the plant's reproductive structures; however bees sometimes extract nectar from a hole in the side of the flower that they or other floral visitors create. This behavior is called "nectar robbing" because bees may acquire the nectar without transporting pollen. We asked whether the presence of a symmetric floral nectar guide pattern on artificial flowers affected bumble bees' (Bombus impatiens propensity to rob or access nectar "legitimately." We discovered that nectar guides made legitimate visits more efficient for bees than robbing, and increased the relative frequency of legitimate visits, compared to flowers lacking nectar guides. This study is the first to show that beyond speeding nectar discovery, a nectar guide pattern can influence bees' flower handling in a way that could benefit the plant.

  3. Nosema ceranae escapes fumagillin control in honey bees.

    Directory of Open Access Journals (Sweden)

    Wei-Fone Huang

    2013-03-01

    Full Text Available Fumagillin is the only antibiotic approved for control of nosema disease in honey bees and has been extensively used in United States apiculture for more than 50 years for control of Nosema apis. It is toxic to mammals and must be applied seasonally and with caution to avoid residues in honey. Fumagillin degrades or is diluted in hives over the foraging season, exposing bees and the microsporidia to declining concentrations of the drug. We showed that spore production by Nosema ceranae, an emerging microsporidian pathogen in honey bees, increased in response to declining fumagillin concentrations, up to 100% higher than that of infected bees that have not been exposed to fumagillin. N. apis spore production was also higher, although not significantly so. Fumagillin inhibits the enzyme methionine aminopeptidase2 (MetAP2 in eukaryotic cells and interferes with protein modifications necessary for normal cell function. We sequenced the MetAP2 gene for apid Nosema species and determined that, although susceptibility to fumagillin differs among species, there are no apparent differences in fumagillin binding sites. Protein assays of uninfected bees showed that fumagillin altered structural and metabolic proteins in honey bee midgut tissues at concentrations that do not suppress microsporidia reproduction. The microsporidia, particularly N. ceranae, are apparently released from the suppressive effects of fumagillin at concentrations that continue to impact honey bee physiology. The current application protocol for fumagillin may exacerbate N. ceranae infection rather than suppress it.

  4. Molecular structure and elastic properties of thermotropic liquid crystals: Integrated molecular dynamics—Statistical mechanical theory vs molecular field approach

    Science.gov (United States)

    Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.

    2013-03-01

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  5. Molecular structure and elastic properties of thermotropic liquid crystals: integrated molecular dynamics--statistical mechanical theory vs molecular field approach.

    Science.gov (United States)

    Ilk Capar, M; Nar, A; Ferrarini, A; Frezza, E; Greco, C; Zakharov, A V; Vakulenko, A A

    2013-03-21

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio

  6. Sandhills native bee survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report includes the results of a bee survey conducted in Sandhills region of north and south Carolina on May 18th and 19th 2006. Part of the survey was...

  7. XOR-based artificial bee colony algorithm for binary optimization

    OpenAIRE

    KIRAN, Mustafa Servet; Gündüz, Mesut

    2012-01-01

    The artificial bee colony (ABC) algorithm, which was inspired by the foraging and dance behaviors of real honey bee colonies, was first introduced for solving numerical optimization problems. When the solution space of the optimization problem is binary-structured, the basic ABC algorithm should be modified for solving this class of problems. In this study, we propose XOR-based modification for the solution-updating equation of the ABC algorithm in order to solve binary optimization pro...

  8. Optimization techniques in molecular structure and function elucidation

    OpenAIRE

    Sahinidis, Nikolaos V.

    2009-01-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly ...

  9. Molecular Structure of DNA by Scanning Tunneling Microscopy

    Science.gov (United States)

    Cricenti, A.; Selci, S.; Felici, A. C.; Generosi, R.; Gori, E.; Djaczenko, W.; Chiarotti, G.

    1989-09-01

    Uncoated DNA molecules marked with an activated tris(1-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 and 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.

  10. THE REFINEMENT OF NMR STRUCTURES BY MOLECULAR-DYNAMICS SIMULATION

    NARCIS (Netherlands)

    TORDA, AE; VANGUNSTEREN, WF

    1991-01-01

    We discuss the use of molecular dynamics simulations as a tool for the refinement of structures based on NMR data. The procedure always involves the construction of a pseudo-energy term to model the experimental data and we consider the various approaches to this problem. We detail recent work where

  11. A SAPO-11 Silicoaluminophosphate Molecular Sieve with Stable Crystal Structure

    Institute of Scientific and Technical Information of China (English)

    Yue Ming LIU; Feng Mei ZHANG; Hai Hong WU; Hai Jiao ZHANG; Jian Guo YANG; Xing Tian SHU; Ming Yuan HE

    2004-01-01

    A SAPO-11 silicoaluminophosphate molecular sieve with stable crystal structure was synthesized for the first time. After removing template by calcination, its crystal space group still retains Icm2 which the as-synthesized has. The catalyst deriving from the present SAPO-11materials shows higher isomerization selectivity and higher paraffin hydroisomerization yield than those reported elsewhere.

  12. Nonlinear excitations in two-dimensional molecular structures with impurities

    DEFF Research Database (Denmark)

    Gaididei, Yuri Borisovich; Rasmussen, Kim; Christiansen, Peter Leth

    1995-01-01

    We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence of the imp...

  13. Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model

    Science.gov (United States)

    Zhao, Song-Feng; Huang, Fang; Wang, Guo-Li; Zhou, Xiao-Xin

    2016-03-01

    We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov-Popov-Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  14. Special Issue: Honey Bee Viruses

    Directory of Open Access Journals (Sweden)

    Sebastian Gisder

    2015-10-01

    Full Text Available Pollination of flowering plants is an important ecosystem service provided by wild insect pollinators and managed honey bees. Hence, losses and declines of pollinating insect species threaten human food security and are of major concern not only for apiculture or agriculture but for human society in general. Honey bee colony losses and bumblebee declines have attracted intensive research interest over the last decade and although the problem is far from being solved we now know that viruses are among the key players of many of these bee losses and bumblebee declines. With this special issue on bee viruses we, therefore, aimed to collect high quality original papers reflecting the current state of bee virus research. To this end, we focused on newly discovered viruses (Lake Sinai viruses, bee macula-like virus, or a so far neglected virus species (Apis mellifera filamentous virus, and cutting edge technologies (mass spectrometry, RNAi approach applied in the field.

  15. Molecular solids of actinide hexacyanoferrate: Structure and bonding

    International Nuclear Information System (INIS)

    The hexacyanometallate family is well known in transition metal chemistry because the remarkable electronic delocalization along the metal-cyano-metal bond can be tuned in order to design systems that undergo a reversible and controlled change of their physical properties. We have been working for few years on the description of the molecular and electronic structure of materials formed with [Fe(CN)6]n- building blocks and actinide ions (An = Th, U, Np, Pu, Am) and have compared these new materials to those obtained with lanthanide cations at oxidation state +III. In order to evaluate the influence of the actinide coordination polyhedron on the three-dimensional molecular structure, both atomic number and formal oxidation state have been varied : oxidation states +III, +IV. EXAFS at both iron K edge and actinide LIII edge is the dedicated structural probe to obtain structural information on these systems. Data at both edges have been combined to obtain a three-dimensional model. In addition, qualitative electronic information has been gathered with two spectroscopic tools : UV-Near IR spectrophotometry and low energy XANES data that can probe each atom of the structural unit : Fe, C, N and An. Coupling these spectroscopic tools to theoretical calculations will lead in the future to a better description of bonding in these molecular solids. Of primary interest is the actinide cation ability to form ionic - covalent bonding as 5f orbitals are being filled by modification of oxidation state and/or atomic number.

  16. Design of Carborane Molecular Architectures via Electronic Structure Computations

    Directory of Open Access Journals (Sweden)

    Josep M. Oliva

    2009-01-01

    Full Text Available Quantum-mechanical electronic structure computations were employed to explore initial steps towards a comprehensive design of polycarborane architectures through assembly of molecular units. Aspects considered were (i the striking modification of geometrical parameters through substitution, (ii endohedral carboranes and proposed ejection mechanisms for energy/ion/atom/energy storage/transport, (iii the excited state character in single and dimeric molecular units, and (iv higher architectural constructs. A goal of this work is to find optimal architectures where atom/ion/energy/spin transport within carborane superclusters is feasible in order to modernize and improve future photoenergy processes.

  17. Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection

    Directory of Open Access Journals (Sweden)

    Evans JD

    2008-06-01

    bees, and give an indication of the specific physiological changes found in parasitized bees. They provide a first step toward better understanding molecular pathways involved in this important host-parasite relationship.

  18. Molecular spectroscopy and molecular structure - Selected communications presented at the 1st International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013)

    Science.gov (United States)

    Durig, James R.; Fausto, Rui; Ünsalan, Ozan; Bayarı, Sevgi; Kuş, Nihal; Ildız, Gülce Ö.

    2016-01-01

    The First International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013) took place at the Harbiye Cultural Center & Museum, Istanbul, Turkey, September 15-20, 2013. The main aim of the congress was to encourage the exchange of scientific ideas and collaborations all around the world, introduce new techniques and instruments, and discuss recent developments in the field of molecular spectroscopy. Among the different subjects covered, particular emphasis was given to the relevance of spectroscopy to elucidate details of the molecular structure and the chemical and physical behavior of systems ranging from simple molecules to complex biochemical molecules. Besides experimental spectroscopic approaches, related computational and theoretical methods were also considered. In this volume, selected contributions presented at the congress were put together.

  19. The influence of Nosema (Microspora: Nosematidae) infection on honey bee (Hymenoptera: Apidae) defense against Varroa destructor (Mesostigmata: Varroidae).

    Science.gov (United States)

    Bahreini, Rassol; Currie, Robert W

    2015-11-01

    The objectives of this study were to quantify the costs and benefits of co-parasitism with Varroa (Varroa destructor Anderson and Trueman) and Nosema (Nosema ceranae Fries and Nosema apis Zander) on honey bees (Apis mellifera L.) with different defense levels. Newly-emerged worker bees from either high-mite-mortality-rate (high-MMR) bees or low-mite-mortality-rate (low-MMR) bees were confined in forty bioassay cages which were either inoculated with Nosema spores [Nosema (+) group] or were left un-inoculated [Nosema (-) group]. Caged-bees were then inoculated with Varroa mites [Varroa (+) group] or were left untreated [Varroa (-) group]. This established four treatment combinations within each Nosema treatment group: (1) low-MMR Varroa (-), (2) high-MMR Varroa (-), (3) low-MMR Varroa (+) and (4) high-MMR Varroa (+), each with five replicates. Overall mite mortality in high-MMR bees (0.12±0.02 mites per day) was significantly greater than in the low-MMR bees (0.06±0.02 mites per day). In the Nosema (-) groups bee mortality was greater in high-MMR bees than low-MMR bees but only when bees had a higher mite burden. Overall, high-MMR bees in the Nosema (-) group showed greater reductions in mean abundance of mites over time compared with low-MMR bees, when inoculated with additional mites. However, high-MMR bees could not reduce mite load as well as in the Nosema (-) group when fed with Nosema spores. Mean abundance of Nosema spores in live bees and dead bees of both strains of bees was significantly greater in the Nosema (+) group. Molecular analyses confirmed the presence of both Nosema species in inoculated bees but N. ceranae was more abundant than N. apis and unlike N. apis increased over the course of the experiment. Collectively, this study showed differential mite mortality rates among different genotypes of bees, however, Nosema infection restrained Varroa removal success in high-MMR bees. PMID:26283465

  20. Ab initio molecular crystal structures, spectra, and phase diagrams.

    Science.gov (United States)

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  1. Spatial patterns of honey bee (Apis mellifera L.) genetic diversity in continental Portugal: the story told by mitochondrial DNA

    OpenAIRE

    Pinto, M. Alice; Muñoz, Irene; Brandão, Andreia; Neto, Margarida; Guedes, Helena; Souza, Larissa; Baptista, Paula; Pires, Sância; De La Rúa, Pilar

    2010-01-01

    Over 24 honey bee (Apis mellifera L.) subspecies occur naturally in Europe, Africa and the Middle East. Morphological and molecular markers have grouped this wide-ranging diversity into four lineages (A, M, C, O). The Iberian Peninsula harbours two of such lineages (A and M) and the greatest honey bee maternal diversity and complexity across Europe. While the Spanish honey bee populations have been extensively surveyed for mtDNA variation, the genetic composition of the populations inhabiting...

  2. Bumblebees and solitary bees

    DEFF Research Database (Denmark)

    Henriksen, Casper Christian I

    quadrupling the organic arable area. Instead, bumblebees responded to perennial flower resources in the road verge/grassy field border and semi-natural habitats in the landscape. Organically managed arable fields with mostly annual non-crop flowering plants in intensively cultivated landscapes probably played......Summary: The effects of farming system, flower resources and semi-natural habitats on bumblebees and solitary bees in intensively cultivated landscapes in Denmark were investigated in two sets of studies, in 2011 and 2012. The pan trap colour preferences of bumblebees and solitary bees were also...... of dicotyledonous herbs in the flowering stage (quantity) and density of plants containing combined high pollen and nectar amounts (quality). Potential flower and nesting resources (referred to as semi-natural habitats) in the surrounding landscape were assessed using up-to-date, spatially precise...

  3. Imaging molecular structure and dynamics using laser driven recollisions

    International Nuclear Information System (INIS)

    Complete test of publication follows. Laser driven electron recollision provides a unique tool for measuring the structure and dynamics of matter. We illustrate this with experiments that use HHG to measure molecular structure with sub-Angstrom spatial and sub-femtosecond temporal resolution. Our recent work has looked in particular at the signal from high order harmonic generation which contains rich information about the structure and intra-molecular dynamics of small molecules. This we will illustrate by two types of experiment; (a) measurements of HHG from aligned molecular samples to observe two-centre recombination interference and electronic structure dependence of the angle dependent yield, (b) reconstruction of intra-molecular proton dynamics from the spectral dependence of the HHG using the intrinsic chirp of recolliding electrons. We experimentally investigate the process of intramolecular quantum interference in high-order harmonic generation in impulsively aligned CO2 molecules. The recombination interference effect is clearly seen through the order dependence of the harmonic yield in an aligned sample. This confirms that the effective de Broglie wavelength of the returning electron wave is not significantly altered by acceleration in the Coulomb field of the molecular ion. For the first time, to our knowledge, we demonstrate that such interference effects can be effectively controlled by changing the ellipticity of the driving laser field. Here we also report the results of angular dependence measurements of high order harmonics (17tth - 27th) from impulsively aligned organic molecules: Acetylene, Ethylene, and Allene. Since these molecules have a relatively low Ip an appropriately short pulse is required to produce as many harmonic orders as possible. This was provided by the ∼ 10 fs beam line of the ASTRA laser at Rutherford Appleton Laboratory whilst a somewhat longer pulse, properly forwarded with respect to the driving pulse, induced the

  4. A Modiifed Molecular Structure Mechanics Method for Analysis of Graphene

    Institute of Scientific and Technical Information of China (English)

    HUA Jun; LI Dongbo; ZHAO Dong; LIANG Shengwei; LIU Qinlong; JIA Ruiyan

    2015-01-01

    Based on molecular mechanics and the deformation characteristics of the atomic lattice structure of graphene, a modiifed molecular structure mechanics method was developed to improve the original one, that is, the semi-rigid connections were used to model the bond angle variations between the C-C bonds in graphene. The simulated results show that the equivalent space frame model with semi-rigid connections for graphene proposed in this article is a simple, efifcient, and accurate model to evaluate the equivalent elastic properties of graphene. Though the present computational model of the semi-rigid connected space frame is only applied to characterize the mechanical behaviors of the space lattices of graphene, it has more potential applications in the static and dynamic analyses of graphene and other nanomaterials.

  5. A new parametrizable model of molecular electronic structure

    OpenAIRE

    Laikov, Dimitri N.

    2011-01-01

    A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good...

  6. Preparation and structure characterization of nanospherical MCM- 41 molecular sieves

    OpenAIRE

    Chen, Ting; WEI Yiting; Guo, Yajun; CHU Lianfeng; Guo, Yaping

    2013-01-01

    Nanospherical MCM-41 molecular sieves have been synthesized by using hexadecyl trimethyl ammonium bromide (CTAB) as templates and tetraethyl orthosilicate (TEOS) as silicon sources. XRD,SEM,FT-IR,TEM,and N2 adsorption-desorption isotherms were used to investigate the effects of the reaction temperature and aging time on the morphology and structure of the samples. The results show that the nanospherical MCM-41 particles can be obtained at reaction temperatures between 20 to 80℃. With the reac...

  7. Improvised Scout Bee Movements in Artificial Bee Colony

    Directory of Open Access Journals (Sweden)

    Tarun Kumar Sharma

    2014-01-01

    Full Text Available In the basic Artificial Bee Colony (ABC algorithm, if the fitness value associated with a food source is not improved for a certain number of specified trials then the corresponding bee becomes a scout to which a random value is assigned for finding the new food source. Basically, it is a mechanism of pulling out the candidate solution which may be entrapped in some local optimizer due to which its value is not improving. In the present study, we propose two new mechanisms for the movements of scout bees. In the first method, the scout bee follows a non-linear interpolated path while in the second one, scout bee follows Gaussian movement. Numerical results and statistical analysis of benchmark unconstrained, constrained and real life engineering design problems indicate that the proposed modifications enhance the performance of ABC.

  8. Dynamical structure of fluid mercury: Molecular-dynamics simulations

    OpenAIRE

    Hoshino, Kozo; Tanaka, Shunichiro; Shimojo, Fuyuki

    2007-01-01

    We have carried out molecular-dynamics simulations for nonmetallic fluid mercury in liquid and vapor phases using a Lennard-Jones type effective potential and shown that the structure factors S(Q) and the dynamic structure factors S(Q, omega) of nonmetallic fluid mercury obtained by our MD simulations are in good agreement with recent X-ray diffraction and inelastic X-ray scattering experiments. We conclude from these results that, though the fluid mercury which shows a metal-nonmetal transit...

  9. Optimization techniques in molecular structure and function elucidation.

    Science.gov (United States)

    Sahinidis, Nikolaos V

    2009-12-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly via combinatorial optimization algorithms that are applied to discrete approximations. The main purpose of the paper is to offer an introduction and motivate further systems approaches to these problems. PMID:20160866

  10. Microspectroscopy as applied to the study of wood molecular structure

    DEFF Research Database (Denmark)

    Fackler, Karin; Thygesen, Lisbeth Garbrecht

    2013-01-01

    -induced dimensional changes, decay resistance or mechanical properties. It is, however, important to choose the right technique for the purpose at hand and to apply it in a suitable way if any new insights are to be gained. This review presents and compares three different microspectroscopic techniques: infrared......Microspectroscopy gives access to spatially resolved information on the molecular structure and chemical composition of a material. For a highly heterogeneous and anisotropic material like wood, such information is essential when assessing structure/property relationships such as moisture...

  11. Bee-inspired protocol engineering

    CERN Document Server

    Farooq, Muddassar

    2008-01-01

    Honey bee colonies demonstrate robust adaptive efficient agent-based communications and task allocations without centralized controls - desirable features in network design. This book introduces a multi path routing algorithm for packet-switched telecommunication networks based on techniques observed in bee colonies.

  12. Safety with Wasps and Bees.

    Science.gov (United States)

    Hackett, Erla

    This guide is designed to provide elementary school teachers with safe learning activities concerning bees and wasps. The following topics are included: (1) the importance of a positive teacher attitude towards bees and wasps; (2) special problems posed by paper wasps; (3) what to do when a child is bothered by a wasp; (4) what to do if a wasp…

  13. 7 CFR 322.29 - Dead bees.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 5 2010-01-01 2010-01-01 false Dead bees. 322.29 Section 322.29 Agriculture..., DEPARTMENT OF AGRICULTURE BEES, BEEKEEPING BYPRODUCTS, AND BEEKEEPING EQUIPMENT Importation and Transit of Restricted Articles § 322.29 Dead bees. (a) Dead bees imported into or transiting the United States must...

  14. Preparation and structure characterization of nanospherical MCM- 41 molecular sieves

    Directory of Open Access Journals (Sweden)

    CHEN Ting

    2013-04-01

    Full Text Available Nanospherical MCM-41 molecular sieves have been synthesized by using hexadecyl trimethyl ammonium bromide (CTAB as templates and tetraethyl orthosilicate (TEOS as silicon sources. XRD,SEM,FT-IR,TEM,and N2 adsorption-desorption isotherms were used to investigate the effects of the reaction temperature and aging time on the morphology and structure of the samples. The results show that the nanospherical MCM-41 particles can be obtained at reaction temperatures between 20 to 80℃. With the reaction temperature increasing,the diameter of the nanospheres increases. When the reaction temperature reaches 110℃,MCM-41 molecular sieves exhibit irregular particle morphology. With the aging time of 0-15 h,the dispersion of nanospherical MCM-41 molecular sieves is very good. However,as the aging time increases,the particle size is also increased,while agglomeration is also more serious. Besides,the optimal synthesis conditions of the nanospherical MCM-41 molecular sieves were obtained by analyzing their formation mechanism.

  15. Molecular descriptor subset selection in theoretical peptide quantitative structure-retention relationship model development using nature-inspired optimization algorithms.

    Science.gov (United States)

    Žuvela, Petar; Liu, J Jay; Macur, Katarzyna; Bączek, Tomasz

    2015-10-01

    In this work, performance of five nature-inspired optimization algorithms, genetic algorithm (GA), particle swarm optimization (PSO), artificial bee colony (ABC), firefly algorithm (FA), and flower pollination algorithm (FPA), was compared in molecular descriptor selection for development of quantitative structure-retention relationship (QSRR) models for 83 peptides that originate from eight model proteins. The matrix with 423 descriptors was used as input, and QSRR models based on selected descriptors were built using partial least squares (PLS), whereas root mean square error of prediction (RMSEP) was used as a fitness function for their selection. Three performance criteria, prediction accuracy, computational cost, and the number of selected descriptors, were used to evaluate the developed QSRR models. The results show that all five variable selection methods outperform interval PLS (iPLS), sparse PLS (sPLS), and the full PLS model, whereas GA is superior because of its lowest computational cost and higher accuracy (RMSEP of 5.534%) with a smaller number of variables (nine descriptors). The GA-QSRR model was validated initially through Y-randomization. In addition, it was successfully validated with an external testing set out of 102 peptides originating from Bacillus subtilis proteomes (RMSEP of 22.030%). Its applicability domain was defined, from which it was evident that the developed GA-QSRR exhibited strong robustness. All the sources of the model's error were identified, thus allowing for further application of the developed methodology in proteomics. PMID:26346190

  16. A 3D visualization system for molecular structures

    Science.gov (United States)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  17. Molecular Structure and Target Recognition of Neuronal Calcium Sensor Proteins

    Directory of Open Access Journals (Sweden)

    James Ames

    2012-02-01

    Full Text Available Neuronal calcium sensor (NCS proteins, a sub-branch of the calmodulin superfamily, are expressed in the brain and retina where they transduce calcium signals and are genetically linked to degenerative diseases. The amino acid sequences of NCS proteins are highly conserved but their physiological functions are quite distinct. Retinal recoverin and guanylate cyclase activating proteins (GCAPs both serve as calcium sensors in retinal rod cells, neuronal frequenin (NCS1 modulates synaptic activity and neuronal secretion, K+ channel interacting proteins (KChIPs regulate ion channels to control neuronal excitability, and DREAM (KChIP3 is a transcriptional repressor that regulates neuronal gene expression. Here we review the molecular structures of myristoylated forms of NCS1, recoverin, and GCAP1 that all look very different, suggesting that the sequestered myristoyl group helps to refold these highly homologous proteins into very different structures. The molecular structure of NCS target complexes have been solved for recoverin bound to rhodopsin kinase, NCS-1 bound to phosphatidylinositol 4-kinase, and KChIP1 bound to A-type K+ channels. We propose that N-terminal myristoylation is critical for shaping each NCS family member into a different structure, which upon Ca2+-induced extrusion of the myristoyl group exposes a unique set of previously masked residues that interact with a particular physiological target.

  18. Tunneling and resonant conductance in one-dimensional molecular structures

    International Nuclear Information System (INIS)

    We present a theory of tunneling and resonant transitions in one-dimensional molecular systems which is based on Green's function theory of electron sub-barrier scattering off the structural units (or functional groups) of a molecular chain. We show that the many-electron effects are of paramount importance in electron transport and they are effectively treated using a formalism of sub-barrier scattering operators. The method which calculates the total scattering amplitude of the bridge molecule not only predicts the enhancement of the amplitude of tunneling transitions in course of tunneling electron transfer through onedimensional molecular structures but also allows us to interpret conductance mechanisms by calculating the bound energy spectrum of the tunneling electron, the energies being obtained as poles of the total scattering amplitude of the bridge molecule. We found that the resonant tunneling via bound states of the tunneling electron is the major mechanism of electron conductivity in relatively long organic molecules. The sub-barrier scattering technique naturally includes a description of tunneling in applied electric fields which allows us to calculate I-V curves at finite bias. The developed theory is applied to explain experimental findings such as bridge effect due to tunneling through organic molecules, and threshold versus Ohmic behavior of the conductance due to resonant electron transfer

  19. Radiation track structure simulation in a molecular medium

    International Nuclear Information System (INIS)

    A problem in the simulation of track structures is identified; because the underlying medium is assumed to be a continuum in the simulation, events (and therefore chemical species) can be generated unphysically close together. The problem is particularly severe for low-energy electrons, which are responsible for inducing most of the observed chemistry. Two modified simulation methods are proposed to investigate this effect. The first method modifies the density of the medium using the radial distribution function, to ensure that events can not be generated closer to one another than nearest neighbour molecules. The second method simulates the track in a molecular medium, using configurations generated by molecular dynamics. When gas phase cross-sections are used these two methods have large effects on the mean electron range and the mean inter-event distance, but surprisingly, they act in opposite directions. When condensed phase cross-sections are used the effects are much smaller. (author)

  20. Molecular structure and pathophysiological roles of the Mitochondrial Calcium Uniporter.

    Science.gov (United States)

    Mammucari, Cristina; Raffaello, Anna; Vecellio Reane, Denis; Rizzuto, Rosario

    2016-10-01

    Mitochondrial Ca(2+) uptake regulates a wide array of cell functions, from stimulation of aerobic metabolism and ATP production in physiological settings, to induction of cell death in pathological conditions. The molecular identity of the Mitochondrial Calcium Uniporter (MCU), the highly selective channel responsible for Ca(2+) entry through the IMM, has been described less than five years ago. Since then, research has been conducted to clarify the modulation of its activity, which relies on the dynamic interaction with regulatory proteins, and its contribution to the pathophysiology of organs and tissues. Particular attention has been placed on characterizing the role of MCU in cardiac and skeletal muscles. In this review we summarize the molecular structure and regulation of the MCU complex in addition to its pathophysiological role, with particular attention to striated muscle tissues. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou. PMID:26968367

  1. Theoretical investigation of the molecular structure of the isoquercitrin molecule

    Science.gov (United States)

    Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

    1999-09-01

    Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

  2. STRUCTURAL ANALYSIS AND MOLECULAR DYNAMICS STUDY OF PHB SYNTHASE

    Directory of Open Access Journals (Sweden)

    T. Femlin Blessia

    2012-02-01

    Full Text Available Polyhydroxybutyrate (PHB is a polyhydroxyalkanoate (PHA, a polymer belonging to polyesters class and is composed of hydroxy fatty acids. PHB is produced by microorganisms apparently in response to conditions of physiological stress. PHB synthases are the key enzymes of PHB biosynthesis. The PHB synthases obtained from Chromobacterium violaceum, belongs to the class I PHA synthases. Due to the limited structural information of PHB synthase, its functional properties including catalysis are unknown. Therefore, this study seeks to investigate the structural and functional properties of PHB synthase (phaC by predicting its three dimensional structure using bioinformatics methods. Present 15 ns molecular dynamics study provides an overall insight about some of the parameters such as energy, RMSD (Root Mean Square Deviation, SASA (Solvent Accessible Surface Area, hydrogen bonds, etc., Protein-protein docking reveals the binding mode of the protein in the active dimer state.

  3. Ordered molecular layer structure of lubricating oil adsorbed films

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Low-angle X-ray diffraction has been applied to analyze the structure of stearic acid LB films and self-grown surface adsorbed films of aluminium product metalworking lubricants. The results show that LB films exhibit a good layer-like ordered structure in the normal direction of film-carrying surface, while in the tangential direction, they do not show a cyclically ordered molecular arrangement; as for the self-grown surface adsorbed films of aluminium sheet and strip metalworking lubricants, their molecules are orderly arranged to certain degree in both the tangential and the normal directions of film-carrying surface, and they have a short-range ordered structure. Moreover, the better the orientation of normal molecules is, the higher the oil film strength is, and the smaller the friction factor is.

  4. III - V semiconductor structures for biosensor and molecular electronics applications

    Energy Technology Data Exchange (ETDEWEB)

    Luber, S.M.

    2007-01-15

    The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed

  5. Red mason bees cannot compete with honey bees for floral resources in a cage experiment

    OpenAIRE

    Hudewenz, Anika; Klein, Alexandra‐Maria

    2015-01-01

    Abstract Intensive beekeeping to mitigate crop pollination deficits and habitat loss may cause interspecific competition between bees. Studies show negative correlations between flower visitation of honey bees (Apis mellifera) and wild bees, but effects on the reproduction of wild bees were not proven. Likely reasons are that honey bees can hardly be excluded from controls and wild bee nests are generally difficult to detect in field experiments. The goal of this study was to investigate whet...

  6. First detection of the larval chalkbrood disease pathogen Ascosphaera apis (Ascomycota: Eurotiomycetes: Ascosphaerales in adult bumble bees.

    Directory of Open Access Journals (Sweden)

    Sarah A Maxfield-Taylor

    Full Text Available Fungi in the genus Ascosphaera (Ascomycota: Eurotiomycetes: Ascosphaerales cause chalkbrood disease in larvae of bees. Here, we report the first-ever detection of the fungus in adult bumble bees that were raised in captivity for studies on colony development. Wild queens of Bombus griseocollis, B. nevadensis and B. vosnesenskii were collected and maintained for establishment of nests. Queens that died during rearing or that did not lay eggs within one month of capture were dissected, and tissues were examined microscopically for the presence of pathogens. Filamentous fungi that were detected were plated on artificial media containing broad spectrum antibiotics for isolation and identification. Based on morphological characters, the fungus was identified as Ascosphaera apis (Maasen ex Claussen Olive and Spiltoir, a species that has been reported earlier only from larvae of the European honey bee, Apis mellifera, the Asian honey bee, Apis cerana, and the carpenter bee Xylocopa californica arizonensis. The identity of the fungus was confirmed using molecular markers and phylogenetic analysis. Ascosphaera apis was detected in queens of all three bumble bee species examined. Of 150 queens dissected, 12 (8% contained vegetative and reproductive stages of the fungus. Both fungal stages were also detected in two workers collected from colonies with Ascosphaera-infected B. nevadensis queens. In this study, wild bees could have been infected prior to capture for rearing, or, the A. apis infection could have originated via contaminated European honey bee pollen fed to the bumble bees in captivity. Thus, the discovery of A. apis in adult bumble bees in the current study has important implications for commercial production of bumble bee colonies and highlights potential risks to native bees via pathogen spillover from infected bees and infected pollen.

  7. The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Neutron diffraction (ND) measurements on liquid methanol (CD3OD, CD3O(H/D), CD3OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), Gdist(r) and inter-molecular, Ginter(r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, GXHo(r) (X=C, O, and H - a methyl hydrogen) and GXX(r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, GXHo(r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct GXX(r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular GXX(r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), gHoHo(r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular GXHo(r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial distribution functions

  8. Surface Structure of Hydroxyapatite from Simulated Annealing Molecular Dynamics Simulations.

    Science.gov (United States)

    Wu, Hong; Xu, Dingguo; Yang, Mingli; Zhang, Xingdong

    2016-05-10

    The surface structure of hydroxyapatite (HAP) is crucial for its bioactivity. Using a molecular dynamics simulated annealing method, we studied the structure and its variation with annealing temperature of the HAP (100) surface. In contrast to the commonly used HAP surface model, which is sliced from HAP crystal and then relaxed at 0 K with first-principles or force-field calculations, a new surface structure with gradual changes from ordered inside to disordered on the surface was revealed. The disordering is dependent on the annealing temperature, Tmax. When Tmax increases up to the melting point, which was usually adopted in experiments, the disordering increases, as reflected by its radial distribution functions, structural factors, and atomic coordination numbers. The disordering of annealed structures does not show significant changes when Tmax is above the melting point. The thickness of disordered layers is about 10 Å. The surface energy of the annealed structures at high temperature is significantly less than that of the crystal structure relaxed at room temperature. A three-layer model of interior, middle, and surface was then proposed to describe the surface structure of HAP. The interior layer retains the atomic configurations in crystal. The middle layer has its atoms moved and its groups rotated about their original locations. In the surface layer, the atomic arrangements are totally different from those in crystal. In particular for the hydroxyl groups, they move outward and cover the Ca(2+) ions, leaving holes occupied by the phosphate groups. Our study suggested a new model with disordered surface structures for studying the interaction of HAP-based biomaterials with other molecules. PMID:27096760

  9. [Cardiac potassium channels: molecular structure, physiology, pathophysiology and therapeutic implications].

    Science.gov (United States)

    Mironov, N Iu; Golitsyn, S P

    2013-01-01

    Potassium channels and currents play essential roles in cardiac repolarization. Potassium channel blockade by class III antiarrhythmic drugs prolongs cardiac repolarization and results in termination and prevention of cardiac arrhythmias. Excessive inhomogeneous repolarization prolongation may lead to electrical instability and proarrhythmia (Torsade de Pointes tachycardia). This review focuses on molecular structure, physiology, pathophysiology and therapeutic potential of potassium channels of cardiac conduction system and myocardium providing information on recent findings in pathogenesis of cardiac arrhythmias, including inherited genetic abnormalities, and future perspectives. PMID:24654438

  10. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  11. Three decades of structure- and property-based molecular design

    DEFF Research Database (Denmark)

    Müller, Klaus

    2014-01-01

    Roche has pioneered structure- and property-based molecular design to drug discovery. While this is an ongoing development, the past three decades feature key events that have revolutionized the way drug discovery is conducted in Big Pharma industry. It has been a great privilege to have been...... of bioinformatics. It describes the strategic shift to large compound libraries and high-throughput screening with the development of novel compound storage and ultra-high-throughput screening facilities, as well as the strategic return to focused screening of small motif-based compound libraries...

  12. Molecular structural order and anomalies in liquid silica.

    Science.gov (United States)

    Shell, M Scott; Debenedetti, Pablo G; Panagiotopoulos, Athanassios Z

    2002-07-01

    The present investigation examines the relationship between structural order, diffusivity anomalies, and density anomalies in liquid silica by means of molecular dynamics simulations. We use previously defined orientational and translational order parameters to quantify local structural order in atomic configurations. Extensive simulations are performed at different state points to measure structural order, diffusivity, and thermodynamic properties. It is found that silica shares many trends recently reported for water [J. R. Errington and P. G. Debenedetti, Nature 409, 318 (2001)]. At intermediate densities, the distribution of local orientational order is bimodal. At fixed temperature, order parameter extrema occur upon compression: a maximum in orientational order followed by a minimum in translational order. Unlike water, however, silica's translational order parameter minimum is broad, and there is no range of thermodynamic conditions where both parameters are strictly coupled. Furthermore, the temperature-density regime where both structural order parameters decrease upon isothermal compression (the structurally anomalous regime) does not encompass the region of diffusivity anomalies, as was the case for water. PMID:12241346

  13. Molecular structure and reversible photodegradation in anthraquinone dyes

    CERN Document Server

    Dhakal, Prabodh

    2016-01-01

    Reversible photodegradation is a process that has been observed in several dye molecules, but the underlying mechanisms are not still well understood. In this contribution, we characterize a series of anthraquinone dyes to determine how self-healing depends on molecular structure. Past studies have used probing techniques that rely on linear absorption, two-photon fluorescence, and amplified spontaneous emission. Each of these probes provide an indirect measure of the populations of the damaged and undamaged species, requiring calibrations or assumptions to be made that might affect the accuracy of the results. The present studies use fluorescence as a probe, which is shown to directly measure the undamaged population. It is found that certain anthraquinone classes share common structural features that are associated with self healing. Furthermore, the time and temperature dependence of photodegradation and self-healing is found to be consistent with the domain model of self healing.

  14. Study on multimers and their structures in molecular association mixture

    Institute of Scientific and Technical Information of China (English)

    YAMAGUCHI; Yoshinori; OZAKI; Yukihiro

    2007-01-01

    Self-association system of(R)-1,3-butanediol in dilute carbon tetrachloride(CCl4)solution is studied as a model of molecular association mixture.Analysis methods including FSMWEFA(fixed-size moving window evolving factor analysis)combined with PCA(principal component analysis),SIMPLISMA (simple-to-use interactive self-modeling mixture analysis),and ITTFA(iterative target transformation factor analysis)are adopted to resolve infrared spectra of(R)-1,3-butanediol solution.Association number and equilibrium constant are computed.(R)-1,3-butanediol in dilute inert solution is determined as a monomer-trimer equilibrium system.Theoretical investigation of trimer structures is carried out with DFT(density functional theory),and structural factors are analyzed.

  15. Structures and physicochemical properties of molecular aggregates of lipids

    International Nuclear Information System (INIS)

    Structures and physicochemical properties of lipids such as fatty acids, alcohols, acylglycerols and steroids in their two- or three-dimensional states were studied through the measurements of surface pressure (π), surface-molecular area (A), vapor-pressure osmosis, radioactivity (R), self-diffusion coefficient (D), density, viscosity, near-infrared spectroscopy (NIR), 13C-NMR spin-lattice relaxation time (T1), ESR, SEM, DSC, X-ray diffraction and small-angle neutron scattering (SANS). Following results are obtained: (1) π-A and R-A relationships indicate that the explanation, being widely believed, of the reaction occurred in the oleic acid or the trioleylglycerol monolayer on the aqueous KMnO4 solution is incorrect. (2) By using the LB film of 3H-labelled fatty acid, the upper limit of the neutrino mass was determined. In addition, by using the LB film of 14C-labelled fatty acid, a new type of crystal-transformation process was found, in which fatty-acid crystal transforms from its unstable state to its stable one by the transfer of the fatty acid molecules through the vapor phase. (3) Fatty acids always exist as their dimers in their liquid state and mostly in non-polar solvents; the dimers are the units of the molecular movements in the molten liquid and in solvents. T1 results clearly showed the internal molecular movements of the dimers. In addition, D and SANS results indicated that two different kinds of fatty acids in their binary mixture make only each homodimers. (4) Furthermore, the study on the liquid structure of fatty acids such as cis-6-, cis-9-, cis-11-, trans-9-octadecenoic acids and stearic acid indicated that these fatty-acid dimers construct the clusters resemble to the smectic-liquid crystal in the liquid state. The clusters determine the physicochemical properties of the liquid of the fatty acid. (author)

  16. Methods for empirical formula, molecular structure determination and colloid characterisation

    International Nuclear Information System (INIS)

    Determination of empirical formula and of molecular structures in issues pertinent to the fuel cycle, waste management and remediation, as well as in risk assessment associated with radionuclide release and its migration to the near and far field of a repository present a particular challenge. Speciation techniques in these areas are needed for extraction chemistry of actinides, aquatic reactions of actinide ions (e.g. tetravalent actinide hydrolysis, formation of ternary complexes and redox chemistry), reactions at the water/mineral interface, formation of secondary phases and the formation of and interaction with colloids. The range of concentrations of interest is extreme, from relatively pure substances such as the fuels themselves, to tracer levels in far-field release scenarios. Actinide speciation in extractant solutions used for separation techniques for partitioning technologies involves investigation of solutions with often acidic pH, whereas speciation in cement pore waters, for example, can involve very basic solutions. Finally, the amount of sample available may be limited, e.g. pore water samples can be as small as μL quantities. There exist a variety of techniques for determining empirical formula and molecular structure of radionuclide species. The actual contents and components of the sample at hand in addition to the degree of complexity required dictates the method that is chosen. The speciation of radionuclides is often governed by their association with or formation to colloids. The characterisation of such colloids is imperative and their quantification and characterisation is, therefore, included as a separate treatise. (author)

  17. Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

    Science.gov (United States)

    Murphy, Peter M.

    2007-01-01

    A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

  18. Molecular Modeling and Structural Analysis of Arylesterase of Ancylostoma Duodenale

    Science.gov (United States)

    Panda, Subhamay; Panda, Santamay; Kumari, Leena

    2016-01-01

    Parasitic worm infection of humans is one of the most commonly prevalent helminth infection that has imposed great impact on society and public health in the developing world. The two species of hookworm, namely Ancylostoma duodenale and Necator americanus may be primarily responsible for causing parasitic infections in human beings. The highly prevalent areas for Ancylostoma duodenale infections are mainly India, Middle East, Australia, northern Africa and other parts of the world. The serum arylesterases/paraoxonases are family of enzymes that is involved in the hydrolysis of a number of organophosphorus insecticides to the nontoxic products. The participation of the enzymes in the breakdown of a variety of organophosphate substrates that is generally made up of paraoxon and numerous aromatic carboxylic acid esters (e.g., phenyl acetate), and hence combats the toxic effect of organophosphates. The aim of the present investigation is to evaluate the arylesterases of Ancylostoma duodenale giving special importance to structure generation, validation of the generated models, distribution of secondary structural elements and positive charge distribution over the structure. By the implementation of comparative modeling approach we propose the first molecular model structure of arylesterases of Ancylostoma duodenale.

  19. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  20. Mathematical analysis of compressive/tensile molecular and nuclear structures

    Science.gov (United States)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  1. ZigBee-2007 Security Essentials

    DEFF Research Database (Denmark)

    Yuksel, Ender; Nielson, Hanne Riis; Nielson, Flemming

    2008-01-01

    ZigBee is a fairly new but promising standard for wireless networks due to its low resource requirements. As in other wireless network standards, security is an important issue and each new version of the ZigBee Specification enhances the level of the ZigBee security. In this paper, we present the...... security essentials of the latest ZigBee Specification, ZigBee-2007. We explain the key concepts, protocols, and computations. In addition, we formulate the protocols using standard protocol narrations. Finally, we identify the key challenges to be considered for consolidating ZigBee....

  2. Molecular graphics-structural and molecular graphics descriptors in a QSAR study of 17-a-acetoxyprogesterones

    OpenAIRE

    Kiralj Rudolf; Ferreira Márcia M. C.

    2003-01-01

    Quantitative Structure-Activity Relationship study on 21 oral progestogens, 19 of which are 17-alpha-acetoxyprogesterones, was performed by using Partial Least Squares. Fairly good regression models were achieved, the best being Q²=0.707, R²=0.811 with two Principal Components and four descriptors. Most of the molecular descriptors were generated from molecular graphics of DFT 6-31G** optimized geometries (molecular graphics descriptors) or were additionally combined with experimental structu...

  3. In-depth Proteomics Characterization of Embryogenesis of the Honey Bee Worker (Apis mellifera ligustica) *

    OpenAIRE

    Fang, Yu; Feng, Mao; Han, Bin; Lu, Xiaoshan; Ramadan, Haitham; Li, Jianke

    2014-01-01

    Identifying proteome changes of honey bee embryogenesis is of prime importance for unraveling the molecular mechanisms that they underlie. However, many proteomic changes during the embryonic period are not well characterized. We analyzed the proteomic alterations over the complete time course of honey bee worker embryogenesis at 24, 48, and 72 h of age, using mass spectrometry-based proteomics, label-free quantitation, and bioinformatics. Of the 1460 proteins identified the embryo of all thr...

  4. A new parametrizable model of molecular electronic structure

    Science.gov (United States)

    Laikov, Dimitri N.

    2011-10-01

    A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good dipole polarizabilities and improved intermolecular potentials with dispersion terms. The molecular integrals include up to three-center one-electron and two-center two-electron terms, all in simple analytical forms. A method to extract the effective one-electron Hamiltonian of nonlocal-exchange Kohn-Sham theory from the coupled-cluster one-electron density matrix is designed and used to get its matrix representation in a molecule-intrinsic minimal basis as an input to the parametrization procedure - making a direct link to the correlated wavefunction theory. The model has been trained for 15 elements (H, Li-F, Na-Cl, 720 parameters) on a set of 5581 molecules (including ions, transition states, and weakly bound complexes) whose first- and second-order properties were computed by the coupled-cluster theory as a reference, and a good agreement is seen. The model looks promising for the study of large molecular systems, it is believed to be an important step forward from the traditional semiempirical models towards higher accuracy at nearly as low a computational cost.

  5. How does the molecular network structure influence PDMS elastomer wettability?

    Science.gov (United States)

    Melillo, Matthew; Genzer, Jan

    Poly(dimethylsiloxane) (PDMS) is one of the most common elastomers, with applications ranging from medical devices to absorbents for water treatment. Fundamental understanding of how liquids spread on the surface of and absorb into PDMS networks is of critical importance for the design and use of another application - microfluidic devices. We have systematically studied the effects of polymer molecular weight, loading of tetra-functional crosslinker, end-group chemical functionality, and the extent of dilution of the curing mixture on the mechanical and surface properties of end-linked PDMS networks. The gel and sol fractions, storage and loss moduli, liquid swelling ratios, and water contact angles have all been shown to vary greatly based on the aforementioned variables. Similar trends were observed for the commercial PDMS material, Sylgard-184. Our results have confirmed theories predicting the relationships between modulus and swelling. Furthermore, we have provided new evidence for the strong influence that substrate modulus and molecular network structure have on the wettability of PDMS elastomers. These findings will aid in the design and implementation of efficient microfluidics and other PDMS-based materials that involve the transport of liquids.

  6. Effect of processing on carbon molecular sieve structure and performance

    KAUST Repository

    Das, Mita

    2010-11-01

    Sub-micron sized carbon molecular sieve (CMS) materials were produced via ball milling for subsequent use in hybrid material formation. A detailed analysis of the effects of the milling process in the presence of different milling environments is reported. The milling process apparently alters the molecular scale structure and properties of the carbon material. Three cases: unmilled, air milled and nitrogen milled, were analyzed in this work. The property changes were probed using equilibrium sorption experiments with different gases. Furthermore, WAXD and BET results also showed differences between milling processes. Finally in order to improve the interfacial polymer-sieve region of hybrid membranes, the CMS surface was chemically modified with a linkage unit capable of covalently bonding the polymer to the sieve. A published single-wall carbon nanotube (SWCNTs) modification method was adopted to attach a primary aromatic amine to the surface. Several aspects including rigidity, chemical composition, bulky groups and length were considered in selecting the preferred linkage unit. Fortunately kinetic and equilibrium sorption properties of the modified sieves showed very little difference from unmodified samples, suggesting that the linkage unit is not excessively filling or obstructing access to the pores of the CMSs during the modification process. © 2010 Elsevier Ltd. All rights reserved.

  7. A new parametrizable model of molecular electronic structure

    CERN Document Server

    Laikov, Dimitri N

    2011-01-01

    A new electronic structure model is developed in which the ground state energy of a molecular system is given by a Hartree-Fock-like expression with parametrized one- and two-electron integrals over an extended (minimal + polarization) set of orthogonalized atom-centered basis functions, the variational equations being solved formally within the minimal basis but the effect of polarization functions being included in the spirit of second-order perturbation theory. It is designed to yield good dipole polarizabilities and improved intermolecular potentials with dispersion terms. The molecular integrals include up to three-center one-electron and two-center two-electron terms, all in simple analytical forms. A method to extract the effective one-electron Hamiltonian of nonlocal-exchange Kohn-Sham theory from the coupled-cluster one-electron density matrix is designed and used to get its matrix representation in a molecule-intrinsic minimal basis as an input to the paramtrization procedure -- making a direct link...

  8. Molecular structure and thermodynamic properties of scandium halides

    International Nuclear Information System (INIS)

    Experimental data on molecular constants of mono-, di- and trihalides of scandium, as well as di-scandium hexahalides of the composition ScXn and Sc2X6 (X = F - I; n = 1 - 3), have been analyzed. Specific features of the compounds molecule structure are considered. The values of molecular constants have been evaluated by the methods of statistical thermodynamics and thermodynamic properties of all scandium halides mentioned in the temperature range of 100 - 6000 K and 298.15 - 1000 K respectively for scandium monohalides and for di-, tri-, hexahalides have been calculated. The values of thermodynamic functions Cp Deg, Φ Deg (T), H Deg (T) - H Deg (0) at 298.15 K published for the first time equal respectively for ScF: 32.734; 192.186; 222.232; 8.958; for ScCl: 45.782; 203.351; 237.356; 10.138; for ScBr: 49.449; 215.090; 252.783; 11.238; for ScI: 42.605; 227.517; 265.635; 12.259

  9. Introductory group theory and its application to molecular structure

    CERN Document Server

    Ferraro, John R

    1975-01-01

    The success of the first edition of this book has encouraged us to revise and update it. In the second edition we have attempted to further clarify por­ tions of the text in reference to point symmetry, keeping certain sections and removing others. The ever-expanding interest in solids necessitates some discussion on space symmetry. In this edition we have expanded the discus­ sion on point symmetry to include space symmetry. The selection rules in­ clude space group selection rules (for k = 0). Numerous examples are pro­ vided to acquaint the reader with the procedure necessary to accomplish this. Recent examples from the literature are given to illustrate the use of group theory in the interpretation of molecular spectra and in the determination of molecular structure. The text is intended for scientists and students with only a limited theoretical background in spectroscopy. For this reason we have presented detailed procedures for carrying out the selection rules and normal coor­ dinate treatment of ...

  10. Towards a molecular description of intermediate filament structure and assembly

    International Nuclear Information System (INIS)

    Intermediate filaments (IFs) represent one of the prominent cytoskeletal elements of metazoan cells. Their constituent proteins are coded by a multigene family, whose members are expressed in complex patterns that are controlled by developmental programs of differentiation. Hence, IF proteins found in epidermis differ significantly from those in muscle or neuronal tissues. Due to their fibrous nature, which stems from a fairly conserved central α-helical coiled-coil rod domain, IF proteins have long resisted crystallization and thus determination of their atomic structure. Since they represent the primary structural elements that determine the shape of the nucleus and the cell more generally, a major challenge is to arrive at a more rational understanding of how their nanomechanical properties effect the stability and plasticity of cells and tissues. Here, we review recent structural results of the coiled-coil dimer, assembly intermediates and growing filaments that have been obtained by a hybrid methods approach involving a rigorous combination of X-ray crystallography, small angle X-ray scattering, cryo-electron tomography, computational analysis and molecular modeling

  11. Electronic Structure and Molecular Dynamics Calculations for KBH4

    Science.gov (United States)

    Papaconstantopoulos, Dimitrios; Shabaev, Andrew; Hoang, Khang; Mehl, Michael; Kioussis, Nicholas

    2012-02-01

    In the search for hydrogen storage materials, alkali borohydrides MBH4 (M=Li, Na, K) are especially interesting because of their light weight and the high number of hydrogen atoms per metal atom. Electronic structure calculations can give insights into the properties of these complex hydrides and provide understanding of the structural properties and of the bonding of hydrogen. We have performed first-principles density-functional theory (DFT) and tight-binding (TB) calculations for KBH4 in both the high temperature (HT) and low temperature (LT) phases to understand its electronic and structural properties. Our DFT calculations were carried out using the VASP code. The results were then used as a database to develop a tight-binding Hamiltonian using the NRL-TB method. This approach allowed for computationally efficient calculations of phonon frequencies and elastic constants using the static module of the NRL-TB, and also using the molecular dynamics module to calculate mean-square displacements and formation energies of hydrogen vacancies.

  12. Tyrosine Aminotransferase: Biochemical and Structural Properties and Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    P Mehere; Q Han; J Lemkul; C Vavricka; H Robinson; D Bevan; J Li

    2011-12-31

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  13. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Mehere, P.; Robinson, H.; Han, Q.; Lemkul, J. A.; Vavricka, C. J.; Bevan, D. R.; Li, J.

    2010-11-01

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  14. Influence of the molecular structure on hydrolyzability of epoxy resins

    International Nuclear Information System (INIS)

    EDF has decided to use glass reinforced composites for certain pipework in Pressurized Water Reactors (service water, emergency-supplied service water, fine pipe works, etc...) as a replacement for traditional materials. In practice, steel is prone to rapid corrosion in these circuits; introducing composites could prove economically viable if their long term behaviour can be demonstrated. However, composite materials can undergo deterioration in service through hydrolysis of the resin or the fibre-matrix interface. Different resins can be chosen depending on the programmed use. A first study has covered the hydrolyzability of polyester and vinyl ester resins. The present document undertakes the resistance to hydrolysis of epoxy resins, concentrating on those reputed to withstand high temperatures. This research uses model monomer, linking the molecular structure of the materials to their resistance to hydrolysis. (author)

  15. Calculations of optical rotation: Influence of molecular structure

    Directory of Open Access Journals (Sweden)

    Yu Jia

    2012-01-01

    Full Text Available Ab initio Hartree-Fock (HF method and Density Functional Theory (DFT were used to calculate the optical rotation of 26 chiral compounds. The effects of theory and basis sets used for calculation, solvents influence on the geometry and values of calculated optical rotation were all discussed. The polarizable continuum model, included in the calculation, did not improve the accuracy effectively, but it was superior to γs. Optical rotation of five or sixmembered of cyclic compound has been calculated and 17 pyrrolidine or piperidine derivatives which were calculated by HF and DFT methods gave acceptable predictions. The nitrogen atom affects the calculation results dramatically, and it is necessary in the molecular structure in order to get an accurate computation result. Namely, when the nitrogen atom was substituted by oxygen atom in the ring, the calculation result deteriorated.

  16. Single Assay Detection of Acute Bee Paralysis Virus, Kashmir Bee Virus and Israeli Acute Paralysis Virus

    DEFF Research Database (Denmark)

    Francis, Roy Mathew; Kryger, Per

    2012-01-01

    A new RT-PCR primer pair designed to identify Acute Bee Paralysis Virus (ABPV), Kashmir Bee Virus (KBV) or Israeli Acute Bee Paralysis Virus (IAPV) of honey bees (Apis mellifera L.) in a single assay is described. These primers are used to screen samples for ABPV, KBV, or IAPV in a single RT...

  17. Assessing the Utility of a PCR Diagnostics Marker for the Identification of Africanized Honey Bee, Apis mellifera L., (Hymenoptera: Apidae in the United States.

    Directory of Open Access Journals (Sweden)

    Allen Szalanski

    2014-07-01

    Full Text Available An assessment of a molecular diagnostic technique for distinguishing Africanized honey bees from European honey bees in the United States was conducted. Results from multiplex PCR diagnostics of a mitochondrial DNA cyt-b marker corresponded with results based on COI-COII sequencing analysis, but differed from morphometric analysis results. We suggest utilizing both multiplex PCR and morphometric methods for Africanized honey bee diagnostics in the United States, when possible.

  18. STUDIES OF RELATIONSHIPS BETWEEN MOLECULAR STRUCTURE AND BIOLOGICAL ACTIVITY BY PATTERN RECOGNITION METHODS

    Science.gov (United States)

    The attempt to rationalize the connections between the molecular structures of organic compounds and their biological activities comprises the field of structure-activity relations (SAR) studies. Correlations between structure and activity are important for the understanding and ...

  19. Collective thermoregulation in bee clusters.

    Science.gov (United States)

    Ocko, Samuel A; Mahadevan, L

    2014-02-01

    Swarming is an essential part of honeybee behaviour, wherein thousands of bees cling onto each other to form a dense cluster that may be exposed to the environment for several days. This cluster has the ability to maintain its core temperature actively without a central controller. We suggest that the swarm cluster is akin to an active porous structure whose functional requirement is to adjust to outside conditions by varying its porosity to control its core temperature. Using a continuum model that takes the form of a set of advection-diffusion equations for heat transfer in a mobile porous medium, we show that the equalization of an effective 'behavioural pressure', which propagates information about the ambient temperature through variations in density, leads to effective thermoregulation. Our model extends and generalizes previous models by focusing the question of mechanism on the form and role of the behavioural pressure, and allows us to explain the vertical asymmetry of the cluster (as a consequence of buoyancy-driven flows), the ability of the cluster to overpack at low ambient temperatures without breaking up at high ambient temperatures, and the relative insensitivity to large variations in the ambient temperature. Our theory also makes testable hypotheses for the response of the cluster to external temperature inhomogeneities and suggests strategies for biomimetic thermoregulation. PMID:24335563

  20. Production of the catechol type siderophore bacillibactin by the honey bee pathogen Paenibacillus larvae.

    Science.gov (United States)

    Hertlein, Gillian; Müller, Sebastian; Garcia-Gonzalez, Eva; Poppinga, Lena; Süssmuth, Roderich D; Genersch, Elke

    2014-01-01

    The Gram-positive bacterium Paenibacillus larvae is the etiological agent of American Foulbrood. This bacterial infection of honey bee brood is a notifiable epizootic posing a serious threat to global honey bee health because not only individual larvae but also entire colonies succumb to the disease. In the recent past considerable progress has been made in elucidating molecular aspects of host pathogen interactions during pathogenesis of P. larvae infections. Especially the sequencing and annotation of the complete genome of P. larvae was a major step forward and revealed the existence of several giant gene clusters coding for non-ribosomal peptide synthetases which might act as putative virulence factors. We here present the detailed analysis of one of these clusters which we demonstrated to be responsible for the biosynthesis of bacillibactin, a P. larvae siderophore. We first established culture conditions allowing the growth of P. larvae under iron-limited conditions and triggering siderophore production by P. larvae. Using a gene disruption strategy we linked siderophore production to the expression of an uninterrupted bacillibactin gene cluster. In silico analysis predicted the structure of a trimeric trithreonyl lactone (DHB-Gly-Thr)3 similar to the structure of bacillibactin produced by several Bacillus species. Mass spectrometric analysis unambiguously confirmed that the siderophore produced by P. larvae is identical to bacillibactin. Exposure bioassays demonstrated that P. larvae bacillibactin is not required for full virulence of P. larvae in laboratory exposure bioassays. This observation is consistent with results obtained for bacillibactin in other pathogenic bacteria. PMID:25237888

  1. Proceedings "… Towards Resilient Honey Bees …"

    OpenAIRE

    Dooremalen, van, C.; Zweep, A.

    2015-01-01

    The Research Roadmap is a co-creation by Bees@wur and the Dutch government, and the (inter)national researchers participating in the workshop Resilient Honey bees 23-24 November 2015, Castle Hoekelum, Bennekom, The Netherlands

  2. Divergent forms of endoplasmic reticulum stress trigger a robust unfolded protein response in honey bees.

    Science.gov (United States)

    Johnston, Brittany A; Hooks, Katarzyna B; McKinstry, Mia; Snow, Jonathan W

    2016-03-01

    Honey bee colonies in the United States have suffered from an increased rate of die-off in recent years, stemming from a complex set of interacting stresses that remain poorly described. While we have some understanding of the physiological stress responses in the honey bee, our molecular understanding of honey bee cellular stress responses is incomplete. Thus, we sought to identify and began functional characterization of the components of the UPR in honey bees. The IRE1-dependent splicing of the mRNA for the transcription factor Xbp1, leading to translation of an isoform with more transactivation potential, represents the most conserved of the UPR pathways. Honey bees and other Apoidea possess unique features in the Xbp1 mRNA splice site, which we reasoned could have functional consequences for the IRE1 pathway. However, we find robust induction of target genes upon UPR stimulation. In addition, the IRE1 pathway activation, as assessed by splicing of Xbp1 mRNA upon UPR, is conserved. By providing foundational knowledge about the UPR in the honey bee and the relative sensitivity of this species to divergent stresses, this work stands to improve our understanding of the mechanistic underpinnings of honey bee health and disease. PMID:26699660

  3. Honey Bees Inspired Optimization Method: The Bees Algorithm.

    Science.gov (United States)

    Yuce, Baris; Packianather, Michael S; Mastrocinque, Ernesto; Pham, Duc Truong; Lambiase, Alfredo

    2013-01-01

    Optimization algorithms are search methods where the goal is to find an optimal solution to a problem, in order to satisfy one or more objective functions, possibly subject to a set of constraints. Studies of social animals and social insects have resulted in a number of computational models of swarm intelligence. Within these swarms their collective behavior is usually very complex. The collective behavior of a swarm of social organisms emerges from the behaviors of the individuals of that swarm. Researchers have developed computational optimization methods based on biology such as Genetic Algorithms, Particle Swarm Optimization, and Ant Colony. The aim of this paper is to describe an optimization algorithm called the Bees Algorithm, inspired from the natural foraging behavior of honey bees, to find the optimal solution. The algorithm performs both an exploitative neighborhood search combined with random explorative search. In this paper, after an explanation of the natural foraging behavior of honey bees, the basic Bees Algorithm and its improved versions are described and are implemented in order to optimize several benchmark functions, and the results are compared with those obtained with different optimization algorithms. The results show that the Bees Algorithm offering some advantage over other optimization methods according to the nature of the problem. PMID:26462528

  4. Honey Bees Inspired Optimization Method: The Bees Algorithm

    Directory of Open Access Journals (Sweden)

    Ernesto Mastrocinque

    2013-11-01

    Full Text Available Optimization algorithms are search methods where the goal is to find an optimal solution to a problem, in order to satisfy one or more objective functions, possibly subject to a set of constraints. Studies of social animals and social insects have resulted in a number of computational models of swarm intelligence. Within these swarms their collective behavior is usually very complex. The collective behavior of a swarm of social organisms emerges from the behaviors of the individuals of that swarm. Researchers have developed computational optimization methods based on biology such as Genetic Algorithms, Particle Swarm Optimization, and Ant Colony. The aim of this paper is to describe an optimization algorithm called the Bees Algorithm, inspired from the natural foraging behavior of honey bees, to find the optimal solution. The algorithm performs both an exploitative neighborhood search combined with random explorative search. In this paper, after an explanation of the natural foraging behavior of honey bees, the basic Bees Algorithm and its improved versions are described and are implemented in order to optimize several benchmark functions, and the results are compared with those obtained with different optimization algorithms. The results show that the Bees Algorithm offering some advantage over other optimization methods according to the nature of the problem.

  5. One moment in time : Gene expression analysis of honey bees; nurse bees v.s. foragers

    OpenAIRE

    Rimestad, Tove

    2012-01-01

    Honey bees live in complex societies based on a division of labour. The honey bee workers specialise in different tasks throughout their lives, starting off as nurse bees and ending as foragers. The nurse bees and foragers display interesting phenotypic differences that do not have its origins in differences at genotype level, but in differences in gene expression. This thesis presents the results from an expression analysis done on honey bee workers comparing the expression profiles of nu...

  6. Honey bees and bumble bees respond differently to inter- and intra-specific encounters

    OpenAIRE

    Rogers, Shelley; Cajamarca, Peter; Tarpy, David; Burrack, Hannah

    2013-01-01

    Multiple bee species may forage simultaneously at a common resource. Physical encounters among these bees may modify their subsequent foraging behavior and shape pollinator distribution and resource utilization in a plant community. We observed physical encounters between honey bees, Apis mellifera, and bumble bees, Bombus impatiens, visiting artificial plants in a controlled foraging arena. Both species were more likely to leave the plant following an encounter with another bee, but differed...

  7. Structural and electronic properties of Diisopropylammonium bromide molecular ferroelectric crystal

    Science.gov (United States)

    Alsaad, A.; Qattan, I. A.; Ahmad, A. A.; Al-Aqtash, N.; Sabirianov, R. F.

    2015-10-01

    We report the results of ab-initio calculations based on Generalized Gradient Approximation (GGA) and hybrid functional (HSE06) of electronic band structure, density of states and partial density of states to get a deep insight into structural and electronic properties of P21 ferroelectric phase of Diisopropylammonium Bromide molecular crystal (DIPAB). We found that the optical band gap of the polar phase of DIPAB is ∼ 5 eV confirming it as a good dielectric. Examination of the density of states and partial density of states reveal that the valence band maximum is mainly composed of bromine 4p orbitals and the conduction band minimum is dominated by carbon 2p, carbon 2s, and nitrogen 2s orbitals. A unique aspect of P21 ferroelectric phase is the permanent dipole within the material. We found that P21 DIPAB has a spontaneous polarization of 22.64 consistent with recent findings which make it good candidate for the creation of ferroelectric tunneling junctions (FTJs) which have the potential to be used as memory devices.

  8. Bonding and structure in dense multi-component molecular mixtures.

    Science.gov (United States)

    Meyer, Edmund R; Ticknor, Christopher; Bethkenhagen, Mandy; Hamel, Sebastien; Redmer, Ronald; Kress, Joel D; Collins, Lee A

    2015-10-28

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10,000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systems engendered by variations in the concentration ratios. A basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers. PMID:26520533

  9. Helping agricultural pollination & bees in farmland

    OpenAIRE

    Balfour, Nicholas James

    2016-01-01

    Previous research has shown that bees are vital to crop pollination. However, modern agricultural practices are occupying an increasing share of the world's land area and have been heavily linked to declining bee populations. This thesis explores: i) the foraging behaviour of the honey bee (Apis mellifera) and its influence on crop pollination, and ii) the impact of current farmland management on bees and other flower visiting insects. Chapter 3 demonstrates, via waggle dance decoding, tha...

  10. Viral diseases in honey bee queens

    OpenAIRE

    Francis, Roy Mathew

    2012-01-01

    Honey bees are one of the most important insects useful to human beings. They provide us with several biological products such as honey and wax, but more importantly carries out the invaluable laborious work of pollination. The honey bee industry in Europe and elsewhere has been plagued by recently introduced pests such as varroa mites and subsequent rise of viruses which has resulted in widespread decline of bee population. Of the numerous pathogens of honey bees that are being studied, viru...

  11. Honey bee genotypes and the environment

    DEFF Research Database (Denmark)

    Meixner, Marina D; Büchler, Ralph; Costa, Cecilia;

    2014-01-01

    Although knowledge about honey bee geographic and genetic diversity has increased tremendously in recent decades, the adaptation of honey bees to their local environment has not been well studied. The current demand for high economic performance of bee colonies with desirable behavioural...

  12. Gardening for Bees in Hampton Roads

    OpenAIRE

    Campbell, Norma; Johnson, Latarsha

    2011-01-01

    Lists plants that will grow well in the Hampton Roads area of Virginia, and will serve as good nectar sources for bees. Also lists a few garden and landscaping plants that bees won't visit for nectar, or could be poisonous to bees.

  13. Viral diseases in honey bee queens

    DEFF Research Database (Denmark)

    Francis, Roy Mathew

    was developed to diagnose three viruses in honey bees. Quantitative PCR was used to investigate the distribution of two popular viruses in five different tissues of 86 honey bee queens. Seasonal variation of viral infection in honey bee workers and varroa mites were determined by sampling 23 colonies...

  14. Antioxidant Activity of Sonoran Desert Bee Pollen

    Science.gov (United States)

    Bee products have been consumed by mankind since antiquity and their health benefits are becoming more apparent. Bee pollen (pollen collected by honey bees) was collected in the high intensity ultraviolet (UV) Sonoran desert and was analyzed by the anti-2,2-diphenyl-1-picryhydrazyl (DPPH) assay and...

  15. Mitochondrial tRNA gene translocations in highly eusocial bees

    Directory of Open Access Journals (Sweden)

    Daniela Silvestre

    2006-01-01

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

  16. Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees.

    Directory of Open Access Journals (Sweden)

    Hui Liu

    2016-06-01

    Full Text Available The emerging field of sociogenomics explores the relations between social behavior and genome structure and function. An important question is the extent to which associations between social behavior and gene expression are conserved among the Metazoa. Prior experimental work in an invertebrate model of social behavior, the honey bee, revealed distinct brain gene expression patterns in African and European honey bees, and within European honey bees with different behavioral phenotypes. The present work is a computational study of these previous findings in which we analyze, by orthology determination, the extent to which genes that are socially regulated in honey bees are conserved across the Metazoa. We found that the differentially expressed gene sets associated with alarm pheromone response, the difference between old and young bees, and the colony influence on soldier bees, are enriched in widely conserved genes, indicating that these differences have genomic bases shared with many other metazoans. By contrast, the sets of differentially expressed genes associated with the differences between African and European forager and guard bees are depleted in widely conserved genes, indicating that the genomic basis for this social behavior is relatively specific to honey bees. For the alarm pheromone response gene set, we found a particularly high degree of conservation with mammals, even though the alarm pheromone itself is bee-specific. Gene Ontology identification of human orthologs to the strongly conserved honey bee genes associated with the alarm pheromone response shows overrepresentation of protein metabolism, regulation of protein complex formation, and protein folding, perhaps associated with remodeling of critical neural circuits in response to alarm pheromone. We hypothesize that such remodeling may be an adaptation of social animals to process and respond appropriately to the complex patterns of conspecific communication essential for

  17. Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees

    Science.gov (United States)

    Robinson, Gene E.; Jakobsson, Eric

    2016-01-01

    The emerging field of sociogenomics explores the relations between social behavior and genome structure and function. An important question is the extent to which associations between social behavior and gene expression are conserved among the Metazoa. Prior experimental work in an invertebrate model of social behavior, the honey bee, revealed distinct brain gene expression patterns in African and European honey bees, and within European honey bees with different behavioral phenotypes. The present work is a computational study of these previous findings in which we analyze, by orthology determination, the extent to which genes that are socially regulated in honey bees are conserved across the Metazoa. We found that the differentially expressed gene sets associated with alarm pheromone response, the difference between old and young bees, and the colony influence on soldier bees, are enriched in widely conserved genes, indicating that these differences have genomic bases shared with many other metazoans. By contrast, the sets of differentially expressed genes associated with the differences between African and European forager and guard bees are depleted in widely conserved genes, indicating that the genomic basis for this social behavior is relatively specific to honey bees. For the alarm pheromone response gene set, we found a particularly high degree of conservation with mammals, even though the alarm pheromone itself is bee-specific. Gene Ontology identification of human orthologs to the strongly conserved honey bee genes associated with the alarm pheromone response shows overrepresentation of protein metabolism, regulation of protein complex formation, and protein folding, perhaps associated with remodeling of critical neural circuits in response to alarm pheromone. We hypothesize that such remodeling may be an adaptation of social animals to process and respond appropriately to the complex patterns of conspecific communication essential for social organization

  18. Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees.

    Science.gov (United States)

    Liu, Hui; Robinson, Gene E; Jakobsson, Eric

    2016-06-01

    The emerging field of sociogenomics explores the relations between social behavior and genome structure and function. An important question is the extent to which associations between social behavior and gene expression are conserved among the Metazoa. Prior experimental work in an invertebrate model of social behavior, the honey bee, revealed distinct brain gene expression patterns in African and European honey bees, and within European honey bees with different behavioral phenotypes. The present work is a computational study of these previous findings in which we analyze, by orthology determination, the extent to which genes that are socially regulated in honey bees are conserved across the Metazoa. We found that the differentially expressed gene sets associated with alarm pheromone response, the difference between old and young bees, and the colony influence on soldier bees, are enriched in widely conserved genes, indicating that these differences have genomic bases shared with many other metazoans. By contrast, the sets of differentially expressed genes associated with the differences between African and European forager and guard bees are depleted in widely conserved genes, indicating that the genomic basis for this social behavior is relatively specific to honey bees. For the alarm pheromone response gene set, we found a particularly high degree of conservation with mammals, even though the alarm pheromone itself is bee-specific. Gene Ontology identification of human orthologs to the strongly conserved honey bee genes associated with the alarm pheromone response shows overrepresentation of protein metabolism, regulation of protein complex formation, and protein folding, perhaps associated with remodeling of critical neural circuits in response to alarm pheromone. We hypothesize that such remodeling may be an adaptation of social animals to process and respond appropriately to the complex patterns of conspecific communication essential for social organization

  19. Gut pathology and responses to the microsporidium Nosema ceranae in the honey bee Apis mellifera.

    Science.gov (United States)

    Dussaubat, Claudia; Brunet, Jean-Luc; Higes, Mariano; Colbourne, John K; Lopez, Jacqueline; Choi, Jeong-Hyeon; Martín-Hernández, Raquel; Botías, Cristina; Cousin, Marianne; McDonnell, Cynthia; Bonnet, Marc; Belzunces, Luc P; Moritz, Robin F A; Le Conte, Yves; Alaux, Cédric

    2012-01-01

    The microsporidium Nosema ceranae is a newly prevalent parasite of the European honey bee (Apis mellifera). Although this parasite is presently spreading across the world into its novel host, the mechanisms by it which affects the bees and how bees respond are not well understood. We therefore performed an extensive characterization of the parasite effects at the molecular level by using genetic and biochemical tools. The transcriptome modifications at the midgut level were characterized seven days post-infection with tiling microarrays. Then we tested the bee midgut response to infection by measuring activity of antioxidant and detoxification enzymes (superoxide dismutases, glutathione peroxidases, glutathione reductase, and glutathione-S-transferase). At the gene-expression level, the bee midgut responded to N. ceranae infection by an increase in oxidative stress concurrent with the generation of antioxidant enzymes, defense and protective response specifically observed in the gut of mammals and insects. However, at the enzymatic level, the protective response was not confirmed, with only glutathione-S-transferase exhibiting a higher activity in infected bees. The oxidative stress was associated with a higher transcription of sugar transporter in the gut. Finally, a dramatic effect of the microsporidia infection was the inhibition of genes involved in the homeostasis and renewal of intestinal tissues (Wnt signaling pathway), a phenomenon that was confirmed at the histological level. This tissue degeneration and prevention of gut epithelium renewal may explain early bee death. In conclusion, our integrated approach not only gives new insights into the pathological effects of N. ceranae and the bee gut response, but also demonstrate that the honey bee gut is an interesting model system for studying host defense responses. PMID:22623972

  20. Gut pathology and responses to the microsporidium Nosema ceranae in the honey bee Apis mellifera.

    Directory of Open Access Journals (Sweden)

    Claudia Dussaubat

    Full Text Available The microsporidium Nosema ceranae is a newly prevalent parasite of the European honey bee (Apis mellifera. Although this parasite is presently spreading across the world into its novel host, the mechanisms by it which affects the bees and how bees respond are not well understood. We therefore performed an extensive characterization of the parasite effects at the molecular level by using genetic and biochemical tools. The transcriptome modifications at the midgut level were characterized seven days post-infection with tiling microarrays. Then we tested the bee midgut response to infection by measuring activity of antioxidant and detoxification enzymes (superoxide dismutases, glutathione peroxidases, glutathione reductase, and glutathione-S-transferase. At the gene-expression level, the bee midgut responded to N. ceranae infection by an increase in oxidative stress concurrent with the generation of antioxidant enzymes, defense and protective response specifically observed in the gut of mammals and insects. However, at the enzymatic level, the protective response was not confirmed, with only glutathione-S-transferase exhibiting a higher activity in infected bees. The oxidative stress was associated with a higher transcription of sugar transporter in the gut. Finally, a dramatic effect of the microsporidia infection was the inhibition of genes involved in the homeostasis and renewal of intestinal tissues (Wnt signaling pathway, a phenomenon that was confirmed at the histological level. This tissue degeneration and prevention of gut epithelium renewal may explain early bee death. In conclusion, our integrated approach not only gives new insights into the pathological effects of N. ceranae and the bee gut response, but also demonstrate that the honey bee gut is an interesting model system for studying host defense responses.

  1. Transcriptome analysis of honey bee larvae following neonicotinoid exposure

    OpenAIRE

    Snart, Charles J. P.

    2011-01-01

    The current decline of the European Honey Bee (Apis Mellifera) has been linked to the increasing use of neonicotinoid pesticides within agriculture. Whilst the toxicity of these pesticides to Apis has long been established, the possibility of low dosages inducing molecular stress has not yet been fully explored. Of particular interest is the action of these nicotine derivatives on the nicotinic acetylcholine receptor, and its association with the DNA methyltransferase family (Dnmts). An ...

  2. Mitochondrial tRNA gene translocations in highly eusocial bees

    OpenAIRE

    Daniela Silvestre; Maria Cristina Arias

    2006-01-01

    Mitochondrial gene rearrangement events, especially involving tRNA genes, have been described more frequently as more complete mitochondrial genome sequences are becoming available. In the present work, we analyzed mitochondrial tRNA gene rearrangements between two bee species belonging to the tribes Apini and Meliponini within the "corbiculate Apidae". Eleven tRNA genes are in different genome positions or strands. The molecular events responsible for each translocation are explained. Consid...

  3. Improvised Scout Bee Movements in Artificial Bee Colony

    OpenAIRE

    Tarun Kumar Sharma; Millie Pant

    2014-01-01

    In the basic Artificial Bee Colony (ABC) algorithm, if the fitness value associated with a food source is not improved for a certain number of specified trials then the corresponding bee becomes a scout to which a random value is assigned for finding the new food source. Basically, it is a mechanism of pulling out the candidate solution which may be entrapped in some local optimizer due to which its value is not improving. In the present study, we propose two new mechanisms for the movements ...

  4. Mineral-Biochar Composites: Molecular Structure and Porosity.

    Science.gov (United States)

    Rawal, Aditya; Joseph, Stephen D; Hook, James M; Chia, Chee H; Munroe, Paul R; Donne, Scott; Lin, Yun; Phelan, David; Mitchell, David R G; Pace, Ben; Horvat, Joseph; Webber, J Beau W

    2016-07-19

    Dramatic changes in molecular structure, degradation pathway, and porosity of biochar are observed at pyrolysis temperatures ranging from 250 to 550 °C when bamboo biomass is pretreated by iron-sulfate-clay slurries (iron-clay biochar), as compared to untreated bamboo biochar. Electron microscopy analysis of the biochar reveals the infusion of mineral species into the pores of the biochar and the formation of mineral nanostructures. Quantitative (13)C nuclear magnetic resonance (NMR) spectroscopy shows that the presence of the iron clay prevents degradation of the cellulosic fraction at pyrolysis temperatures of 250 °C, whereas at higher temperatures (350-550 °C), the clay promotes biomass degradation, resulting in an increase in both the concentrations of condensed aromatic, acidic, and phenolic carbon species. The porosity of the biochar, as measured by NMR cryoporosimetry, is altered by the iron-clay pretreatment. In the presence of the clay, at lower pyrolysis temperatures, the biochar develops a higher pore volume, while at higher temperature, the presence of clay causes a reduction in the biochar pore volume. The most dramatic reduction in pore volume is observed in the kaolinite-infiltrated biochar at 550 °C, which is attributed to the blocking of the mesopores (2-50 nm pore) by the nonporous metakaolinite formed from kaolinite. PMID:27284608

  5. Crystal and molecular structure of four adamantyl-substituted tetrazoles

    International Nuclear Information System (INIS)

    Four adamantyltetrazoles-1-(1-adamantyl)tetrazole (I), 2-(1-adamantyl)tetrazole (II), 2-(3-aminoadamantyl-1)tetrazole (III), and 2-(3-aminoadamantyl-1)-5-methyltetrazole (IV)-are synthesized, and their crystal structures are studied. It is found that the tetrazole rings in the 1-substituted molecule I and 2-substituted molecules II-IV have close linear parameters but differ significantly in endocyclic angles. The degree of delocalization of double bonds in I is somewhat smaller than that in II-IV. The identical relative orientation of the tetrazole ring and adamantyl fragment in I-IV is stabilized by intramolecular C-H...N interactions (H...N, 2.57(2)-2.76(2) A). The molecular packings of crystals I-IV are determined by weak intermolecular C-H...N interactions; in III and IV, the packings are in addition affected by N-H...N interactions that involve NH2 groups. In the series of compounds I-IV, a qualitative dependence of the lengths of intermolecular H...N contacts and antiviral activity on the basicity of nitrogen atoms in the molecules is revealed.

  6. Crystal and molecular structure of four adamantyl-substituted tetrazoles

    Energy Technology Data Exchange (ETDEWEB)

    Polyakova, I. N., E-mail: polyakova@igic.ras.ru [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Saraev, V. V.; Gavrilov, A. S.; Golod, E. L. [St. Petersburg State Technological Institute (Technical University) (Russian Federation)

    2009-05-15

    Four adamantyltetrazoles-1-(1-adamantyl)tetrazole (I), 2-(1-adamantyl)tetrazole (II), 2-(3-aminoadamantyl-1)tetrazole (III), and 2-(3-aminoadamantyl-1)-5-methyltetrazole (IV)-are synthesized, and their crystal structures are studied. It is found that the tetrazole rings in the 1-substituted molecule I and 2-substituted molecules II-IV have close linear parameters but differ significantly in endocyclic angles. The degree of delocalization of double bonds in I is somewhat smaller than that in II-IV. The identical relative orientation of the tetrazole ring and adamantyl fragment in I-IV is stabilized by intramolecular C-H...N interactions (H...N, 2.57(2)-2.76(2) A). The molecular packings of crystals I-IV are determined by weak intermolecular C-H...N interactions; in III and IV, the packings are in addition affected by N-H...N interactions that involve NH{sub 2} groups. In the series of compounds I-IV, a qualitative dependence of the lengths of intermolecular H...N contacts and antiviral activity on the basicity of nitrogen atoms in the molecules is revealed.

  7. Death Associated Protein Kinases: Molecular Structure and Brain Injury

    Directory of Open Access Journals (Sweden)

    Claire Thornton

    2013-07-01

    Full Text Available Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1.

  8. Automatic molecular structure perception for the universal force field.

    Science.gov (United States)

    Artemova, Svetlana; Jaillet, Léonard; Redon, Stephane

    2016-05-15

    The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well-adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self-contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience (http://www.samson-connect.net). We validate both the automatic perception method and the UFF implementation on a series of benchmarks. PMID:26927616

  9. Modeling Carbon and Hydrocarbon Molecular Structures in EZTB

    Science.gov (United States)

    Lee, Seungwon; vonAllmen, Paul

    2007-01-01

    A software module that models the electronic and mechanical aspects of hydrocarbon molecules and carbon molecular structures on the basis of first principles has been written for incorporation into, and execution within, the Easy (Modular) Tight-Binding (EZTB) software infrastructure, which is summarized briefly in the immediately preceding article. Of particular interest, this module can model carbon crystals and nanotubes characterized by various coordinates and containing defects, without need to adjust parameters of the physical model. The module has been used to study the changes in electronic properties of carbon nanotubes, caused by bending of the nanotubes, for potential utility as the basis of a nonvolatile, electriccharge- free memory devices. For example, in one application of the module, it was found that an initially 50-nmlong carbon, (10,10)-chirality nanotube, which is a metallic conductor when straight, becomes a semiconductor with an energy gap of .3 meV when bent to a lateral displacement of 4 nm at the middle.

  10. Molecular Diversity and Genetic Structure of Durum Wheat Landraces

    Directory of Open Access Journals (Sweden)

    GULNAR SHIKHSEYIDOVA

    2015-06-01

    Full Text Available To determine the genetic diversity of durum wheat, 41 accessions from Morocco, Ethiopia, Turkey, Lebanon, Kazakhstan, China, and Mongolia were analyzed through Inter-Simple Sequence Repeats (ISSR molecular markers. Out of the used twenty primers, 15 primers that included a considerable polymorphism were selected for the analyses. Among the genotypes under study, 163 fragments (73.7% were polymorph. Several indexes were used to determine the most appropriate primers. While UBC812, UBC864, UBC840, and UBC808 primers were among those markers which produced the highest number of bands and polymorphic bands, they also dedicated the highest rate of polymorphic index content (PIC. These primers also possessed the highest amounts of effective multiplex ratio (EMR and marker index (MI. Therefore, these primers can be recommended for genetic evaluation of the durum wheat. The results of cluster analysis and principle component analysis indicated that the observed genetic diversity in wheat materials under study is geographically structured. The results also indicated that the genetic diversity index based on ISSR markers was higher for Turkey, Lebanon, Morocco, and Ethiopia accessions than for other countries. The high level of polymorphism in this collections durum wheat would agree with the suggestion that Fertile Crescent and parts of Africa are first possible diversity center of this crop.

  11. A fluorescent method for visualization of Nosema infection in whole-mount honey bee tissues.

    Science.gov (United States)

    Snow, Jonathan W

    2016-03-01

    Honey bees are critical pollinators in both agricultural and ecological settings. The Nosema species, ceranae and apis, are microsporidian parasites that are pathogenic to honey bees. While current methods for detecting Nosema infection have key merits, additional techniques with novel properties for studying the cell biology of Nosema infection are highly desirable. We demonstrate that whole-mount staining of honey bee midgut tissue with chitin-binding agent Fluorescent Brightener 28 and DNA dye Propidium Iodide allows for observation of Nosema infection in structurally intact tissue, providing a new tool for increasing our understanding of Nosema infection at the cellular and tissue level. PMID:26802732

  12. The plight of the bees

    Science.gov (United States)

    Spivak, M.; Mader, E.; Vaughan, M.; Euliss, N.H.

    2011-01-01

    The loss of biodiversity is a trend that is garnering much concern. As organisms have evolved mutualistic and synergistic relationships, the loss of one or a few species can have a much wider environmental impact. Since much pollination is facilitated by bees, the reported colony collapse disorder has many worried of widespread agricultural fallout and thus deleterious impact on human foodstocks. In this Feature, Spivak et al. review what is known of the present state of bee populations and provide information on how to mitigate and reverse the trend. ?? 2010 American Chemical Society.

  13. Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach

    OpenAIRE

    Gutierrez, R.; Caetano, R.; Woiczikowski, P. B.; Kubar, T.; Elstner, M; Cuniberti, G.

    2009-01-01

    Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations arising either fr...

  14. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    International Nuclear Information System (INIS)

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method

  15. Compact structure and proteins of pasta retard in vitro digestive evolution of branched starch molecular structure.

    Science.gov (United States)

    Zou, Wei; Sissons, Mike; Warren, Frederick J; Gidley, Michael J; Gilbert, Robert G

    2016-11-01

    The roles that the compact structure and proteins in pasta play in retarding evolution of starch molecular structure during in vitro digestion are explored, using four types of cooked samples: whole pasta, pasta powder, semolina (with proteins) and extracted starch without proteins. These were subjected to in vitro digestion with porcine α-amylase, collecting samples at different times and characterizing the weight distribution of branched starch molecules using size-exclusion chromatography. Measurement of α-amylase activity showed that a protein (or proteins) from semolina or pasta powder interacted with α-amylase, causing reduced enzymatic activity and retarding digestion of branched starch molecules with hydrodynamic radius (Rh)protein(s) was susceptible to proteolysis. Thus the compact structure of pasta protects the starch and proteins in the interior of the whole pasta, reducing the enzymatic degradation of starch molecules, especially for molecules with Rh>100nm. PMID:27516291

  16. Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia.

    Directory of Open Access Journals (Sweden)

    Charles Runckel

    Full Text Available Honey bees (Apis mellifera play a critical role in global food production as pollinators of numerous crops. Recently, honey bee populations in the United States, Canada, and Europe have suffered an unexplained increase in annual losses due to a phenomenon known as Colony Collapse Disorder (CCD. Epidemiological analysis of CCD is confounded by a relative dearth of bee pathogen field studies. To identify what constitutes an abnormal pathophysiological condition in a honey bee colony, it is critical to have characterized the spectrum of exogenous infectious agents in healthy hives over time. We conducted a prospective study of a large scale migratory bee keeping operation using high-frequency sampling paired with comprehensive molecular detection methods, including a custom microarray, qPCR, and ultra deep sequencing. We established seasonal incidence and abundance of known viruses, Nosema sp., Crithidia mellificae, and bacteria. Ultra deep sequence analysis further identified four novel RNA viruses, two of which were the most abundant observed components of the honey bee microbiome (∼10(11 viruses per honey bee. Our results demonstrate episodic viral incidence and distinct pathogen patterns between summer and winter time-points. Peak infection of common honey bee viruses and Nosema occurred in the summer, whereas levels of the trypanosomatid Crithidia mellificae and Lake Sinai virus 2, a novel virus, peaked in January.

  17. Undergraduate chemistry students' conceptions of atomic structure, molecular structure and chemical bonding

    Science.gov (United States)

    Campbell, Erin Roberts

    The process of chemical education should facilitate students' construction of meaningful conceptual structures about the concepts and processes of chemistry. It is evident, however, that students at all levels possess concepts that are inconsistent with currently accepted scientific views. The purpose of this study was to examine undergraduate chemistry students' conceptions of atomic structure, chemical bonding and molecular structure. A diagnostic instrument to evaluate students' conceptions of atomic and molecular structure was developed by the researcher. The instrument incorporated multiple-choice items and reasoned explanations based upon relevant literature and a categorical summarization of student responses (Treagust, 1988, 1995). A covalent bonding and molecular structure diagnostic instrument developed by Peterson and Treagust (1989) was also employed. The ex post facto portion of the study examined the conceptual understanding of undergraduate chemistry students using descriptive statistics to summarize the results obtained from the diagnostic instruments. In addition to the descriptive portion of the study, a total score for each student was calculated based on the combination of correct and incorrect choices made for each item. A comparison of scores obtained on the diagnostic instruments by the upper and lower classes of undergraduate students was made using a t-Test. This study also examined an axiomatic assumption that an understanding of atomic structure is important in understanding bonding and molecular structure. A Pearson Correlation Coefficient, ṟ, was calculated to provide a measure of the strength of this association. Additionally, this study gathered information regarding expectations of undergraduate chemistry students' understanding held by the chemical community. Two questionnaires were developed with items based upon the propositional knowledge statements used in the development of the diagnostic instruments. Subgroups of items from

  18. Honey Bee Gut Microbiome Is Altered by In-Hive Pesticide Exposures.

    Science.gov (United States)

    Kakumanu, Madhavi L; Reeves, Alison M; Anderson, Troy D; Rodrigues, Richard R; Williams, Mark A

    2016-01-01

    Honey bees (Apis mellifera) are the primary pollinators of major horticultural crops. Over the last few decades, a substantial decline in honey bees and their colonies have been reported. While a plethora of factors could contribute to the putative decline, pathogens, and pesticides are common concerns that draw attention. In addition to potential direct effects on honey bees, indirect pesticide effects could include alteration of essential gut microbial communities and symbionts that are important to honey bee health (e.g., immune system). The primary objective of this study was to determine the microbiome associated with honey bees exposed to commonly used in-hive pesticides: coumaphos, tau-fluvalinate, and chlorothalonil. Treatments were replicated at three independent locations near Blacksburg Virginia, and included a no-pesticide amended control at each location. The microbiome was characterized through pyrosequencing of V2-V3 regions of the bacterial 16S rRNA gene and fungal ITS region. Pesticide exposure significantly affected the structure of bacterial but not fungal communities. The bee bacteriome, similar to other studies, was dominated by sequences derived from Bacilli, Actinobacteria, α-, β-, γ-proteobacteria. The fungal community sequences were dominated by Ascomycetes and Basidiomycetes. The Multi-response permutation procedures (MRPP) and subsequent Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated that chlorothalonil caused significant change to the structure and functional potential of the honey bee gut bacterial community relative to control. Putative genes for oxidative phosphorylation, for example, increased while sugar metabolism and peptidase potential declined in the microbiome of chlorothalonil exposed bees. The results of this field-based study suggest the potential for pesticide induced changes to the honey bee gut microbiome that warrant further investigation. PMID:27579024

  19. Honey Bee Gut Microbiome Is Altered by In-Hive Pesticide Exposures

    Science.gov (United States)

    Kakumanu, Madhavi L.; Reeves, Alison M.; Anderson, Troy D.; Rodrigues, Richard R.; Williams, Mark A.

    2016-01-01

    Honey bees (Apis mellifera) are the primary pollinators of major horticultural crops. Over the last few decades, a substantial decline in honey bees and their colonies have been reported. While a plethora of factors could contribute to the putative decline, pathogens, and pesticides are common concerns that draw attention. In addition to potential direct effects on honey bees, indirect pesticide effects could include alteration of essential gut microbial communities and symbionts that are important to honey bee health (e.g., immune system). The primary objective of this study was to determine the microbiome associated with honey bees exposed to commonly used in-hive pesticides: coumaphos, tau-fluvalinate, and chlorothalonil. Treatments were replicated at three independent locations near Blacksburg Virginia, and included a no-pesticide amended control at each location. The microbiome was characterized through pyrosequencing of V2–V3 regions of the bacterial 16S rRNA gene and fungal ITS region. Pesticide exposure significantly affected the structure of bacterial but not fungal communities. The bee bacteriome, similar to other studies, was dominated by sequences derived from Bacilli, Actinobacteria, α-, β-, γ-proteobacteria. The fungal community sequences were dominated by Ascomycetes and Basidiomycetes. The Multi-response permutation procedures (MRPP) and subsequent Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated that chlorothalonil caused significant change to the structure and functional potential of the honey bee gut bacterial community relative to control. Putative genes for oxidative phosphorylation, for example, increased while sugar metabolism and peptidase potential declined in the microbiome of chlorothalonil exposed bees. The results of this field-based study suggest the potential for pesticide induced changes to the honey bee gut microbiome that warrant further investigation. PMID:27579024

  20. Neurobiological mechanisms of treatment resistant depression: Functional, structural and molecular imaging studies

    NARCIS (Netherlands)

    B.P. de Kwaasteniet

    2015-01-01

    This thesis investigated the neurobiological mechanisms of TRD using functional, structural and molecular imaging studies. First the neurobiological mechanisms of MDD were investigated and revealed decreased functional connectivity between the ventral and dorsal network. Thereafter, structural conne

  1. From silkworms to bees: Diseases of beneficial insects

    Science.gov (United States)

    The diseases of the silkworm (Bombyx mori) and managed bees, including the honey bee (Apis mellifera), bumbles bees (Bombus spp.), the alfalfa leafcutting bee (Megachile rotundata), and mason bees (Osmia spp.) are reviewed, with diagnostic descriptions and a summary of control methods for production...

  2. Effect of molecular structure and slump loss resistance of polycarboxylate superplasticizers on self-compacting concrete

    Institute of Scientific and Technical Information of China (English)

    LAN Zi-dong

    2016-01-01

    A new kind of polycarboxylate superplasticizer with high slump loss resistance was obtained by designing scheduled molecular structure. The number average molecular mass of the polymer was characterized by thegel permeation chromatography measurements. And chemical structure of the polymer was observed by the Fouriertransform infrared spectroscopy(FT-IR). The results showthat the good workablemaintaining ofself-compacting concretecould be achieved through direct adjustmentof number average molecular mass and different unsaturated monomer in synthetic process. The FT-IR analysis illustrated that the high slump loss resistance of polycarboxylate superplasticizers with ester and carboxyl group and expectations of molecular structure were designed.

  3. Molecular Structural and Properties of 3-chloro-4 (dichloromethyl)-5-hydroxy-2 [5H] -furanone (MX)

    Institute of Scientific and Technical Information of China (English)

    李欣; 龙运前; 齐晶瑶; 王郁萍

    2004-01-01

    3 - chloro - 4 (dichloromethyl) - 5 - hydroxy - 2 [5H] - furanone (MX) formed during chlorination of water containing natural organic substances, is a very potent bacterial mutgen. Molecular mechanics calculations to evaluate the conformation of structure, and to determine structure relationship properties are put forward. The investigations allow the correlation of molecular structures of MX with its properties, such as mass,partial charges, steric energy, frontier molecular orbital. The VRML molecular models have been investigated using Virtual Reality software. The spectral simulation of MX is illustrated. The principal aim is to develop an efficient method which control of MX.

  4. Structural Characteristics of Low Molecular Weight Laminarin Prepared by Ionizing Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jong-il [Chonnam National University, Gwangju (Korea, Republic of)

    2013-12-15

    Recently, it has been reported that low molecular weight laminarin had the enhanced biological activities. In this study, molecular structure of low molecular weight laminarin prepared by ionizing irradiation was studied. Low molecular weight laminarin samples of 13.5, 8.5, 7, and 6 kDa were obtained from 15 kDa laminarin by irradiation. From gel permeation chromatography data, low molecular weight laminarin was shown to have low polydispersity. To define the changes of functional groups in laminarin with different molecular weights, Fourier-transform infrared analysis was carried out. There was found no significant changes of functional groups in low molecular weight laminarin, except the increase of carbonyl group. The granular fissures from scanning electron microscopy showed the breakage of glycosidic bond in low molecular weight laminarin. These results could be utilized for the investigation of the enhanced biological activities of low molecular weight polysaccharides including laminarin.

  5. Structural Characteristics of Low Molecular Weight Laminarin Prepared by Ionizing Irradiation

    International Nuclear Information System (INIS)

    Recently, it has been reported that low molecular weight laminarin had the enhanced biological activities. In this study, molecular structure of low molecular weight laminarin prepared by ionizing irradiation was studied. Low molecular weight laminarin samples of 13.5, 8.5, 7, and 6 kDa were obtained from 15 kDa laminarin by irradiation. From gel permeation chromatography data, low molecular weight laminarin was shown to have low polydispersity. To define the changes of functional groups in laminarin with different molecular weights, Fourier-transform infrared analysis was carried out. There was found no significant changes of functional groups in low molecular weight laminarin, except the increase of carbonyl group. The granular fissures from scanning electron microscopy showed the breakage of glycosidic bond in low molecular weight laminarin. These results could be utilized for the investigation of the enhanced biological activities of low molecular weight polysaccharides including laminarin

  6. Chronic bee paralysis virus and Nosema ceranae experimental co-infection of winter honey bee workers (Apis mellifera L.)

    Science.gov (United States)

    Chronic bee paralysis virus (CBPV) is an important viral disease of adult bees which induces significant losses in honey bee colonies. In this study winter worker bees were experimentally infected using three different experiments. Bees were inoculated orally or topically with CBPV to evaluate the l...

  7. Hey! A Bee Stung Me!

    Science.gov (United States)

    ... feeding on pollen and honey, wasps eat animal food, other insects, or spiders. They are not fuzzy like bees, ... Wear shoes outdoors. Don't disturb hives or insect nests. Don't wear sweet-smelling perfume, ... food when eating outdoors. Be careful when outside with ...

  8. Sickness Behavior in Honey Bees

    Science.gov (United States)

    Kazlauskas, Nadia; Klappenbach, Martín; Depino, Amaicha M.; Locatelli, Fernando F.

    2016-01-01

    During an infection, animals suffer several changes in their normal physiology and behavior which may include lethargy, appetite loss, and reduction in grooming and general movements. This set of alterations is known as sickness behavior and although it has been extensively believed to be orchestrated primarily by the immune system, a relevant role for the central nervous system has also been established. The aim of the present work is to develop a simple animal model to allow studying how the immune and the nervous systems interact coordinately during an infection. We administered a bacterial lipopolysaccharide (LPS) into the thorax of honey bees to mimic a bacterial infection, and then we evaluated a set of stereotyped behaviors of the animals that might be indicative of sickness behavior. First, we show that this immune challenge reduces the locomotor activity of the animals in a narrow time window after LPS injection. Furthermore, bees exhibit a loss of appetite 60 and 90 min after injection, but not 15 h later. We also demonstrate that LPS injection reduces spontaneous antennal movements in harnessed animals, which suggests a reduction in the motivational state of the bees. Finally, we show that the LPS injection diminishes the interaction between animals, a crucial behavior in social insects. To our knowledge these results represent the first systematic description of sickness behavior in honey bees and provide important groundwork for the study of the interaction between the immune and the neural systems in an insect model. PMID:27445851

  9. Furosemide's one little hydrogen atom: NMR crystallography structure verification of powdered molecular organics.

    Science.gov (United States)

    Widdifield, Cory M; Robson, Harry; Hodgkinson, Paul

    2016-05-10

    The potential of NMR crystallography to verify molecular crystal structures deposited in structural databases is evaluated, with two structures of the pharmaceutical furosemide serving as examples. While the structures differ in the placement of one H atom, using this approach, we verify one of the structures in the Cambridge Structural Database using quantitative tools, while establishing that the other structure does not meet the verification criteria. PMID:27115483

  10. Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

    OpenAIRE

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E.

    2001-01-01

    An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit discusses methods used to treat the energy and to sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.

  11. Evaluation of specimen preservatives for DNA analyses of bees

    Science.gov (United States)

    Frampton, M.; Droege, S.; Conrad, T.; Prager, S.; Richards, M.H.

    2008-01-01

    Large-scale insect collecting efforts that are facilitated by the use of pan traps result in large numbers of specimens being collected. Storage of these specimens can be problematic if space and equipment are limited. In this study, we investigated the effects of various preservatives (alcohol solutions and DMSO) on the amount and quality of DNA extracted from bees (specifically Halictidae, Apidae, and Andrenidae). In addition, we examined the amount and quality of DNA obtained from bee specimens killed and stored at -80 degrees C and from specimens stored for up to 24 years in ethanol. DNA quality was measured in terms of how well it could be PCR-amplified using a set of mitochondrial primers that are commonly used in insect molecular systematics. Overall the best methods of preservation were ultra-cold freezing and dimethyl sulfoxide, but these are both expensive and in the case of ultra-cold freezing, somewhat impractical for field entomologists. Additionally, dimethyl sulfoxide was shown to have adverse effects on morphological characters that are typically used for identification to the level of species. We therefore recommend that the best alternative is 95% ethanol, as it preserves bee specimens well for both morphological and molecular studies.

  12. Molecular weight dependence of domain structure in silica-siloxane molecular composites

    International Nuclear Information System (INIS)

    This paper reports that a detailed investigation of the molecular weight dependence of silica growth in in situ filled polydimethylsiloxane/tetraethylorthosilicate (PDMS/TEOS) materials was conducted using small angle neutron scattering (SANS). Composite materials were produced by using TEOS to simultaneously produce the glassy filler phase and to crosslink linear, hydroxyl terminated PDMS of variable molecular weight, M. Correlated domains of glassy filler were produced. The morphology of the in situ filled material showed a definite dependence on the molecular weight of the precursor polymer. The scale, R, of the glassy domains follows de Gennes' description of phase separation in a crosslinked system (R α M1/2)

  13. Monogamy in large bee societies: a stingless paradox

    Science.gov (United States)

    Jaffé, Rodolfo; Pioker-Hara, Fabiana C.; dos Santos, Charles F.; Santiago, Leandro R.; Alves, Denise A.; de M. P. Kleinert, Astrid; Francoy, Tiago M.; Arias, Maria C.; Imperatriz-Fonseca, Vera L.

    2014-03-01

    High genetic diversity is important for the functioning of large insect societies. Across the social Hymenoptera (ants, bees, and wasps), species with the largest colonies tend to have a high colony-level genetic diversity resulting from multiple queens (polygyny) or queens that mate with multiple males (polyandry). Here we studied the genetic structure of Trigona spinipes, a stingless bee species with colonies an order of magnitude larger than those of polyandrous honeybees. Genotypes of adult workers and pupae from 43 nests distributed across three Brazilian biomes showed that T. spinipes colonies are usually headed by one singly mated queen. Apart from revealing a notable exception from the general incidence of high genetic diversity in large insect societies, our results reinforce previous findings suggesting the absence of polyandry in stingless bees and provide evidence against the sperm limitation hypothesis for the evolution of polyandry. Stingless bee species with large colonies, such as T. spinipes, thus seem promising study models to unravel alternative mechanisms to increase genetic diversity within colonies or understand the adaptive value of low genetic diversity in large insect societies.

  14. A honey bee (Apis mellifera L. PeptideAtlas crossing castes and tissues

    Directory of Open Access Journals (Sweden)

    Deutsch Eric W

    2011-06-01

    Full Text Available Abstract Background Honey bees are a mainstay of agriculture, contributing billions of dollars through their pollination activities. Bees have been a model system for sociality and group behavior for decades but only recently have molecular techniques been brought to study this fascinating and valuable organism. With the release of the first draft of its genome in 2006, proteomics of bees became feasible and over the past five years we have amassed in excess of 5E+6 MS/MS spectra. The lack of a consolidated platform to organize this massive resource hampers our ability, and that of others, to mine the information to its maximum potential. Results Here we introduce the Honey Bee PeptideAtlas, a web-based resource for visualizing mass spectrometry data across experiments, providing protein descriptions and Gene Ontology annotations where possible. We anticipate that this will be helpful in planning proteomics experiments, especially in the selection of transitions for selected reaction monitoring. Through a proteogenomics effort, we have used MS/MS data to anchor the annotation of previously undescribed genes and to re-annotate previous gene models in order to improve the current genome annotation. Conclusions The Honey Bee PeptideAtlas will contribute to the efficiency of bee proteomics and accelerate our understanding of this species. This publicly accessible and interactive database is an important framework for the current and future analysis of mass spectrometry data.

  15. Phylogenomics Controlling for Base Compositional Bias Reveals a Single Origin of Eusociality in Corbiculate Bees.

    Science.gov (United States)

    Romiguier, Jonathan; Cameron, Sydney A; Woodard, S Hollis; Fischman, Brielle J; Keller, Laurent; Praz, Christophe J

    2016-03-01

    As increasingly large molecular data sets are collected for phylogenomics, the conflicting phylogenetic signal among gene trees poses challenges to resolve some difficult nodes of the Tree of Life. Among these nodes, the phylogenetic position of the honey bees (Apini) within the corbiculate bee group remains controversial, despite its considerable importance for understanding the emergence and maintenance of eusociality. Here, we show that this controversy stems in part from pervasive phylogenetic conflicts among GC-rich gene trees. GC-rich genes typically have a high nucleotidic heterogeneity among species, which can induce topological conflicts among gene trees. When retaining only the most GC-homogeneous genes or using a nonhomogeneous model of sequence evolution, our analyses reveal a monophyletic group of the three lineages with a eusocial lifestyle (honey bees, bumble bees, and stingless bees). These phylogenetic relationships strongly suggest a single origin of eusociality in the corbiculate bees, with no reversal to solitary living in this group. To accurately reconstruct other important evolutionary steps across the Tree of Life, we suggest removing GC-rich and GC-heterogeneous genes from large phylogenomic data sets. Interpreted as a consequence of genome-wide variations in recombination rates, this GC effect can affect all taxa featuring GC-biased gene conversion, which is common in eukaryotes. PMID:26576851

  16. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: a non-equilibrium molecular dynamics study

    CERN Document Server

    Lemarchand, Claire A; Todd, Billy D; Daivis, Peter J; Hansen, Jesper S

    2015-01-01

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear is investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity and normal stress differences of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid. The corresponding molecular structure is studied at the same shear rates and temperatures. The Cooee bitumen is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. The nanoaggregates are shown to break up at very high shear rates, leading only to a minor effect on the viscosity of the mixture. At low shear rates, bitumen can be seen as a colloidal suspension of nanoaggregates in a solvent. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified...

  17. Designing π-stacked molecular structures to control heat transport through molecular junctions

    Energy Technology Data Exchange (ETDEWEB)

    Kiršanskas, Gediminas [Center for Quantum Devices, Niels Bohr Institute, University of Copenhagen, DK-2100 Copenhagen Ø (Denmark); Mathematical Physics and Nanometer Structure Consortium (nmC-LU), Lund University, Box 118, 221 00 Lund (Sweden); Li, Qian; Solomon, Gemma C. [Nano-Science Center and Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø (Denmark); Flensberg, Karsten [Center for Quantum Devices, Niels Bohr Institute, University of Copenhagen, DK-2100 Copenhagen Ø (Denmark); Leijnse, Martin [Solid State Physics and Nanometer Structure Consortium (nmC-LU), Lund University, 221 00 Lund (Sweden)

    2014-12-08

    We propose and analyze a way of using π stacking to design molecular junctions that either enhance or suppress a phononic heat current, but at the same time remain conductors for an electric current. Such functionality is highly desirable in thermoelectric energy converters, as well as in other electronic components where heat dissipation should be minimized or maximized. We suggest a molecular design consisting of two masses coupled to each other with one mass coupled to each lead. By having a small coupling (spring constant) between the masses, it is possible to either reduce or perhaps more surprisingly enhance the phonon conductance. We investigate a simple model system to identify optimal parameter regimes and then use first principle calculations to extract model parameters for a number of specific molecular realizations, confirming that our proposal can indeed be realized using standard molecular building blocks.

  18. Insights from the Molecular Dynamics Simulation of Cellobiohydrolase Cel6A Molecular Structural Model from Aspergillus fumigatus NITDGPKA3.

    Science.gov (United States)

    Dodda, Subba Reddy; Sarkar, Nibedita; Aikat, Kaustav; Krishnaraj, Navanietha R; Bhattacharjee, Sanchari; Bagchi, Angshuman; Mukhopadhyay, Sudit S

    2016-01-01

    Global demand for bioethanol is increasing tremendously as it could help to replace the conventional fossil fuel and at the same time supporting the bioremediation of huge volume of cellulosic wastes generated from different sources. Ideal genetic engineering approaches are essential to improve the efficacy of the bioethanol production processes for real time applications. A locally isolated fungal strain Aspergillus fumigatus NITDGPKA3 was used in our laboratory for the hydrolysis of lignocellulose with good cellulolytic activity when compared with other contemporary fungal strains. An attempt is made to sequence the cellobiohydrolases (CBHs) of A. fumigatus NITDGPKA3, model its structure to predict its catalytic activity towards improving the protein by genetic engineering approaches. Herein, the structure of the sequenced Cellobiohydrolases (CBHs) of A. fumigatus NITDGPKA3, modelled by homology modelling and its validation is reported. Further the catalytic activity of the modelled CBH enzyme was assessed by molecular docking analysis. Phylogenetic analysis showed that CBH from A. fumigatus NITDGPKA3 belongs to the Glycohydro 6 (Cel6A) super family. Molecular modeling and molecular dynamics simulation suggest the structural and functional mechanism of the enzyme. The structures of both the cellulose binding (CBD) and catalytic domain (CD) have been compared with most widely studied CBH of Trichoderma reesei. The molecular docking with cellulose suggests that Gln 248, Pro 287, Val236, Asn284, and Ala288 are the main amino acids involved in the hydrolysis of the β, 1-4, glycosidic bonds of cellulose. PMID:27109185

  19. Graph of atomic orbitals and the molecular structure-descriptors based on it

    Directory of Open Access Journals (Sweden)

    ANDREY A. TOROPOV

    2005-04-01

    Full Text Available The graph of atomic orbitals (GAO is a novel type of molecular graph, recently proposed by one of the authors. Various molecular structure-descriptors computed for GAO are compared with their analogs computed for ordinary molecular graphs. The quality of these structure-descriptors was tested for correlation with the normal boiling points of alkanes and cycloalkanes. In all the studied cases, the results based on GAO are similar to, and usually slightly better than, those obtained by means of ordinary molecular graps.

  20. Autogrooming by resistant honey bees challenged with individual tracheal mites

    OpenAIRE

    Danka, Robert; Villa, José

    2003-01-01

    Autogrooming responses of resistant and susceptible strains of honey bees were measured when bees were challenged by placing adult female tracheal mites on their thoraces. Marked, young adult workers of the two strains of bees were added to colonies in observation hives. We transferred a single, live, adult, female mite onto the mesoscutum of a marked bee, monitored the bee for seven minutes and then removed it and searched for the mite. Greater proportions of resistant bees autogroomed, and ...

  1. Do managed bees drive parasite spread and emergence in wild bees?

    OpenAIRE

    Graystock, Peter; Blane, Edward J; McFrederick, Quinn S.; Goulson, Dave; Hughes, William O. H.

    2015-01-01

    Bees have been managed and utilised for honey production for centuries and, more recently, pollination services. Since the mid 20th Century, the use and production of managed bees has intensified with hundreds of thousands of hives being moved across countries and around the globe on an annual basis. However, the introduction of unnaturally high densities of bees to areas could have adverse effects. Importation and deployment of managed honey bee and bumblebees may be responsible for parasite...

  2. Bee Venom Alleviates Motor Deficits and Modulates the Transfer of Cortical Information through the Basal Ganglia in Rat Models of Parkinson’s Disease

    OpenAIRE

    Maurice, Nicolas; Deltheil, Thierry; Melon, Christophe; Degos, Bertrand; Mourre, Christiane; Amalric, Marianne; Kerkerian-Le Goff, Lydia

    2015-01-01

    Recent evidence points to a neuroprotective action of bee venom on nigral dopamine neurons in animal models of Parkinson’s disease (PD). Here we examined whether bee venom also displays a symptomatic action by acting on the pathological functioning of the basal ganglia in rat PD models. Bee venom effects were assessed by combining motor behavior analyses and in vivo electrophysiological recordings in the substantia nigra pars reticulata (SNr, basal ganglia output structure) in pharmacological...

  3. 蜂毒的主要成分及药理作用的研究进展%Advances in main compositions and pharmacological effects of bee venom

    Institute of Scientific and Technical Information of China (English)

    张冰清; 刘晓波

    2016-01-01

    Bee venom is a kind of active compounds secreted by the gland,which have many active ingredients like anti-inflammatory,anti -tumor,analgesic,anti -hypertensive and so on.In recent years,many scientists had been made im-portant progress in research of the active ingredient analysis,genetic structure,pharmacological action mechanism and mo-lecular biology of bee venom.The purpose of this article was to summarize main active ingredients of bee venom and the main pharmacological actions and provide theoretical basis for the clinical used.%蜂毒是由蜜蜂毒腺分泌的活性物质,其中很多活性成分具有抗炎、抗肿瘤、镇痛、降压的作用。近年来,国内外很多科学家对蜂毒的活性成分及其基因结构、药理作用机制、分子生物学等方面进行了研究,并且取得了重要的研究进展。本文总结了蜂毒的主要活性成分以及主要的药理作用,为蜂毒的临床应用提供理论基础。

  4. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  5. Chronic Bee Paralysis Virus in Honeybee Queens

    DEFF Research Database (Denmark)

    Amiri, Esmaeil; Meixner, Marina; Büchler, Ralph;

    2014-01-01

    Chronic bee paralysis virus (CBPV) is known as a disease of worker honey bees. To investigate pathogenesis of the CBPV on the queen, the sole reproductive individual in a colony, we conducted experiments regarding the susceptibility of queens to CBPV. Results from susceptibility experiment showed a...... similar disease progress in the queens compared to worker bees after infection. Infected queens exhibit symptoms by Day 6 post infection and virus levels reach 1011 copies per head. In a transmission experiment we showed that social interactions may affect the disease progression. Queens with forced...... contact to symptomatic worker bees acquired an overt infection with up to 1011 virus copies per head in six days. In contrast, queens in contact with symptomatic worker bees, but with a chance to receive food from healthy bees outside the cage appeared healthy. The virus loads did not exceed 107 in the...

  6. Differential sensitivity of honey bees and bumble bees to a dietary insecticide (imidacloprid).

    Science.gov (United States)

    Cresswell, James E; Page, Christopher J; Uygun, Mehmet B; Holmbergh, Marie; Li, Yueru; Wheeler, Jonathan G; Laycock, Ian; Pook, Christopher J; de Ibarra, Natalie Hempel; Smirnoff, Nick; Tyler, Charles R

    2012-12-01

    Currently, there is concern about declining bee populations and the sustainability of pollination services. One potential threat to bees is the unintended impact of systemic insecticides, which are ingested by bees in the nectar and pollen from flowers of treated crops. To establish whether imidacloprid, a systemic neonicotinoid and insect neurotoxin, harms individual bees when ingested at environmentally realistic levels, we exposed adult worker bumble bees, Bombus terrestris L. (Hymenoptera: Apidae), and honey bees, Apis mellifera L. (Hymenoptera: Apidae), to dietary imidacloprid in feeder syrup at dosages between 0.08 and 125μg l(-1). Honey bees showed no response to dietary imidacloprid on any variable that we measured (feeding, locomotion and longevity). In contrast, bumble bees progressively developed over time a dose-dependent reduction in feeding rate with declines of 10-30% in the environmentally relevant range of up to 10μg l(-1), but neither their locomotory activity nor longevity varied with diet. To explain their differential sensitivity, we speculate that honey bees are better pre-adapted than bumble bees to feed on nectars containing synthetic alkaloids, such as imidacloprid, by virtue of their ancestral adaptation to tropical nectars in which natural alkaloids are prevalent. We emphasise that our study does not suggest that honey bee colonies are invulnerable to dietary imidacloprid under field conditions, but our findings do raise new concern about the impact of agricultural neonicotinoids on wild bumble bee populations. PMID:23044068

  7. Host Range Expansion of Honey Bee Black Queen Cell Virus in the Bumble Bee, Bombus huntii

    Science.gov (United States)

    Honey bee viruses display a host range that is not restricted to their original host, European honey bees, Apis mellifera. Here we provide the first evidence that Black Queen Cell Virus (BQCV), one of the most prevalent honey bee viruses, can cause an infection in both laboratory-reared and field-co...

  8. Comparative Analyses of Proteome Complement Between Worker Bee Larvae of High Royal Jelly Producing Bees (A. m. ligustica) and Carniolian Bees (A. m. carnica)

    Institute of Scientific and Technical Information of China (English)

    CHEN Jian; LI Jian-ke

    2009-01-01

    This study is to compare the protein composition of the high royal jelly producing bee (A. m. ligustica) with that of Carniolian bee (A. m. carnica) during their worker larval developmental stage. The experiment was carried out by two-dimensional gel electrophoresis. The results showed that significant higher numbers of total proteins (283) were detected in larvae of high royal jelly producing bees (Jelly bee) than those of Camiolian bees (152) on 2-d-old larvae. Among them, 110 proteins were presented on both strains of bee larvae, whereas 173 proteins were specific to larvae of Jelly bees, and 42 proteins were exclusive to Carniolian larvae. However, on the 4th d, a significant higher number of total proteins (290) were detected in larvae of Jelly bees than those of Camiolian bees (240), 163 proteins resolved to both bee larvae, and 127 proteins were specific to Jelly bees and 77 proteins to Camiolian bees. Until the 6th d, also a significant higher number of total proteins (236) were detected in larvae of Jelly bees than those of Carniolian bees (180), 132 proteins were constantly expressed in two bee larvae, whereas 104 and 48 proteins are unique to Jelly bee and Camiolian bee larvae, respectively. We tentatively concluded that the metabolic rate and gene expression of Jelly bees larvae is higher than those of Carniolian bees based proteins detected as total proteins and proteins specific to each stage of two strains of bee larvae. Proteins constantly expressed on 3 stages of larval development with some significant differences between two bee strains, and proteins unique to each stage expressed differences in term of quality and quantity, indicating that larval development needed house keeping and specific proteins to regulate its growth at different development phage, but the expression mold is different between two strains of larval development.

  9. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to...

  10. How bees distinguish patterns by green and blue modulation

    Directory of Open Access Journals (Sweden)

    Horridge A

    2015-10-01

    Full Text Available Adrian Horridge Biological Sciences, Australian National University, Canberra, ACT, Australia Abstract: In the 1920s, Mathilde Hertz found that trained bees discriminated between shapes or patterns of similar size by something related to total length of contrasting contours. This input is now interpreted as modulation in green and blue receptor channels as flying bees scan in the horizontal plane. Modulation is defined as total contrast irrespective of sign multiplied by length of edge displaying that contrast, projected to vertical, therefore, combining structure and contrast in a single input. Contrast is outside the eye; modulation is a phasic response in receptor pathways inside. In recent experiments, bees trained to distinguish color detected, located, and measured three independent inputs and the angles between them. They are the tonic response of the blue receptor pathway and modulation of small-field green or (less preferred blue receptor pathways. Green and blue channels interacted intimately at a peripheral level. This study explores in more detail how various patterns are discriminated by these cues. The direction of contrast at a boundary was not detected. Instead, bees located and measured total modulation generated by horizontal scanning of contrasts, irrespective of pattern. They also located the positions of isolated vertical edges relative to other landmarks and distinguished the angular widths between vertical edges by green or blue modulation alone. The preferred inputs were the strongest green modulation signal and angular width between outside edges, irrespective of color. In the absence of green modulation, the remaining cue was a measure and location of blue modulation at edges. In the presence of green modulation, blue modulation was inhibited. Black/white patterns were distinguished by the same inputs in blue and green receptor channels. Left–right polarity and mirror images could be discriminated by retinotopic green

  11. Pathogen Webs in Collapsing Honey Bee Colonies

    OpenAIRE

    Cornman, R Scott; Tarpy, David R.; Chen, Yanping; Jeffreys, Lacey; Lopez, Dawn; Pettis, Jeffery S.; vanEngelsdorp, Dennis; Jay D. Evans

    2012-01-01

    Recent losses in honey bee colonies are unusual in their severity, geographical distribution, and, in some cases, failure to present recognized characteristics of known disease. Domesticated honey bees face numerous pests and pathogens, tempting hypotheses that colony collapses arise from exposure to new or resurgent pathogens. Here we explore the incidence and abundance of currently known honey bee pathogens in colonies suffering from Colony Collapse Disorder (CCD), otherwise weak colonies, ...

  12. Bee sting after seizure and ischemic attack

    Directory of Open Access Journals (Sweden)

    Aynur Yurtseven

    2015-09-01

    Full Text Available Insect bites, bee stings are the most frequently encountered. Often seen after bee stings usually only local allergic reactions. Sometimes with very serious clinical condition may also be confronted. Of this rare clinical findings; polyneuritis, parkinsonism, encephalitis, acute disseminated encephalomyelitis, Guillain-Barre syndrome, myocardial infarction, pulmonary edema, hemorrhage, hemolytic anemia and renal disease has. Here a rare convulsions after a bee sting is presented.

  13. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    Science.gov (United States)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  14. Molecular and structural preservation of dehydrated bio-tissue for THz spectroscopy

    Science.gov (United States)

    Png, Gretel M.; Choi, Jin Wook; Guest, Ian; Ng, Brian W.-H.; Mickan, Samuel P.; Abbott, Derek; Zhang, Xi-Cheng

    2007-12-01

    Terahertz transmission through freshly excised biological tissue is limited by the tissue's high water content. Tissue fixation methods that remove water, such as fixation in Formalin, destroy the structural information of proteins hence are not suitable for THz applications. Dehydration is one possible method for revealing the tissue's underlying molecular structure and components. In this study, we measured the THz responses over time of dehydrating fresh, necrotic and lyophilized rat tissue. Our results show that as expected, THz absorption increases dramatically with drying and tissue freshness can be maintained through lyophilization. Dehydrated biological tissue with retained molecular structure can be useful for future laser-based THz wave molecular analysis.

  15. A parity function for studying the molecular electronic structure

    DEFF Research Database (Denmark)

    Schmider, Hartmut

    1996-01-01

    Sections through the molecular Wigner function with zero momentum variable are shown to provide important information about the off-diagonal regions of the spinless one-particle reduced density matrix. Since these regions are characteristic for the bonding situation in molecules, the sections...

  16. A Molecular Dynamics Approach to Grain Boundary Structure and Migration

    DEFF Research Database (Denmark)

    Cotterill, R. M. J.; Leffers, Torben; Lilholt, Hans

    1974-01-01

    It has been demonstrated that grain boundary formation from the melt can be simulated by the molecular dynamics method. The space between two mutually-misoriented crystal slabs was filled with atoms in a random manner and this liquid was then cooled until crystallization occurred. The general...

  17. Molecular conformation and structural correlations of liquid D-1-propanol through neutron diffraction

    Indian Academy of Sciences (India)

    A Sahoo; S Sarkar; P S R Krishna; V Bhagat; R N Joarder

    2008-07-01

    An analysis of neutron diffraction data of liquid deuterated 1-propanol at room temperature to extract its molecular conformation is presented. Being a big molecule with twelve atomic sites, the analysis is tricky and needs careful consideration. The resulting molecular parameters are compared with electron diffraction (gas phase), X-ray diffraction (liquid phase) and MD simulation results. Information about the hydrogen-bonded intermolecular structure in liquid is extracted and nature of the probable molecular association suggested.

  18. Molecular Characterisation of Structural Chromosomal Abnormalities Associated with Congenital Disorders

    OpenAIRE

    Mansouri, Mahmoud R.

    2006-01-01

    Chromosomal abnormalities are defined as changes in the chromosome structure and fall in one of two categories. The first category is numerical alterations while the second category consists of structural abnormalities. Structural chromosomal abnormalities do not always interrupt genes in order to cause disease. They can also affect gene expression by separating a gene and its promoter element from distant regulatory elements. We have used characterisation of structural chromosomal abnormalit...

  19. Clinical Studies of Sweet Bee Venom to the Effect of Abdominal Fat Accumulation

    Directory of Open Access Journals (Sweden)

    Chung San, Lim

    2008-06-01

    Full Text Available Objective : Sweet bee venom is made by removing allergen from the bee venom through gel filtration chromatography and propionic acid/urea polyacrylamide gel electrophoresis. The aim of this study was to verify allergy inhibitory action in Sweet Bee Venom(SBV and New Sweet Bee Venom(NSBV removed enzymes and compounds of low molecular weight. Methods : 84 healthy adult men and women were selected through a survey whom had never received the bee venom therapy in the past. The concentration of Normal Saline, SBV and NSBV pharmacopuncture was equally at 0.1mg/mL and the experiment was conducted as the double blind test. Results : Participants of the study was comprised of 63 men and 21 women with the average age of 28.3 years. According to results of pain sense, SBV group showed significant higher score compared with NS group and NSBV group using VAS in treating time. And SBV and NSBV group showed significant higher score compared with NS group after 30 minutes. Other allergic responses were insignificant between the groups. Conclusions : As a result of removed allergen and compounds of low molecular weight, NSBV significantly inhibits pain sense in treating time compared with SBV. This indicates wider and easier application of NSBV for the useful application in clinical treatment. Further comparative studies should be conducted to yield more objective verification.

  20. Bee Queen Breeding Methods - Review

    Directory of Open Access Journals (Sweden)

    Silvia Patruica

    2016-05-01

    Full Text Available The biological potential of a bee family is mainly generated by the biological value of the queen. Whether we grow queens widely or just for our own apiaries, we must consider the acquisition of high-quality biological material, and also the creation of optimal feeding and caring conditions, in order to obtain high genetic value queens. Queen breeding technology starts with the setting of hoeing families, nurse families, drone-breeding families – necessary for the pairing of young queens, and also of the families which will provide the bees used to populate the nuclei where the next queens will hatch. The complex of requirements for the breeding of good, high-production queens is sometimes hard to met, under the application of artificial methods. The selection of breeding method must rely on all these requirements and on the beekeeper’s level of training.

  1. Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations.

    Science.gov (United States)

    Fang, Jiansong; Pang, Xiaocong; Wu, Ping; Yan, Rong; Gao, Li; Li, Chao; Lian, Wenwen; Wang, Qi; Liu, Ai-Lin; Du, Guan-Hua

    2016-05-01

    A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2) ) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw ) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives. PMID:26648584

  2. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    Energy Technology Data Exchange (ETDEWEB)

    Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J., E-mail: fwilliams@qi.fcen.uba.ar [INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química-Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EHA (Argentina)

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  3. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    Science.gov (United States)

    de la Llave, Ezequiel; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J.

    2015-11-01

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  4. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    International Nuclear Information System (INIS)

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge

  5. To Bee or Not to Be : Critical Floral Resources of Wild-Bees

    OpenAIRE

    Larsson, Magnus

    2006-01-01

    In recent decades, the development of strategies to prevent or slow the loss of biodiversity has become an important task for ecologists. In most terrestrial ecosystems wild-bees play a key role as pollinators of herbs, shrubs and trees. The scope of this thesis was to study 1) pollinator effectiveness of specialist bees vs. generalist flower-visitors, 2) critical floral resources for wild-bees, and 3) methods to estimate the size of wild-bee populations. The wild-bee species Andrena hattorfi...

  6. In vitro infection of pupae with Israeli acute paralysis virus suggests disturbance of transcriptional homeostasis in honey bees (Apis mellifera.

    Directory of Open Access Journals (Sweden)

    Humberto F Boncristiani

    Full Text Available The ongoing decline of honey bee health worldwide is a serious economic and ecological concern. One major contributor to the decline are pathogens, including several honey bee viruses. However, information is limited on the biology of bee viruses and molecular interactions with their hosts. An experimental protocol to test these systems was developed, using injections of Israeli Acute Paralysis Virus (IAPV into honey bee pupae reared ex-situ under laboratory conditions. The infected pupae developed pronounced but variable patterns of disease. Symptoms varied from complete cessation of development with no visual evidence of disease to rapid darkening of a part or the entire body. Considerable differences in IAPV titer dynamics were observed, suggesting significant variation in resistance to IAPV among and possibly within honey bee colonies. Thus, selective breeding for virus resistance should be possible. Gene expression analyses of three separate experiments suggest IAPV disruption of transcriptional homeostasis of several fundamental cellular functions, including an up-regulation of the ribosomal biogenesis pathway. These results provide first insights into the mechanisms of IAPV pathogenicity. They mirror a transcriptional survey of honey bees afflicted with Colony Collapse Disorder and thus support the hypothesis that viruses play a critical role in declining honey bee health.

  7. Structure of Ionic Liquids and their Mixtures with Molecular Solvents

    Czech Academy of Sciences Publication Activity Database

    Rotrekl, Jan

    Prague : Institute of Chemical Process Fundamentals of the ASCR, v. v. i, 2014 - (Bendová, M.; Wagner, Z.), s. 10-11 ISBN 978-80-86186-61-0. [Bažant Postgraduate Conference 2014. Prague (CZ), 19.06.2014] R&D Projects: GA MŠk LD14090 Institutional support: RVO:67985858 Keywords : molecular solvent * ionic liquids * thermodynamic characterization Subject RIV: CF - Physical ; Theoretical Chemistry

  8. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    Energy Technology Data Exchange (ETDEWEB)

    Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche

    1997-09-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.

  9. The large-scale structure of molecular clouds

    International Nuclear Information System (INIS)

    This thesis deals with the large-scale properties of molecular clouds. Most extensive studies of these clouds are made in 12CO line at 2.6 mm and this line being optically thick, the analysis is strongly dependent on the much less abundant 13CO. In addition there exists some discord about the abundance of CO with respect to H2. The results of observations of large clouds in the local arm are presented: the clouds near Mon OB 1 and Mon OB 2, the Ophiuchus complex near Sco OB2 and the extended complexes of molecular clouds in Taurus. Observations of local clouds between l = 1000 and l = 1400 near the galactic plane are also discussed, as is the distribution of molecular clouds and other spiral arm tracers in the Perseus arm. The author concludes with a comparison of different models of cloud formation. In his opinion the model of Blitz and Shu agrees best with the observations in this part of the galaxy. However he considers it improbable that every individual cloud was formed in that way. It is more likely that a number of clouds with a range of sizes is formed at the same time and that they gradually move apart, which may be the situation in the Perseus arm around l = 1100. (Auth.)

  10. No intracolonial nepotism during colony fissioning in honey bees

    OpenAIRE

    Rangel, Juliana; Mattila, Heather R.; Seeley, Thomas D.

    2009-01-01

    Most species of social insects have singly mated queens, but in some species each queen mates with numerous males to create a colony whose workers belong to multiple patrilines. This colony genetic structure creates a potential for intracolonial nepotism. One context with great potential for such nepotism arises in species, like honey bees, whose colonies reproduce by fissioning. During fissioning, workers might nepotistically choose between serving a young (sister) queen or the old (mother) ...

  11. Low Cost ZigBee Protocol Based Laboratory Platforms

    OpenAIRE

    Alvaro Romero-Acero; Alejandro Marín-Cano; Eliana I. Arango-Zuluaga

    2013-01-01

    This paper presents a low cost wireless communication platform, based on the ZigBee protocol. It is designed with the purpose to strengthen the use of information technology in the classroom. Guides laboratory practices are focused on developing undergraduate engineering students to the area of telecommunications. The platform structure is composed of: Labs custom designed, web tools embedded wireless communication system for data acquisition in real time, and the Human Machine Interface (HMI...

  12. Molecular dynamics simulations on structural conformations of rhodopsin and prion proteins

    International Nuclear Information System (INIS)

    Molecular dynamics simulations were performed to investigate the structural conformation of the rhodopsin and prion proteins. We have estimated the effect of specific disease-related amino acid mutations on the dynamics and conformational changes

  13. SERS and RAIR for Molecular Structure of Phenylazonaphthalene terminated Self-Assembled Monolayer

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The SAMs of 10-[4-(4-phenylazo)naphth-l-oxyl]-l-decanethiol (Compound 1) on gold were prepared. Their molecular structures were determined by surface enhanced Raman spectroscopy (SERS) and reflection absorption infrared spectroscopy (RAIR).

  14. Adsorption and double layer charging in molecular sieve carbons in relation to molecular dimensions and pore structures

    International Nuclear Information System (INIS)

    The pore structure of a fibrous carbon molecular sieve was studied by adsorption of molecular probes. Mild activation steps enabled the graduated opening of critical pore dimensions in the range 3.1-5.0 A, which keeps adsorption selectivity between molecules differing by 0.2 A in cross section diameter, to be considerably greater than 100/1. High adsorption stereospecificity over a wide pore dimension range enabled the studied adsorbates to be ordered in a sequence of increasing critical molecular dimension. Estimation of molecular dimensions by various experimental methods was discussed and their relevance to nonspherical molecules was evaluated. Polar molecules assume different dimensions depending on whether the carbon surface was polar (oxidized) or not. Hydrogen acquires, surprisingly, large width in accordance with its high liquid molar volume. Adsorbent-adsorbate interactions play a crucial role in determining molecular dimensions. Adsorption of ions from aqueous solutions into the developed ultramicropores of fibrous carbon electrodes was also studied. The dependence of the double layer capacitance and the charging rate on the pore critical dimension and on surface oxidation was studied using linear potential sweep voltametry. (Author)

  15. Bumble bee fauna of Palouse Prairie: survey of native bee pollinators in a fragmented ecosystem.

    Science.gov (United States)

    Hatten, T D; Looney, C; Strange, J P; Bosque-Pérez, N A

    2013-01-01

    Bumble bees, Bombus Latreille (Hymenoptera: Apidae:), are dominant pollinators in the northern hemisphere, providing important pollination services for commercial crops and innumerable wild plants. Nationwide declines in several bumble bee species and habitat losses in multiple ecosystems have raised concerns about conservation of this important group. In many regions, such as the Palouse Prairie, relatively little is known about bumble bee communities, despite their critical ecosystem functions. Pitfall trap surveys for ground beetles in Palouse prairie remnants conducted in 2002-2003 contained considerable by-catch of bumble bees. The effects of landscape context, remnant features, year, and season on bumble bee community composition were examined. Additionally, bees captured in 2002-2003 were compared with historic records for the region to assess changes in the presence of individual species. Ten species of bumble bee were captured, representing the majority of the species historically known from the region. Few detectable differences in bumble bee abundances were found among remnants. Community composition differed appreciably, however, based on season, landscape context, and elevation, resulting in different bee assemblages between western, low-lying remnants and eastern, higherelevation remnants. The results suggest that conservation of the still species-rich bumble bee fauna should take into account variability among prairie remnants, and further work is required to adequately explain bumble bee habitat associations on the Palouse. PMID:23902138

  16. Knowledge-Based Optimization of Molecular Geometries Using Crystal Structures.

    Science.gov (United States)

    Cole, Jason C; Groom, Colin R; Korb, Oliver; McCabe, Patrick; Shields, Gregory P

    2016-04-25

    This paper describes a novel way to use the structural information contained in the Cambridge Structural Database (CSD) to drive geometry optimization of organic molecules. We describe how CSD structural information is transformed into objective functions for gradient-based optimization to provide good quality geometries for a large variety of organic molecules. Performance is assessed by minimizing different sets of organic molecules reporting RMSD movements for bond lengths, valence angles, torsion angles, and heavy atom positions. PMID:26977906

  17. Molecular Structures and Functional Relationships in Clostridial Neurotoxins

    Energy Technology Data Exchange (ETDEWEB)

    Swaminathan S.

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.

  18. Influence of the molecular structure of biofuels on combustion in a compression ignition engine

    OpenAIRE

    Schönborn, A

    2009-01-01

    This thesis presents an experimental study on the influence of the molecular structure of potential biofuels on combustion in a compression ignition engine. The molecular structure of a fuel is amongst the most fundamental parameter controlling its physical and chemical characteristics, and is thus critical to the combustion process within an engine. The approach employed in this work was to study the combustion of several individual molecules in a series of experiments whilst var...

  19. Cyclo (Tyrosyl-Prolyl) Produced by Streptomyces sp.: Bioactivity and Molecular Structure Elucidation

    OpenAIRE

    ROFIQ SUNARYANTO; BAMBANG MARWOTO; LIESBETINI HARTOTO; ZAINAL ALIM MAS'UD; TUN TEDJA IRAWADI

    2011-01-01

    Determination of bioactivity by minimum inhibitory concentration (MIC) methods and molecular structure identification of antibiotic produced by Streptomyces sp. have been carried out. The antibiotic was produced by liquid culture using Streptomyces sp. isolate. Purification of antibiotic was carried out by silica gel column chromatography and preparative HPLC. Molecular structure identification was carried out using ESI-MS, 1H NMR, 13C NMR, and 13C DEPT NMR. Pure antibiotic showed inhibition ...

  20. The transcription factor Krüppel homolog 1 is linked to hormone mediated social organization in bees

    Directory of Open Access Journals (Sweden)

    Fan Yongliang

    2010-04-01

    Full Text Available Abstract Background Regulation of worker behavior by dominant queens or workers is a hallmark of insect societies, but the underlying molecular mechanisms and their evolutionary conservation are not well understood. Honey bee and bumble bee colonies consist of a single reproductive queen and facultatively sterile workers. The queens' influences on the workers are mediated largely via inhibition of juvenile hormone titers, which affect division of labor in honey bees and worker reproduction in bumble bees. Studies in honey bees identified a transcription factor, Krüppel-homolog 1 (Kr-h1, whose expression in worker brains is significantly downregulated in the presence of a queen or queen pheromone and higher in forager bees, making this gene an ideal candidate for examining the evolutionary conservation of socially regulated pathways in Hymenoptera. Results In contrast to honey bees, bumble bees foragers do not have higher Kr-h1 levels relative to nurses: in one of three colonies levels were similar in nurses and foragers, and in two colonies levels were higher in nurses. Similarly to honey bees, brain Kr-h1 levels were significantly downregulated in the presence versus absence of a queen. Furthermore, in small queenless groups, Kr-h1 levels were downregulated in subordinate workers with undeveloped ovaries relative to dominant individuals with active ovaries. Brain Kr-h1 levels were upregulated by juvenile hormone treatment relative to a vehicle control. Finally, phylogenetic analysis indicates that KR-H1 orthologs are presence across insect orders. Though this protein is highly conserved between honey bees and bumble bees, there are significant differences between orthologs of insects from different orders. Conclusions Our results suggest that Kr-h1 is associated with juvenile hormone mediated regulation of reproduction in bumble bees. The expression of this transcription factor is inhibited by the queen and associated with endocrine mediated

  1. Molecular weight and antioxidant effects on the structure of irradiated linear low density polyethylene

    International Nuclear Information System (INIS)

    Linear copolymers of ethylene and butene-1 with uniform chemical microstructure and very narrow molecular weight distribution are used to study the effects of ionizing radiation. The well characterized copolymers are irradiated at room temperature with γ-rays from a 60Co source. To follow the evolution of the molecular structure with the radiation doses, changes in molecular weight averages Mn and Mw are measured by membrane osmometry, light scattering and GPC. The influence of the original linear polymer molecular weight is examined in the range of 50,000-100,000. The effects of antioxidant are explored irradiating samples with and without additive. (author)

  2. Representation of molecular structure using quantum topology with inductive logic programming in structure-activity relationships.

    Science.gov (United States)

    Buttingsrud, Bård; Ryeng, Einar; King, Ross D; Alsberg, Bjørn K

    2006-06-01

    The requirement of aligning each individual molecule in a data set severely limits the type of molecules which can be analysed with traditional structure activity relationship (SAR) methods. A method which solves this problem by using relations between objects is inductive logic programming (ILP). Another advantage of this methodology is its ability to include background knowledge as 1st-order logic. However, previous molecular ILP representations have not been effective in describing the electronic structure of molecules. We present a more unified and comprehensive representation based on Richard Bader's quantum topological atoms in molecules (AIM) theory where critical points in the electron density are connected through a network. AIM theory provides a wealth of chemical information about individual atoms and their bond connections enabling a more flexible and chemically relevant representation. To obtain even more relevant rules with higher coverage, we apply manual postprocessing and interpretation of ILP rules. We have tested the usefulness of the new representation in SAR modelling on classifying compounds of low/high mutagenicity and on a set of factor Xa inhibitors of high and low affinity. PMID:17054018

  3. External and internal detection of Nosema ceranae on honey bees using real-time PCR

    Science.gov (United States)

    There are numerous methods for molecular-based detection of the microsporidian parasite of honey bees, Nosema ceranae. Here we test for both external and internal parasite loads using a quantitative assay to determine the optimum tissue for pathogen detection and the likely sources of variability am...

  4. Structural basis for molecular recognition at serotonin receptors.

    Science.gov (United States)

    Wang, Chong; Jiang, Yi; Ma, Jinming; Wu, Huixian; Wacker, Daniel; Katritch, Vsevolod; Han, Gye Won; Liu, Wei; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D; Gao, Xiang; Zhou, X Edward; Melcher, Karsten; Zhang, Chenghai; Bai, Fang; Yang, Huaiyu; Yang, Linlin; Jiang, Hualiang; Roth, Bryan L; Cherezov, Vadim; Stevens, Raymond C; Xu, H Eric

    2013-05-01

    Serotonin or 5-hydroxytryptamine (5-HT) regulates a wide spectrum of human physiology through the 5-HT receptor family. We report the crystal structures of the human 5-HT1B G protein-coupled receptor bound to the agonist antimigraine medications ergotamine and dihydroergotamine. The structures reveal similar binding modes for these ligands, which occupy the orthosteric pocket and an extended binding pocket close to the extracellular loops. The orthosteric pocket is formed by residues conserved in the 5-HT receptor family, clarifying the family-wide agonist activity of 5-HT. Compared with the structure of the 5-HT2B receptor, the 5-HT1B receptor displays a 3 angstrom outward shift at the extracellular end of helix V, resulting in a more open extended pocket that explains subtype selectivity. Together with docking and mutagenesis studies, these structures provide a comprehensive structural basis for understanding receptor-ligand interactions and designing subtype-selective serotonergic drugs. PMID:23519210

  5. Evolution of molecular structure in alkoxide-derived lithium niobate

    International Nuclear Information System (INIS)

    This paper reports on structural rearrangements during the sol-gel processing of lithium niobate investigated by FTIR and Raman spectroscopic methods. The reaction of lithium ethoxide with niobium ethoxide resulted in the formation of a bimetallic alkoxide, LiNb(OEt)6, which could be crystallized from solution. Single crystals were comprised of helical polymeric units consisting of niobium octahedra linked by lithium in cetrahedral (distorted) coordination. Successive crystallizations from solution allowed for the enhanced purification of the alkoxide precursor. Hydrolysis of the bimetallic alkoxide resulted in the formation of an amorphous network structure, which contained niobium-oxygen octahedral units modified by lithium. Heat-treatment facilitated structural rearrangements for the niobium environment, which allowed for the formation of the lithium niobate crystal structure. Further heat-treatment above 700 degrees C resulted in structural changes associated with lithium oxide volatility

  6. No apparent correlation between honey bee forager gut microbiota and honey production.

    Science.gov (United States)

    Horton, Melissa A; Oliver, Randy; Newton, Irene L

    2015-01-01

    One of the best indicators of colony health for the European honey bee (Apis mellifera) is its performance in the production of honey. Recent research into the microbial communities naturally populating the bee gut raise the question as to whether there is a correlation between microbial community structure and colony productivity. In this work, we used 16S rRNA amplicon sequencing to explore the microbial composition associated with forager bees from honey bee colonies producing large amounts of surplus honey (productive) and compared them to colonies producing less (unproductive). As supported by previous work, the honey bee microbiome was found to be dominated by three major phyla: the Proteobacteria, Bacilli and Actinobacteria, within which we found a total of 23 different bacterial genera, including known "core" honey bee microbiome members. Using discriminant function analysis and correlation-based network analysis, we identified highly abundant members (such as Frischella and Gilliamella) as important in shaping the bacterial community; libraries from colonies with high quantities of these Orbaceae members were also likely to contain fewer Bifidobacteria and Lactobacillus species (such as Firm-4). However, co-culture assays, using isolates from these major clades, were unable to confirm any antagonistic interaction between Gilliamella and honey bee gut bacteria. Our results suggest that honey bee colony productivity is associated with increased bacterial diversity, although this mechanism behind this correlation has yet to be determined. Our results also suggest researchers should not base inferences of bacterial interactions solely on correlations found using sequencing. Instead, we suggest that depth of sequencing and library size can dramatically influence statistically significant results from sequence analysis of amplicons and should be cautiously interpreted. PMID:26623177

  7. Object Recognition in Flight: How Do Bees Distinguish between 3D Shapes?

    Science.gov (United States)

    Werner, Annette; Stürzl, Wolfgang; Zanker, Johannes

    2016-01-01

    Honeybees (Apis mellifera) discriminate multiple object features such as colour, pattern and 2D shape, but it remains unknown whether and how bees recover three-dimensional shape. Here we show that bees can recognize objects by their three-dimensional form, whereby they employ an active strategy to uncover the depth profiles. We trained individual, free flying honeybees to collect sugar water from small three-dimensional objects made of styrofoam (sphere, cylinder, cuboids) or folded paper (convex, concave, planar) and found that bees can easily discriminate between these stimuli. We also tested possible strategies employed by the bees to uncover the depth profiles. For the card stimuli, we excluded overall shape and pictorial features (shading, texture gradients) as cues for discrimination. Lacking sufficient stereo vision, bees are known to use speed gradients in optic flow to detect edges; could the bees apply this strategy also to recover the fine details of a surface depth profile? Analysing the bees' flight tracks in front of the stimuli revealed specific combinations of flight maneuvers (lateral translations in combination with yaw rotations), which are particularly suitable to extract depth cues from motion parallax. We modelled the generated optic flow and found characteristic patterns of angular displacement corresponding to the depth profiles of our stimuli: optic flow patterns from pure translations successfully recovered depth relations from the magnitude of angular displacements, additional rotation provided robust depth information based on the direction of the displacements; thus, the bees flight maneuvers may reflect an optimized visuo-motor strategy to extract depth structure from motion signals. The robustness and simplicity of this strategy offers an efficient solution for 3D-object-recognition without stereo vision, and could be employed by other flying insects, or mobile robots. PMID:26886006

  8. Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

    International Nuclear Information System (INIS)

    Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided

  9. Molecular-Field Calculation of the Magnetic Structure in Erbium

    DEFF Research Database (Denmark)

    Jensen, J.

    1976-01-01

    A molecular-field calculation of the magnetic configurations in Er is found to reproduce the neutron diffraction results of the three different magnetic phases and to give a reasonable fit to the magnetization data at 4.2K. The two-ion coupling is considered to be described by the inter......-planar coupling parameters deduced from the dispersion of the spin waves in the low temperature conical phases. The four (effective) crystal-field parameters are determined by the fit to the experimental data. Projecting the magnetic moments present in the intermediate phase of Er (18-52.4K) to a common origin...

  10. The structural biology of molecular recognition by vancomycin.

    Science.gov (United States)

    Loll, P J; Axelsen, P H

    2000-01-01

    Vancomycin is the archetype among naturally occurring compounds known as glycopeptide antibiotics. Because it is a vital therapeutic agent used world-wide for the treatment of infections with gram-positive bacteria, emerging bacterial resistance to vancomycin is a major public health threat. Recent investigations into the mechanisms of action of glycopeptide antibiotics are driven by a need to understand their detailed mechanism of action so that new agents can be developed to overcome resistance. These investigations have revealed that glycopeptide antibiotics exhibit a rich array of complex cooperative phenomena when they bind target ligands, making them valuable model systems for the study of molecular recognition. PMID:10940250

  11. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement.

    Science.gov (United States)

    García-Iriepa, Cristina; Gueye, Moussa; Léonard, Jérémie; Martínez-López, David; Campos, Pedro J; Frutos, Luis Manuel; Sampedro, Diego; Marazzi, Marco

    2016-03-01

    In spite of considerable interest in the design of molecular switches towards photo-controllable (bio)materials, few studies focused on the major influence of the surrounding environment on the switch photoreactivities. We present a combined experimental and computational study of a retinal-like molecular switch linked to a peptide, elucidating the effects on the photoreactivity and on the α-helix secondary structure. Temperature-dependent, femtosecond UV-vis transient absorption spectroscopy and high-level hybrid quantum mechanics/molecular mechanics methods were applied to describe the photoisomerization process and the subsequent peptide rearrangement. It was found that the conformational heterogeneity of the ground state peptide controls the excited state potential energy surface and the thermally activated population decay. Still, a reversible α-helix to α-hairpin conformational change is predicted, paving the way for a fine photocontrol of different secondary structure elements, hence (bio)molecular functions, using retinal-inspired molecular switches. PMID:26876376

  12. Bees prefer foods containing neonicotinoid pesticides

    Science.gov (United States)

    Kessler, Sébastien C.; Tiedeken, Erin Jo; Simcock, Kerry L.; Derveau, Sophie; Mitchell, Jessica; Softley, Samantha; Stout, Jane C.; Wright, Geraldine A.

    2015-05-01

    The impact of neonicotinoid insecticides on insect pollinators is highly controversial. Sublethal concentrations alter the behaviour of social bees and reduce survival of entire colonies. However, critics argue that the reported negative effects only arise from neonicotinoid concentrations that are greater than those found in the nectar and pollen of pesticide-treated plants. Furthermore, it has been suggested that bees could choose to forage on other available flowers and hence avoid or dilute exposure. Here, using a two-choice feeding assay, we show that the honeybee, Apis mellifera, and the buff-tailed bumblebee, Bombus terrestris, do not avoid nectar-relevant concentrations of three of the most commonly used neonicotinoids, imidacloprid (IMD), thiamethoxam (TMX), and clothianidin (CLO), in food. Moreover, bees of both species prefer to eat more of sucrose solutions laced with IMD or TMX than sucrose alone. Stimulation with IMD, TMX and CLO neither elicited spiking responses from gustatory neurons in the bees' mouthparts, nor inhibited the responses of sucrose-sensitive neurons. Our data indicate that bees cannot taste neonicotinoids and are not repelled by them. Instead, bees preferred solutions containing IMD or TMX, even though the consumption of these pesticides caused them to eat less food overall. This work shows that bees cannot control their exposure to neonicotinoids in food and implies that treating flowering crops with IMD and TMX presents a sizeable hazard to foraging bees.

  13. Biological effects of ultraviolet irradiation on bees

    International Nuclear Information System (INIS)

    The influence of natural solar and artificial ultraviolet irradiation on developing bees was studied. Lethal exposures to irradiation at different stages of development were determined. The influence of irradiation on the variability of the morphometric features of bees was revealed. 5 refs., 1 fig

  14. Salt preferences of honey bee water foragers.

    Science.gov (United States)

    Lau, Pierre W; Nieh, James C

    2016-03-15

    The importance of dietary salt may explain why bees are often observed collecting brackish water, a habit that may expose them to harmful xenobiotics. However, the individual salt preferences of water-collecting bees were not known. We measured the proboscis extension reflex (PER) response of Apis mellifera water foragers to 0-10% w/w solutions of Na, Mg and K, ions that provide essential nutrients. We also tested phosphate, which can deter foraging. Bees exhibited significant preferences, with the most PER responses for 1.5-3% Na and 1.5% Mg. However, K and phosphate were largely aversive and elicited PER responses only for the lowest concentrations, suggesting a way to deter bees from visiting contaminated water. We then analyzed the salt content of water sources that bees collected in urban and semi-urban environments. Bees collected water with a wide range of salt concentrations, but most collected water sources had relatively low salt concentrations, with the exception of seawater and swimming pools, which had >0.6% Na. The high levels of PER responsiveness elicited by 1.5-3% Na may explain why bees are willing to collect such salty water. Interestingly, bees exhibited high individual variation in salt preferences: individual identity accounted for 32% of variation in PER responses. Salt specialization may therefore occur in water foragers. PMID:26823100

  15. The Plight of the Honey Bee

    Science.gov (United States)

    Hockridge, Emma

    2010-01-01

    The decline of colonies of honey bees across the world is threatening local plant biodiversity and human food supplies. Neonicotinoid pesticides have been implicated as a major cause of the problem and are banned or suspended in several countries. Other factors could also be lowering the resistance of bees to opportunist infections by, for…

  16. Crystal and molecular structure of Np(4) sulfate

    International Nuclear Information System (INIS)

    Monocrystals are prepared and crystal structure of Np(SO4)2·4H2O is detected: a=14.597(4), b=11.036(2), c=5.663(2) A, space group - Pnma. The structure is layered, electroneutral layers of [Np(SO4)2(H2O)4]n are perpendicular to [100] direction, hydrogen bonds combine layers into three-dimensional packing. Coordination Np(4) polyhedron is quadratic prism and is formed by oxygen atoms of bidentate-bridge sulfate ions and four water molecules. Np-O bond lengths and bond angles are determined. Peculiarities of structure of double neptunium sulfates with K, Na, Cs in dependence on ligand number and effect of outer spheric cations and water molecules on structure of coordination spheres of Np atoms are considered

  17. Structural Basis for Molecular Recognition at Serotonin Receptors

    OpenAIRE

    Wang, Chong; Jiang, Yi; Ma, Jinming; Wu, Huixian; Wacker, Daniel; Katritch, Vsevolod; Han, Gye Won; Liu, Wei; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D.; Gao, Xiang; Zhou, Edward X.; Melcher, Karsten; Zhang, Chenghai

    2013-01-01

    Serotonin or 5-hydroxytryptamine (5-HT) regulates a wide spectrum of human physiology through the 5-HT receptor family. We report the crystal structures of the human 5-HT1B G protein-coupled receptor bound to the agonist anti-migraine medications ergotamine and dihydroergotamine. The structures reveal similar binding modes for these ligands, which occupy the orthosteric pocket and an extended binding pocket close to the extracellular loops. The orthosteric pocket is formed by residues conserv...

  18. Allee effects and colony collapse disorder in honey bees

    Science.gov (United States)

    We propose a mathematical model to quantify the hypothesis that a major ultimate cause of Colony Collapse Disorder (CCD) in honey bees is the presence of an Allee effect in the growth dynamics of honey bee colonies. In the model, both recruitment of adult bees as well as mortality of adult bees have...

  19. Assessing grooming behavior of Russian honey bees toward Varroa destructor.

    Science.gov (United States)

    The grooming behavior of Russian bees was compared to Italian bees. Overall, Russian bees had significantly lower numbers of mites than the Italian bees with a mean of 1,937 ± 366 and 5,088 ± 733 mites, respectively. This low mite population in the Russian colonies was probably due to the increased ...

  20. Optimizing ZigBee Security using Stochastic Model Checking

    DEFF Research Database (Denmark)

    Yuksel, Ender; Nielson, Hanne Riis; Nielson, Flemming;

    ZigBee is a fairly new but promising wireless sensor network standard that offers the advantages of simple and low resource communication. Nevertheless, security is of great concern to ZigBee, and enhancements are prescribed in the latest ZigBee specication: ZigBee-2007. In this technical report...

  1. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    International Nuclear Information System (INIS)

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

  2. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    Energy Technology Data Exchange (ETDEWEB)

    Marcia, Marco, E-mail: marco.marcia@yale.edu; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas [Yale University, New Haven, CT 06511 (United States); Rajashankar, Kanagalaghatta [Argonne National Laboratory, Argonne, IL 60439 (United States); Pyle, Anna Marie, E-mail: marco.marcia@yale.edu [Yale University, New Haven, CT 06511 (United States); Yale University, New Haven, CT 06511 (United States); Howard Hughes Medical Institute, Chevy Chase, MD 20815 (United States)

    2013-11-01

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

  3. THE CHARACTERISTICS OF BIOACTIVE PEPTIDES AND ANTIBACTERIAL ACTIVITY OF HONEY BEE (Apis nigrocincta SMITH VENOM, ENDEMIC TO SULAWESI

    Directory of Open Access Journals (Sweden)

    Mokosuli Yermia Semuel

    2015-11-01

    Full Text Available Apis nigrocincta Smith is a species of honey bee cavity nesting, endemic to Sulawesi. Research that aims to find the composition of the bioactive content of peptides and antibacterial activity of honey bee venom A. nigrocincta Smith has been conducted. Honey bee venom composition was analyzed using Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE Method and Spectrophotometer UV-Vis Method. Analysis of antibacterial activity, was conducted using a modified agar diffusion method. The results showed that the venom of the honey bee Apis nigrocincta Smith has five bands of molecules with a molecular weight i.e. 33.54kDa; 21 kDa and 15.43 kDa. The peptide detected were hyaluronidase, fosfolipase A, mellitin, lysofosfolipase or antigen 5. Antibacterial activity was higher than the control ampisilin and antibiotic streptomycin.

  4. Involvement of secondary metabolites in the pathogenesis of the American foulbrood of honey bees caused by Paenibacillus larvae.

    Science.gov (United States)

    Müller, Sebastian; Garcia-Gonzalez, Eva; Genersch, Elke; Süssmuth, Roderich D

    2015-06-01

    The Gram-positive, spore-forming bacterium Paenibacillus larvae (P. larvae) is the causative agent of the epizootic American Foulbrood (AFB), a fatal brood disease of the western honey bee (Apis mellifera). AFB is one of the most destructive honey bee diseases since it is not only lethal for infected larvae but also for the diseased colonies. Due to the high impact of honey bees on ecology and economy this epizootic is a severe and pressing problem. Knowledge about virulence mechanisms and the underlying molecular mechanisms remain largely elusive. Recent genome sequencing of P. larvae revealed its potential to produce unknown secondary metabolites, like nonribosomal peptides and peptide-polyketide hybrids. This article highlights recent findings on secondary metabolites synthesized by P. larvae and discusses their role in virulence and pathogenicity towards the bee larvae. PMID:25904391

  5. Pharmacological evaluation of bee venom and melittin

    Directory of Open Access Journals (Sweden)

    Camila G. Dantas

    2014-01-01

    Full Text Available The objective of this study was to identify the pharmacological effects of bee venom and its major component, melittin, on the nervous system of mice. For the pharmacological analysis, mice were treated once with saline, 0.1 or 1.2 mg/kg of bee venom and 0.1 mg/kg of melittin, subcutaneously, 30 min before being submitted to behavioral tests: locomotor activity and grooming (open-field, catalepsy, anxiety (elevated plus-maze, depression (forced swimming test and apomorphine-induced stereotypy. Haloperidol, imipramine and diazepam were administered alone (positive control or as a pre-treatment (haloperidol.The bee venom reduced motor activity and promoted cataleptic effect, in a similar manner to haloperidol.These effects were decreased by the pretreatment with haloperidol. Both melittin and bee venom decreased the apomorphine-induced stereotypies. The data indicated the antipsychotic activity of bee venom and melittin in a murine model.

  6. An Experimental Study on Production of Egg Yolk Antibody(IgY) against Bee Venom

    OpenAIRE

    Hwang, Tae-Jun; Lee, Seung-bae; Gwon, Gi-Rok

    2001-01-01

    This study was carried out for production of neutral antibody to bee venom(anti-phospholipase A2 IgY). Hen layings were injected repeatedly with bee venom and phospholipase A2 with Freund's adjuvant. Specific antibody in egg yolk from immunized hen laying was separated, and purified, also immunological characteristics of anti-phospholipase A2 IgY was invested. The results were summarized as follows : 1. Phospholipase A2 was showed single band at molecular weight 17,000 in SDS-PAGE and b...

  7. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    OpenAIRE

    Sha, Wei

    2008-01-01

    In this seminar, I will talk about the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscopy (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics simulations were then carried out to investigate the ...

  8. Larval starvation improves metabolic response to adult starvation in honey bees (Apis mellifera L.).

    Science.gov (United States)

    Wang, Ying; Campbell, Jacob B; Kaftanoglu, Osman; Page, Robert E; Amdam, Gro V; Harrison, Jon F

    2016-04-01

    Environmental changes during development have long-term effects on adult phenotypes in diverse organisms. Some of the effects play important roles in helping organisms adapt to different environments, such as insect polymorphism. Others, especially those resulting from an adverse developmental environment, have a negative effect on adult health and fitness. However, recent studies have shown that those phenotypes influenced by early environmental adversity have adaptive value under certain (anticipatory) conditions that are similar to the developmental environment, though evidence is mostly from morphological and behavioral observations and it is still rare at physiological and molecular levels. In the companion study, we applied a short-term starvation treatment to fifth instar honey bee larvae and measured changes in adult morphology, starvation resistance, hormonal and metabolic physiology and gene expression. Our results suggest that honey bees can adaptively respond to the predicted nutritional stress. In the present study, we further hypothesized that developmental starvation specifically improves the metabolic response of adult bees to starvation instead of globally affecting metabolism under well-fed conditions. Here, we produced adult honey bees that had experienced a short-term larval starvation, then we starved them for 12 h and monitored metabolic rate, blood sugar concentrations and metabolic reserves. We found that the bees that experienced larval starvation were able to shift to other fuels faster and better maintain stable blood sugar levels during starvation. However, developmental nutritional stress did not change metabolic rates or blood sugar levels in adult bees under normal conditions. Overall, our study provides further evidence that early larval starvation specifically improves the metabolic responses to adult starvation in honey bees. PMID:27030776

  9. Combinatorial Evolution and Forecasting of Communication Protocol ZigBee

    CERN Document Server

    Levin, Mark Sh; Kistler, Rolf; Klapproth, Alexander

    2012-01-01

    The article addresses combinatorial evolution and forecasting of communication protocol for wireless sensor networks (ZigBee). Morphological tree structure (a version of and-or tree) is used as a hierarchical model for the protocol. Three generations of ZigBee protocol are examined. A set of protocol change operations is generated and described. The change operations are used as items for forecasting based on combinatorial problems (e.g., clustering, knapsack problem, multiple choice knapsack problem). Two kinds of preliminary forecasts for the examined communication protocol are considered: (i) direct expert (expert judgment) based forecast, (ii) computation of the forecast(s) (usage of multicriteria decision making and combinatorial optimization problems). Finally, aggregation of the obtained preliminary forecasts is considered (two aggregation strategies are used).

  10. Introductory group theory and its application to molecular structure

    CERN Document Server

    Ferraro, John R

    1969-01-01

    This volume is a consequence of a series of seminars presented by the authors at the Infrared Spectroscopy Institute, Canisius College, Buffalo, New York, over the last nine years. Many participants on an intermediate level lacked a sufficient background in mathematics and quantum mechan­ ics, and it became evident that a non mathematical or nearly nonmathe­ matical approach would be necessary. The lectures were designed to fill this need and proved very successful. As a result of the interest that was developed in this approach, it was decided to write this book. The text is intended for scientists and students with only limited theore­ tical background in spectroscopy, but who are sincerely interested in the interpretation of molecular spectra. The book develops the detailed selection rules for fundamentals, combinations, and overtones for molecules in several point groups. Detailed procedures used in carrying out the normal coordinate treatment for several molecules are also presented. Numerous examples...

  11. The Molecular Structure of the Liquid Ordered Phase

    Science.gov (United States)

    Lyman, Edward

    2014-03-01

    Molecular dynamics simulations reveal substructures within the liquid-ordered phase of lipid bilayers. These substructures, identified in a 10 μsec all-atom trajectory of liquid-ordered/liquid-disordered coexistence (Lo/Ld) , are composed of saturated hydrocarbon chains packed with local hexagonal order, and separated by interstitial regions enriched in cholesterol and unsaturated chains. Lipid hydrocarbon chain order parameters calculated from the Lo phase are in excellent agreement with 2H NMR measurements; the local hexagonal packing is also consistent with 1H-MAS NMR spectra of the Lo phase, NMR diffusion experiments, and small angle X-ray- and neutron scattering. The balance of cholesterol-rich to local hexagonal order is proposed to control the partitioning of membrane components into the Lo regions. The latter have been frequently associated with formation of so-called rafts, platforms in the plasma membranes of cells that facilitate interaction between components of signaling pathways.

  12. The Structural, Functional and Molecular Organization of the Brainstem

    Directory of Open Access Journals (Sweden)

    Rudolf eNieuwenhuys

    2011-06-01

    Full Text Available According to Wilhelm His (1891, 1893 the brainstem consists of two longitudinal zones, the dorsal alar plate (sensory in nature and the ventral basal plate (motor in nature. Johnston and Herrick indicated that both plates can be subdivided into separate somatic and visceral zones, distinguishing somatosensory and viscerosensory zones within the alar plate, and visceromotor and somatomotor zones within the basal plate. To test the validity of this ‘four-functional-zones’ concept, I developed a topological procedure, surveying the spatial relationships of the various cell masses in the brainstem in a single figure. Brainstems of 16 different anamniote species were analyzed, and revealed that the brainstems are clearly divisible into four morphological zones, which correspond largely with the functional zones of Johnston and Herrick. Exceptions include (1 the magnocellular vestibular nucleus situated in the viscerosensory zone; (2 the basal plate containing a number of evidently non-motor centres (superior and inferior olives. Nevertheless the ‘functional zonal model’ has explanatory value. Thus, it is possible to interpret certain brain specializations related to particular behavioural profiles, as ‘local hypertrophies’ of one or two functional columns. Recent developmental molecular studies on brains of birds and mammals confirmed the presence of longitudinal zones, and also showed molecularly defined transverse bands or neuromeres throughout development. The intersecting boundaries of the longitudinal zones and the transverse bands appeared to delimit radially arranged histogenetic domains. Because neuromeres have been observed in embryonic and larval stages of numerous anamniote species, it may be hypothesized that the brainstems of all vertebrates share a basic organizational plan, in which intersecting longitudinal and transverse zones form fundamental histogenetic and genoarchitectonic units.

  13. Bug City: Bees [Videotape].

    Science.gov (United States)

    1998

    "Bug City" is a video series created to help children learn about insects and other small critters. All aspects of bug life are touched upon including body structure, food, habitat, life cycle, mating habits, camouflage, mutualism (symbiosis), adaptations, social behavior, and more. Each program features dramatic microscopic photography, fun…

  14. The effects of Bee Venom and Sweet Bee Venom to the preadipocyte proliferation and lipolysis of adipocyte, localized fat accumulation

    Directory of Open Access Journals (Sweden)

    Min-Ki Kim

    2007-12-01

    Full Text Available Objectives : The purpose of this study was to investigate the effects of Bee Venom and Sweet Bee Venom to the primary cultured preadipocyte, adipocytes, and localized fat tissue. Methods : Decreased preadipocyte proliferation and decreased lipogenesis are mechanisms to reduce obesity. So, preadipocytes and adipocytes were performed on cell cultures using Sprague-Dawley Rats and treated with 0.01-1mg/㎖ Bee Venom and Sweet Bee Venom. And porcine skin including fat tissue after treated Bee Venom and Sweet Bee Venom according to the dosage dependent variation are investigated the histologic changes after injection of these Pharmacopuncture. Result : Following results were obtained from the preadipocyte proliferation and lipolysis of adipocyte and histologic investigation of fat tissue. 1. Bee Venom and Sweet Bee Venom showed the effect of decreased preadipocyte proliferation depend on concentration. 2. Bee Venom and Sweet Bee Venom showed the effect of decreased the activity of glycerol-3-phosphate dehydrogenase(GPDH significantly. 3. Bee Venom was not showed the effect of lipolysis, but Sweet Bee Venom was increased in low dosage and decreased in high dosage. 4. Investigated the histologic changes in porcine fat tissue after treated Bee Venom and Sweet Bee Venom, we knew that these Pharmacopuncture was activated nonspecific lysis of cell membranes depend on concentration. Conclusion : These results suggest that Bee Venom and Sweet Bee Venom efficiently induces decreased proliferation of preadipocyte and lipolysis in adipose tissue

  15. Effect of Molecular Structure on the Performance of Polyacrylic Acid Superplasticizer

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rongguo; GUO Huiling; LEI Jiaheng; ZHANG Anfu; GU Huajun

    2007-01-01

    The effects of structure parameters, such as molecular structure, segment kinds, molecular weight, and organic functional groups, on the performance of polyacrylic acid superplasticizer were discussed. According to the differences of chain sections, functional groups, etc, polyacrylic acid superplasticizer could be divided into A, B, C three parts. Among them, A chain section included sulfonic acid groups, B chain section carboxyl groups, C chain section polyester. Polyacrylic acid superplasticizers with different matching of A, B, C chain sections, different length of C chain section and different molecular weights were synthesized by acrylic acid, polyethylene glycol, sodium methyl allylsulfonate; the relation between the molecular structure and performance was also studied. The expetimental results indicate that the water-reduction ratio increases obviously with the increment of the proportion of sodium methyl allylsulfonate chain section in the molecular; the slump retention increases greatly with the increment of the proportion of acrylic acid chain section; the dispersion of cement particles increases with the increment of the chain length of polyethylene glycol; when the molecular weight is in the range of 5000, the dispersion and slump retentibity increase with the increment of the average molecular weight of polymers.

  16. Biology of Paenibacillus larvae, a deadly pathogen of honey bee larvae.

    Science.gov (United States)

    Ebeling, Julia; Knispel, Henriette; Hertlein, Gillian; Fünfhaus, Anne; Genersch, Elke

    2016-09-01

    The gram-positive bacterium Paenibacillus larvae is the etiological agent of American Foulbrood of honey bees, a notifiable disease in many countries. Hence, P. larvae can be considered as an entomopathogen of considerable relevance in veterinary medicine. P. larvae is a highly specialized pathogen with only one established host, the honey bee larva. No other natural environment supporting germination and proliferation of P. larvae is known. Over the last decade, tremendous progress in the understanding of P. larvae and its interactions with honey bee larvae at a molecular level has been made. In this review, we will present the recent highlights and developments in P. larvae research and discuss the impact of some of the findings in a broader context to demonstrate what we can learn from studying "exotic" pathogens. PMID:27394713

  17. Molecular structure and nonequilibrium polarizations: recent experiments on polar gases

    International Nuclear Information System (INIS)

    Senftleben-Beenakker experiments are reported on the thermal conductivity and visosity of polyatomic gases. Polar molecules of linear and symmetric top structure have been investigated in a magnetic field. NH3-noble gas mixtures and CH3CN mixtures have been studied. The results indicate the concentration dependence of the various non-equilibrium polarizations for these specific systems. (C.F.)

  18. Teaching the Structure of Immunoglobulins by Molecular Visualization and SDS-PAGE Analysis

    Science.gov (United States)

    Rižner, Tea Lanišnik

    2014-01-01

    This laboratory class combines molecular visualization and laboratory experimentation to teach the structure of the immunoglobulins (Ig). In the first part of the class, the three-dimensional structures of the human IgG and IgM molecules available through the RCSB PDB database are visualized using freely available software. In the second part, IgG…

  19. Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry.

    Science.gov (United States)

    Reading, Eamonn; Munoz-Muriedas, Jordi; Roberts, Andrew D; Dear, Gordon J; Robinson, Carol V; Beaumont, Claire

    2016-02-16

    Ion mobility-mass spectrometry (IM-MS) in combination with molecular modeling offers the potential for small molecule structural isomer identification by measurement of their gas phase collision cross sections (CCSs). Successful application of this approach to drug metabolite identification would facilitate resource reduction, including animal usage, and may benefit other areas of pharmaceutical structural characterization including impurity profiling and degradation chemistry. However, the conformational behavior of drug molecules and their metabolites in the gas phase is poorly understood. Here the gas phase conformational space of drug and drug-like molecules has been investigated as well as the influence of protonation and adduct formation on the conformations of drug metabolite structural isomers. The use of CCSs, measured from IM-MS and molecular modeling information, for the structural identification of drug metabolites has also been critically assessed. Detection of structural isomers of drug metabolites using IM-MS is demonstrated and, in addition, a molecular modeling approach has been developed offering rapid conformational searching and energy assessment of candidate structures which agree with experimental CCSs. Here it is illustrated that isomers must possess markedly dissimilar CCS values for structural differentiation, the existence and extent of CCS differences being ionization state and molecule dependent. The results present that IM-MS and molecular modeling can inform on the identity of drug metabolites and highlight the limitations of this approach in differentiating structural isomers. PMID:26752623

  20. Pulsed mass recruitment by a stingless bee, Trigona hyalinata.

    OpenAIRE

    Nieh, James C.; Contrera, Felipe A L; Nogueira-Neto, Paulo

    2003-01-01

    Research on bee communication has focused on the ability of the highly social bees, stingless bees (Hymenoptera, Apidae, Meliponini) and honeybees (Apidae, Apini), to communicate food location to nest-mates. Honeybees can communicate food location through the famous waggle dance. Stingless bees are closely related to honeybees and communicate food location through a variety of different mechanisms, many of which are poorly understood. We show that a stingless bee, Trigona hyalinata, uses a pu...

  1. Management of corneal bee sting

    Directory of Open Access Journals (Sweden)

    Razmjoo H

    2011-12-01

    Full Text Available Hassan Razmjoo1,2, Mohammad-Ali Abtahi1,2,4, Peyman Roomizadeh1,3, Zahra Mohammadi1,2, Seyed-Hossein Abtahi1,3,41Medical School, Isfahan University of Medical Sciences (IUMS; 2Ophthalmology Ward, Feiz Hospital, IUMS; 3Isfahan Medical Students Research Center (IMSRC, IUMS; 4Isfahan Ophthalmology Research Center (IORC, Feiz Hospital, IUMS, Isfahan, IranAbstract: Corneal bee sting is an uncommon environmental eye injury that can result in various ocular complications with an etiology of penetrating, immunologic, and toxic effects of the stinger and its injected venom. In this study we present our experience in the management of a middle-aged male with a right-sided deep corneal bee sting. On arrival, the patient was complaining of severe pain, blurry vision with acuity of 160/200, and tearing, which he had experienced soon after the injury. Firstly, we administered conventional drugs for eye injuries, including topical antibiotic, corticosteroid, and cycloplegic agents. After 2 days, corneal stromal infiltration and edema developed around the site of the sting, and visual acuity decreased to 100/200. These conditions led us to remove the stinger surgically. Within 25 days of follow-up, the corneal infiltration decreased gradually, and visual acuity improved to 180/200. We suggest a two-stage management approach for cases of corneal sting. For the first stage, if the stinger is readily accessible or primary dramatic reactions, including infiltration, especially on the visual axis, exist, manual or surgical removal would be indicated. Otherwise, we recommend conventional treatments for eye injuries. Given this situation, patients should be closely monitored for detection of any worsening. If the condition does not resolve or even deteriorates, for the second stage, surgical removal of the stinger under local or generalized anesthesia is indicated.Keywords: bee sting, stinger, cornea, removal, management, surgery

  2. Molecular conformation and liquid structure of 2-propanol through neutron diffraction

    Indian Academy of Sciences (India)

    A Sahoo; S Sarkar; P S R Krishna; R N Joarder

    2010-05-01

    The neutron diffraction data analysis of deuterated liquid 2-propanol at room temperature to define its molecular conformation is presented. 2-Propanol being a large molecule with twelve atomic sites, the conformation analysis is tricky and an improved method of data analysis is given. The intermolecular structural correlations, i.e., hydrogen-bonded liquid structure, can be modelled accurately to extract the nature of the average hydrogen-bonded molecular association in liquid state at room temperature. Like other alcohols these are mostly hexamer ring chain (HRC) clusters. The cluster analysis of recent X-ray data available in the literature also support the same liquid structure.

  3. Using molecular structure for reliable predicting enthalpy of melting of nitroaromatic energetic compounds

    International Nuclear Information System (INIS)

    In this work, a reliable simple method has been introduced for predicting enthalpy of melting of nitroaromatic energetic compounds through their molecular structures. This method can be used for a wide range of nitroaromatics including halogenated nitroaromatic compounds. The contribution of hydrogen bonding and polar groups as well as structural parameters can be used to improve the predicted values on the basis of the number of carbon, nitrogen and oxygen atoms. The predicted results show that this method gives reliable prediction of standard enthalpy of melting with respect to the best available methods for different nitroaromatic compounds including high explosives with complex molecular structures.

  4. Structure of bee-flower system in the coastal sand dune of Abaeté, northeastern Brazil Estrutura do sistema abelha-flor nas dunas litorâneas de Abaeté, Nordeste do Brasil

    Directory of Open Access Journals (Sweden)

    Blandina F. Viana

    2006-03-01

    Full Text Available For twelve months (from January to December of 1996 we investigated bee-flower interactions in a sea coastal ecosystem in Bahia, Brazil. Samples were taken three times each month. 3983 individuals belonging to 49 bee species, grouped in 13 morph-functional categories, visited 66 plant species belonging to 39 botanic families. It was observed 310 interactions between bees and plants at species level. The use of floral resources by bees was not homogeneous; most of the plant species received a low number of visitors. No restricted plant-bee species relationship in resource use concerning the subset of analyzed interactions was detected. In Abaeté the generalist relationships predominated.As interações entre abelhas e flores foram investigadas três vezes por mês, durante doze meses (entre janeiro a dezembro de 1996 em um ambiente de dunas litorâneas com vegetação de restinga no Nordeste do Brasil. Foram amostrados 3983 indivíduos de abelhas pertencentes a 49 espécies, agrupadas em 13 categorias morfo-funcionais. Essas visitaram 66 espécies de plantas pertencentes a 39 famílias vegetais. Trezentos e dez (310 interações entre abelhas e plantas, em nível de espécie foram observadas. O uso de recursos florais por abelhas não foi homogêneo, a maioria das espécies de plantas recebeu um baixo número de visitantes. Não foi notada nenhuma relação especializada, em nível de espécie, entre plantas e abelhas no subconjunto de interações analisadas. Em Abaeté, houve predominância de relações de generalistas.

  5. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    International Nuclear Information System (INIS)

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  6. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    Energy Technology Data Exchange (ETDEWEB)

    Eisenberg, David S.

    2008-07-15

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  7. NATO Advanced Study Institute on Electronic Structure of Polymers and Molecular Crystals

    CERN Document Server

    Ladik, János

    1975-01-01

    The NATO Advanced Study Institute on "Electronic Structure of Polymers and Molecular Crystals" was held at the Facultes Universi­ taires de Namur (F.U.N.) from September 1st till September 14th, 1974. We wish to express our appreciation to the NATO Scientific Affairs Division whose generous support made this Institute possible and to the Facultes Universitaires de Namur and the Societe Chimique de Belgique which provided fellowships and travel grants to a number of students. This volume contains the main lectures about the basic principles of the field and about different recent developments of the theory of the electronic structure of polymers and molecular crystals. The school started with the presentation of the basic SCF-LCAO theory of the electronic structure of periodic polymers and molecular crystals (contributions by Ladik, Andre & Delhalle) showing how a combination of quantum chemical and solid state physical methods can provide band structures for these systems. The numerical aspects of these ...

  8. A holistic molecular docking approach for predicting protein-protein complex structure

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure selection.This article explains the detailed steps and applications for CAPRI Target 39.The CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

  9. Do Giant Molecular Clouds Care About the Galactic Structure?

    CERN Document Server

    Fujimoto, Yusuke; Wakayama, Mariko; Habe, Asao

    2014-01-01

    We investigate the impact of galactic environment on the properties of simulated giant molecular clouds formed in a M83-type barred spiral galaxy. Our simulation uses a rotating stellar potential to create the grand design features and resolves down to 1.5 pc. From the comparison of clouds found in the bar, spiral and disc regions, we find that the typical GMC is environment independent, with a mass of 5e+5 Msun and radius 11 pc. However, the fraction of clouds in the property distribution tails varies between regions, with larger, more massive clouds with a higher velocity dispersion being found in greatest proportions in the bar, spiral and then disc. The bar clouds also show a bimodality that is not reflected in the spiral and disc clouds except in the surface density, where all three regions show two distinct peaks. We identify these features as being due to the relative proportion of three cloud types, classified via the mass-radius scaling relation, which we label A, B and C. Type A clouds have the typi...

  10. Crystal and molecular structure of perindopril erbumine salt

    Science.gov (United States)

    Remko, M.; Bojarska, J.; Ježko, P.; Sieroń, L.; Olczak, A.; Maniukiewicz, W.

    2011-06-01

    The crystal structure of perindopril (2S,3aS,7aS)-1-[(2S)-2-[[(2S)-1-ethoxy-1-oxopentan-2-yl]amino]propanoyl]-2,3,3a,4,5,6,7,7a-octahydroindole-2-carboxylic acid) erbumine salt C 23H 43N 3O 5, angiotensin-converting enzyme inhibitor, was determined from single-crystal X-ray diffraction data. The compound crystallizes in the triclinic, non-centrosymetric space group P1, with unit cell dimensions a = 6.575(3), b = 12.165(5), c = 16.988(8) Å and α = 97.153(4), β = 94.417(4), γ = 90.349(4)°, Z = 2. The structure was refined by full matrix least squares methods to R = 0.037. In the solid state ionized molecules of perindopril and erbumine are linked together forming a complex via O⋯HN + hydrogen bonds between the positively charged amino groups of the erbuminium cations and oxygen atoms of the perindopril carboxylate groups. Intermolecular N sbnd H⋯O and C sbnd H⋯O contacts seem to be effective in the stabilization of the structure, resulting in the formation of a three-dimensional network. The gas-phase structure of perindopril-erbumine complex was optimized by the HF/6-31G(d) and Becke3LYP/6-31G(d) methods. The conformational behavior of this salt in water was examined using the CPCM and Onsager models. In both the gas phase and water solution the perindopril erbumine will exist in prevailing triclinic form.

  11. Molecular Structure of Humin and Melanoidin via Solid State NMR

    OpenAIRE

    Herzfeld, Judith; Rand, Danielle; Matsuki, Yoh; Daviso, Eugenio; Mak-Jurkauskas, Melody; Mamajanov, Irena

    2011-01-01

    Sugar-derived humins and melanoidins figure significantly in food chemistry, agricultural chemistry, biochemistry and prebiotic chemistry. Despite wide interest and significant experimental attention, the amorphous and insoluble nature of the polymers has made them resistant to conventional structural characterization. Here we make use of solid-state NMR methods, including selective 13C substitution, 1H-dephasing, and double quantum filtration. The spectra, and their interpretation, are simpl...

  12. Structure, phase transitions and molecular motions in 4-aminopyridinium perchlorate

    Science.gov (United States)

    Czupinski, O.; Bator, G.; Ciunik, Z.; Jakubas, R.; Medycki, W.; Swiergiel, J.

    2002-09-01

    The crystal structure of the 4-aminopyridinium perchlorate (4-apyH)ClO4 has been determined at 100 K by means of x-ray diffraction as monoclinic, with space group P 21, with Z = 8. The crystal undergoes two structural phase transitions: one of first-order type, reversible, at 241/243 K (on cooling/heating respectively) and one of weakly first-order type, irreversible, at 277 K (on heating). The crystal dynamics is discussed on the basis of the temperature dependence of the 1 H nuclear magnetic resonance second moment (M2) and spin-lattice relaxation time T1. Both phase transitions are interpreted in terms of the changes in the motional state of (4-apyH)+ cations and ClO4- anions. The dielectric dispersion studies disclose a relaxation process over the high-temperature phase (above 241 K) in the audio-frequency region. The dielectric results are described by a Cole-Cole equation. The title crystal reveals pyroelectric properties below 241 K. The ferroelastic domain structure of (4-apyH)ClO4 is observed over the whole temperature range studied.

  13. Structure, phase transitions and molecular motions in 4-aminopyridinium perchlorate

    International Nuclear Information System (INIS)

    The crystal structure of the 4-aminopyridinium perchlorate (4-apyH)ClO4 has been determined at 100 K by means of x-ray diffraction as monoclinic, with space group P 21, with Z=8. The crystal undergoes two structural phase transitions: one of first-order type, reversible, at 241/243 K (on cooling/heating respectively) and one of weakly first-order type, irreversible, at 277 K (on heating). The crystal dynamics is discussed on the basis of the temperature dependence of the 1H nuclear magnetic resonance second moment (M2) and spin-lattice relaxation time T1. Both phase transitions are interpreted in terms of the changes in the motional state of (4-apyH)+ cations and ClO4- anions. The dielectric dispersion studies disclose a relaxation process over the high-temperature phase (above 241 K) in the audio-frequency region. The dielectric results are described by a Cole-Cole equation. The title crystal reveals pyroelectric properties below 241 K. The ferroelastic domain structure of (4-apyH)ClO4 is observed over the whole temperature range studied. (author)

  14. Structure, phase transitions and molecular motions in 4-aminopyridinium perchlorate

    Energy Technology Data Exchange (ETDEWEB)

    Czupinski, O.; Bator, G.; Ciunik, Z.; Jakubas, R. [Faculty of Chemistry, University of Wroclaw, Wroclaw (Poland); Medycki, W.; Swiergiel, J. [Institute of Molecular Physics, PAS, Poznan (Poland)

    2002-09-16

    The crystal structure of the 4-aminopyridinium perchlorate (4-apyH)ClO{sub 4} has been determined at 100 K by means of x-ray diffraction as monoclinic, with space group P 2{sub 1}, with Z=8. The crystal undergoes two structural phase transitions: one of first-order type, reversible, at 241/243 K (on cooling/heating respectively) and one of weakly first-order type, irreversible, at 277 K (on heating). The crystal dynamics is discussed on the basis of the temperature dependence of the {sup 1}H nuclear magnetic resonance second moment (M{sub 2}) and spin-lattice relaxation time T{sub 1}. Both phase transitions are interpreted in terms of the changes in the motional state of (4-apyH){sup +} cations and ClO{sub 4}- anions. The dielectric dispersion studies disclose a relaxation process over the high-temperature phase (above 241 K) in the audio-frequency region. The dielectric results are described by a Cole-Cole equation. The title crystal reveals pyroelectric properties below 241 K. The ferroelastic domain structure of (4-apyH)ClO{sub 4} is observed over the whole temperature range studied. (author)

  15. First principles investigations of electronic structure and transport properties of graphitic structures and single molecular junctions

    Science.gov (United States)

    Owens, Jonathan R.

    properties of the IV curves of single molecule nano-junctions. Specifically, these systems consist of a zinc-porphyrin molecule coupled between two gold electrodes, i.e., a nano-gap. The first observation we want to explain is the asymmetric nature of the experimental IV curve for this porphyrin system, where the IV curve is skewed heavily to the negative bias region. Using a plane-wave DFT calculation, we present the density of states of the porphyrin molecule (both in the presence and absence of the electrodes) and indeed see highly delocalized states (as confirmed by site-projection of the DOS) only in the negative bias region, meaning that the channels with high transmission probability reside there, in agreement with experimental observation. The next problem studied pertains to observed switching in an experimentally-measured IV curve, this time of a longer zinc porphyrin molecule, still within a gold nano-gap. The switching behavior is observed only at 300K, not at 4.2K. The temperature-dependance of this problem renders our previous toolset of DFT calculations void; DFT is a ground-state theory. Instead, we employ a density functional-based tight-binding (DFTB) approach in a molecular dynamics simulation. Basically, the structural configuration evaluated at each time step is based on a tight-binding electronic structure calculation, instead of a typical MD force field. Trajectories are presented at varying temperatures and electric field strengths. Indeed, we observe a conformation of the porphyrin molecule between two configurations of the dihedral angle of the central nitrogen ring, ±15. {o} at 300K, but not 4.2K. These confirmations are equally likely, i.e., the structure assumes these configurations an equal number of teams, meaning the average structure has an angle of 0. {o}. After computing the DOS of all three aforementioned configurations (0. {text{o}} and ±15. {text{o}}), we indeed see a difference between the DOS curves at ±15. {text{o}} (which are

  16. A Quantitative Structure Property Relationship for Prediction of Flash Point of Alkanes Using Molecular Connectivity Indices

    Institute of Scientific and Technical Information of China (English)

    Morteza Atabati; Reza Emamalizadeh

    2013-01-01

    Many structure-property/activity studies use graph theoretical indices,which are based on the topological properties of a molecule viewed as a graph.Since topological indices can be derived directly from the molecular structure without any experimental effort,they provide a simple and straightforward method for property prediction.In this work the flash point of alkanes was modeled by a set of molecular connectivity indices (x),modified molecular connectivity indices (mx(1)h) and valance molecular connectivity indices (mxv),with mxv calculated using the hydrogen perturbation.A stepwise Multiple Linear Regression (MLR) method was used to select the best indices.The predicted flash points are in good agreement with the experimental data,with the average absolute deviation 4.3 K.

  17. Advances in Rosetta structure prediction for difficult molecular-replacement problems

    International Nuclear Information System (INIS)

    Modeling advances using Rosetta structure prediction to aid in solving difficult molecular-replacement problems are discussed. Recent work has shown the effectiveness of structure-prediction methods in solving difficult molecular-replacement problems. The Rosetta protein structure modeling suite can aid in the solution of difficult molecular-replacement problems using templates from 15 to 25% sequence identity; Rosetta refinement guided by noisy density has consistently led to solved structures where other methods fail. In this paper, an overview of the use of Rosetta for these difficult molecular-replacement problems is provided and new modeling developments that further improve model quality are described. Several variations to the method are introduced that significantly reduce the time needed to generate a model and the sampling required to improve the starting template. The improvements are benchmarked on a set of nine difficult cases and it is shown that this improved method obtains consistently better models in less running time. Finally, strategies for best using Rosetta to solve difficult molecular-replacement problems are presented and future directions for the role of structure-prediction methods in crystallography are discussed

  18. FlaME: Flash Molecular Editor - a 2D structure input tool for the web

    Directory of Open Access Journals (Sweden)

    Dallakian Pavel

    2011-02-01

    Full Text Available Abstract Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME. In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol( and setMol(. In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application and the HTML elements on a web page, using JavaScript functions.

  19. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    Directory of Open Access Journals (Sweden)

    Peiqiang Yu

    2007-01-01

    Full Text Available The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1 using the newly advanced synchrotron technology (S-FTIR as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2 revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3 prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4 obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  20. Molecular modeling of the ion channel-like nanotube structure of amyloid β-peptide

    Institute of Scientific and Technical Information of China (English)

    JIAO Yong; YANG Pin

    2007-01-01

    The ion channel-like nanotube structure of the oligomers of amyloid β-peptide (Aβ) was first investigated by molecular modeling. The results reveal that the hydrogen bond net is one of the key factors to stabilize the structure. The hydrophobicity distribution mode of the side chains is in favor of the structure inserting into the bilayers and forming a hydrophilic pore. The lumen space is under the control of the negative potential, weaker but spreading continuously, to which the cation selectivity attributes; meanwhile, the alternate distribution of the stronger positive and negative potentials makes the electrostatic distribution of the structure framework balance, which is also one of the key factors stabilizing the structure. The results lay the theoretical foundation for illuminating the structure stability and the ion permeability, and give a clue to elucidating the molecular mechanism of Alzheimer's disease (AD) and designing novel drugs to prevent or reverse AD at the root.

  1. Prolonged postdiapause: influence on some indicators of carbohydrate and lipid metabolism of the red mason bee, Osmia rufa.

    Science.gov (United States)

    Dmochowska, Kamila; Giejdasz, Karol; Fliszkiewicz, Monika; Zółtowska, Krystyna

    2013-01-01

    Bees of the genus Osmia are being used in crop pollination at an increasing rate. However, a short life expectancy of adult individuals limits the feasibility of their use. Cocoons of the red mason bee, Osmia rufa L. (Hymenoptera: Megachilidae), can be stored at 4° C in a postdiapause state, and adult bees can be used for pollination outside their natural flight period. The period of storage in this form has an unfavorable influence on the survival rate, life expectancy, and fertility of the bee. It was suggested that the negative results are connected with exhaustion of energy reserves. To test this hypothesis, the present study examined the contents of protein, carbohydrates, lipids, and the activities of some enzymes, and their degradation in red mason bees that emerged in spring according to their biological clock and in summer after elongated diapause. It was found that postdiapause artificially elongated by 3 months caused significant decreases in body weight, total sugar, glycogen, lipids, and protein content in O. rufa. Glucose level was highest in bees that emerged in the summer, which was coincident with increased activities of maltase and trehalase. The activities of sucrase and cellobiase were not changed, while amylase activity was considerably decreased. The activities of triacylglycerols lipase and C2, C4, C10 carboxylesterases were highest in bees that emerged in July. Low temperatures restrict O. rufa emergence, and during prolonged postdiapause, metabolic processes lead to significant reductions of structural and energetic compounds. PMID:24219557

  2. Structure of beryllium isotopes in fermionic molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Torabi, Bahram Ramin

    2009-02-16

    Modern theoretical nuclear physics faces two major challenges. The first is finding a suitable interaction, which describes the forces between nucleons. The second challenge is the solution of the nuclear many-body problem for a given nucleus while applying a realistic potential. The potential used in the framework of this thesis is based on the Argonne AV18 potential. It was transformed by means of the Unitary Correlation Operator Method (UCOM) to optimize convergence. The usual phenomenological corrections were applied to improve the potential for the Hilbert space used in Fermionic Molecular Dynamics (FMD). FMD is an approach to solve the nuclear many-body problem. It uses a single-particle basis which is a superposition of Gaussian distributions in phase-space. The most simple many-body state is the antisymmetric product of the singleparticle states: a Slater determinant, the so called intrinsic state. This intrinsic state is projected on parity, total angular momentum and a center of mass momentum zero. The Hilbert space is spanned by several of these projected states. The states are obtained by minimizing their energy while demanding certain constraints. The expectation values of Slater determinants, parity projected and additionally total angular momentum projected Slater determinants are used. The states that are relevant in the low energy regime are obtained by diagonalization. The lowest moments of the mass-, proton- or neutron-distribution and the excitation in proton- and neutron-shells of a harmonic oscillator are some of the used constraints. The low energy regime of the Beryllium isotopes with masses 7 to 14 is calculated by using these states. Energies, radii, electromagnetic transitions, magnetic moments and point density distributions of the low lying states are calculated and are presented in this thesis. (orig.)

  3. Structure of beryllium isotopes in fermionic molecular dynamics

    International Nuclear Information System (INIS)

    Modern theoretical nuclear physics faces two major challenges. The first is finding a suitable interaction, which describes the forces between nucleons. The second challenge is the solution of the nuclear many-body problem for a given nucleus while applying a realistic potential. The potential used in the framework of this thesis is based on the Argonne AV18 potential. It was transformed by means of the Unitary Correlation Operator Method (UCOM) to optimize convergence. The usual phenomenological corrections were applied to improve the potential for the Hilbert space used in Fermionic Molecular Dynamics (FMD). FMD is an approach to solve the nuclear many-body problem. It uses a single-particle basis which is a superposition of Gaussian distributions in phase-space. The most simple many-body state is the antisymmetric product of the singleparticle states: a Slater determinant, the so called intrinsic state. This intrinsic state is projected on parity, total angular momentum and a center of mass momentum zero. The Hilbert space is spanned by several of these projected states. The states are obtained by minimizing their energy while demanding certain constraints. The expectation values of Slater determinants, parity projected and additionally total angular momentum projected Slater determinants are used. The states that are relevant in the low energy regime are obtained by diagonalization. The lowest moments of the mass-, proton- or neutron-distribution and the excitation in proton- and neutron-shells of a harmonic oscillator are some of the used constraints. The low energy regime of the Beryllium isotopes with masses 7 to 14 is calculated by using these states. Energies, radii, electromagnetic transitions, magnetic moments and point density distributions of the low lying states are calculated and are presented in this thesis. (orig.)

  4. Population structure and genetic diversity of the orchid bee Eufriesea violacea (Hymenoptera, Apidae, Euglossini) from Atlantic Forest remnants in southern and southeastern Brazil

    OpenAIRE

    Freiria, Gabriele; Ruim, Juliana; Souza, Rogério; Sofia, Silvia

    2012-01-01

    In this study, both the genetic diversity and population genetic structure of Eufriesea violacea from six Atlantic Forest fragments, located in four Brazilian states, were assessed using microsatellite markers. The results showed that genetic diversity was high in all populations and the genetic differentiation (Φ ST), based on allelic frequency differences, for all population pairwise comparisons was found to be significantly different from zero, indicating from low to moderate genetic diffe...

  5. Study of the molecular structure of uranium hexafluoride

    International Nuclear Information System (INIS)

    The vibrational spectrum of uranium hexafluoride has been studied in both the gaseous and solid states. The study of gaseous UF6 confirms the regular octahedral structure of the fluorine atoms around the central U atom and makes it possible to evaluate some of the vibrational frequencies. From these, some new force constants have been determined. A tetragonal distortion is observed on solid UF6; this distortion has only observed up till now by means of X-ray diffraction and nuclear magnetic resonance techniques. (author)

  6. Molecular structure and biological function of proliferating cell nuclear antigen

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Proliferating cell nuclear antigen (PCNA) is the core component of replication complex in eukaryote.As a processive factor of DNA polymerase delta, PCNA coordinates the replication process by interacting with various replication proteins. PCNA appears to play an essential role in many cell events, such as DNA damage repair, cell cycle regulation, and apoptosis, through the coordination or organization of different partners. PCNA is an essential factor in cell proliferation, and has clinical significance in tumor research. In this article we review the functional structure of PCNA, which acts as a function switch in different cell events.

  7. Lithium diffusion in silicon and induced structure disorder: A molecular dynamics study

    OpenAIRE

    Huanyu Wang; Xiao Ji; Chi Chen; Kui Xu; Ling Miao

    2013-01-01

    Using molecular dynamics method, we investigate the diffusion property of lithium in different silicon structures and silicon structure's disorder extent during lithium's diffusion process. We find that the pathway and the incident angle between the direction of barrier and diffusion of lithium are also the essential factors to the lithium's diffusion property in silicon anode besides the barrier. Smaller incident angle could decrease the scattering of lithium in silicon structure effectively...

  8. Crystal and molecular structure of N-(-nitrobenzylidene)-3-chloro-4-fluoroaniline

    Indian Academy of Sciences (India)

    K V Arjuna Gowda; M K Kokila; Puttaraja; M V Kulkarni; N C Shivaprakash

    2000-09-01

    The crystal structure of N-(-nitrobenzylidene)-3-chloro-4-fluoroaniline (II) has been determined by X-ray structure analysis. This belongs to a class of benzylidene anilines. The structure was solved by direct method. The molecular packing of the non-planar molecules are held by Van der Waals and F$\\cdots\\cdot$H7, O$\\cdots\\cdot$Cl, F$\\cdots\\cdot$F and N$\\cdots\\cdot$H interactions.

  9. Structural and dipolar fluctuations in liquid water: A Car-Parrinello molecular dynamics study

    Science.gov (United States)

    Skarmoutsos, Ioannis; Masia, Marco; Guardia, Elvira

    2016-03-01

    A Car-Parrinello molecular dynamics simulation was performed to investigate the local tetrahedral order, molecular dipole fluctuations and their interrelation with hydrogen bonding in liquid water. Water molecules were classified in three types, exhibiting low, intermediate and high tetrahedral order. Transitions from low to high tetrahedrally ordered structures take place only through transitions to the intermediate state. The molecular dipole moments depend strongly on the tetrahedral order and hydrogen bonding. The average dipole moment of water molecules with a strong tetrahedral order around them comes in excellent agreement with previous estimations of the dipole moment of ice Ih molecules.

  10. Correlations between molecular structure and charge distribution in organometallic complexes of lanthanoids and actinoids

    International Nuclear Information System (INIS)

    The correlation between molecular structure and charge distribution was investigated in organometallic compounds of the lanthanoid (4f-) and actinoid (5f-) elements. These compounds are suitable models for two reasons: a) they are soluble in nonpolar solvents and b) in both series, there is a possibility for continuous variation of the ionic size of the central ion. Detailed investigation of several compound-classes with different molecular symmetry, has given important information concerning the influence of the molecular structure on the macroscopic charge distribution in the molecule. The anisotropy of the charge distribution in the molecule increases with decreasing of the molecular symmetry. Contrary to predictions previously discussed in the literature, it has been shown, that the molecular symmetry primarily does not depend on sterical interactions, but on the Coulomb-interaction between the central ion and the ligand. Using different models which take into account the molecular geometry and the charge distribution, it was possible to calculate the partial electrical moments between ligand and central ion for several coordinating atoms of the used ligands. The contribution of the f-electrons to the total charge distribution around the central ion can be quantitatively calculated from the molecular polarizability and the total charge distribution of the investigated molecule. (orig./RB)

  11. Molecular Clouds in the North American and Pelican Nebulae: Structures

    CERN Document Server

    Zhang, Shaobo; Yang, Ji

    2013-01-01

    We present observations of 4.25 square degree area toward the North American and Pelican Nebulae in the $J = 1-0$ transitions of $^{12}$CO, $^{13}$CO, and C$^{18}$O. Three molecules show different emission area with their own distinct structures. These different density tracers reveal several dense clouds with surface density over 500 $M_\\odot$ pc$^{-2}$ and a mean H$_2$ column density of 5.8, 3.4, and 11.9$\\times10^{21}$ cm$^{-2}$ for $^{12}$CO, $^{13}$CO, and C$^{18}$O, respectively. We obtain a total mass of $5.4\\times10^4 M_\\odot$ ($^{12}$CO), $2.0\\times10^4 M_\\odot$ ($^{13}$CO), and $6.1\\times10^3 M_\\odot$ (C$^{18}$O) in the complex. The distribution of excitation temperature shows two phase of gas: cold gas ($\\sim$10 K) spreads across the whole cloud; warm gas ($>$20 K) outlines the edge of cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud including t...

  12. Enhanced production of parthenocarpic cucumbers pollinated with stingless bees and Africanized honey bees in greenhouses

    Directory of Open Access Journals (Sweden)

    Euclides Braga Malheiros

    2013-12-01

    Full Text Available Crops have different levels of dependence on pollinators; this holds true even for cultivars of the same species, as in the case of cucumber (Cucumis sativus. The aim of this research was to assess the attractiveness of flowers of three Japanese parthenocarpic cucumber cultivars and evaluate the importance of Africanized bees (Apis mellifera, and the Brazilian native stingless bees, Jataí (Tetragonisca angustula and Iraí (Nannotrigona testaceicornis on fruit production. Several parameters, including frequency of bee visits to flowers as well as duration of nectar collection and fruit set were examined; additionally, fruit weight, length and diameter were evaluated. Three greenhouses located in Ribeirão Preto, SP, were used for planting three cucumber cultivars (Hokushin, Yoshinari and Soudai. The female flowers were more attractive than male flowers; however, Jataí bees were not observed visiting the flowers. The Africanized and the Iraí bees collected only nectar, with a visitation peak between 10 and 12h. Visits to female flowers had a longer duration than visits to male flower visits in all three cultivars. Africanized bee colonies declined due to loss of bees while in the greenhouse; the native stingless bee colonies did not suffer these losses. When bees were excluded, fruit set was 78%; however, when bees had access to the flowers, fruit set was significantly (19.2% higher. Fruit size and weight did not differ with and without bees. This demonstrates that even in parthenocarpic cucumber cultivars, which do not require pollination in order to from fruits, fruit production is significantly increased by bee pollination.

  13. Coalescence of silver unidimensional structures by molecular dynamics simulation; Coalescencia de estructuras unidimensionales de plata por simulacion dinamica molecular

    Energy Technology Data Exchange (ETDEWEB)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G. [ININ, 52750 La Marquesa, Estado de Mexico (Mexico); Arenas, J. [IFUNAM, 04510 Mexico D.F. (Mexico)

    2007-07-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  14. EFFECTS OF MATRIX MOLECULAR WEIGHT ON STRUCTURE AND REINFORCEMENT OF HIGH DENSITY POLYETHYLENE/MICA COMPOSITES

    Institute of Scientific and Technical Information of China (English)

    Li Chen; Yu-fang Xiang; Ke Wang; Qin Zhang; Rong-ni Du; Qiang Fu

    2011-01-01

    Three types of high-density polyethylene (HDPE) with different molecular weights (high, medium and Iow) were adopted to evaluate the influence of matrix molecular weight on the structure-property relation of injection-molded HDPE/mica composites through a combination of SEM, 2d-WAXS, DSC, DMA and tensile testing. Various structural factors including orientation, filler dispersion, interfacial interaction between HDPE and mica, etc., which can impact the macroscopic mechanics, were compared in detail among the three HDPE/mica composites. The transcrystallization of HDPE on the mica surface was observed and it exhibited strong matrix molecular weight dependence. Obvious transcrystalline structure was found in the composite with Iow molecular weight HDPE, whereas it was hard to be detected in the composites with increased HDPE molecular weight. The best reinforcement effect in the composite with low molecular weight HDPE can be understood as mainly due to substantially improved interracial adhesion between matrix and mica filler, which arises from the transerystallization mechanism.

  15. Two-dimensional topological insulator molecular networks: dependence on structure, symmetry, and composition

    Science.gov (United States)

    Tan, Liang Z.; Louie, Steven G.

    2014-03-01

    2D molecular networks can be fabricated from a wide variety of molecular building blocks, arranged in many different configurations. Interactions between neighboring molecular building blocks result in the formation of new 2D materials. Examples of 2D organic topological insulators, that contain molecular building blocks and heavy elements arranged in a hexagonal lattice, have been recently proposed by Feng Liu and coworkers (Nano Lett., 13, 2842 (2013)). In this work, we present a systematic study of the design space of 2D molecular network topological insulators, elucidating the role of structure, symmetry, and composition of the networks. We show that the magnitude and presence of spin-orbit gaps in the electronic band structure is strongly dependent on the symmetry properties and arrangement of the individual components of the molecular lattice. We present general rules to maximize the magnitude of spin-orbit gaps and perform ab-initio calculations on promising structures derived from these guidelines. This work was supported by National Science Foundation Grant No. DMR10-1006184, the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Computational resources have been provided by the NSF through XSEDE resources at NICS.

  16. Transcriptome analysis of the Asian honey bee Apis cerana cerana.

    Directory of Open Access Journals (Sweden)

    Zi Long Wang

    Full Text Available BACKGROUND: The Eastern hive honey bee, Apis cerana cerana is a native and widely bred honey bee species in China. Molecular biology research about this honey bee species is scarce, and genomic information for A. c. cerana is not currently available. Transcriptome and expression profiling data for this species are therefore important resources needed to better understand the biological mechanisms of A. c. cerana. In this study, we obtained the transcriptome information of A. c. cerana by RNA-sequencing and compared gene expression differences between queens and workers of A. c. cerana by digital gene expression (DGE analysis. RESULTS: Using high-throughput Illumina RNA sequencing we obtained 51,581,510 clean reads corresponding to 4.64 Gb total nucleotides from a single run. These reads were assembled into 46,999 unigenes with a mean length of 676 bp. Based on a sequence similarity search against the five public databases (NR, Swissport, GO, COG, KEGG with a cut-off E-value of 10(-5 using BLASTX, a total of 24,630 unigenes were annotated with gene descriptions, gene ontology terms, or metabolic pathways. Using these transcriptome data as references we analyzed the gene expression differences between the queens and workers of A. c. cerana using a tag-based digital gene expression method. We obtained 5.96 and 5.66 million clean tags from the queen and worker samples, respectively. A total of 414 genes were differentially expressed between them, with 189 up-regulated and 225 down-regulated in queens. CONCLUSIONS: Our transcriptome data provide a comprehensive sequence resource for future A. c. cerana study, establishing an important public information platform for functional genomic studies in A. c. cerana. Furthermore, the DGE data provide comprehensive gene expression information for the queens and workers, which will facilitate our understanding of the molecular mechanisms of the different physiological aspects of the two castes.

  17. Landscape heterogeneity predicts gene flow in a widespread polymorphic bumble bee, Bombus bifarius (Hymentoptera: Apidae).

    Science.gov (United States)

    Bombus bifarius is a widespread bumble bee that occurs in montane regions of western North America. This species has several major color polymorphisms, and shows evidence of genetic structuring among regional populations. We test whether this structure is evidence for discrete gene flow barriers tha...

  18. Crystal and molecular structure of cadmium diformiatodiaquo-bis-(nicotinamide)

    International Nuclear Information System (INIS)

    The structural investigation of the cadmium formiate complex with nicotinamide Cd(HCOO)2(AHA)2(H2O)2, AHA=NC5H4-CONH2, is performed. The parameters of the triclinic lattice are α=7.451 (1), b=7.549(2), c=8.787(3)A, α=109.88(2), β=100.16(2), γ=96.92(2), space group. P anti 1, Z=1. Each of the ligands occupies a coordination place, forming transoctahedral surroundings around Cd. The AHA ligand is coordinated by pyridine nitrogen Cd-N 2.336(5), distances Cd-O(HCOO) 2.285(7), Cd-O(H2O) 2.342(7)

  19. Molecular Variability in Barley Structural Mutants Produced by Gamma Irradiation

    International Nuclear Information System (INIS)

    Single Sequence Repeat (SSR) and Amplified Fragment Length Polymorphism (AFLP) markers were used to survey gamma ray induced genetic variation in a set of 13 originally produced structural barley (H. vulgare L.) mutants from cv. Freya; including 8 single translocation lines, 3 double translocation lines and 2 multiple reconstructed karyotypes. Both marker systems contributed to the evaluation of the radiation induced DNA alterations and revealed in general 0.49% polymorphisms in the studied genotypes. AFLPs were observed with 3 out of 10 PstI/MseI primer combinations. Transmissible microsatellite instability at loci with perfect (AT)n repeats located in the introns of the rubisco activase and waxy was documented in three mutant lines. The results emphasize that in addition to point mutations, small indels (2bp) form the major group of the gamma induced DNA alterations. (author)

  20. Synergistic effects of non-Apis bees and honey bees for pollination services.

    Science.gov (United States)

    Brittain, Claire; Williams, Neal; Kremen, Claire; Klein, Alexandra-Maria

    2013-03-01

    In diverse pollinator communities, interspecific interactions may modify the behaviour and increase the pollination effectiveness of individual species. Because agricultural production reliant on pollination is growing, improving pollination effectiveness could increase crop yield without any increase in agricultural intensity or area. In California almond, a crop highly dependent on honey bee pollination, we explored the foraging behaviour and pollination effectiveness of honey bees in orchards with simple (honey bee only) and diverse (non-Apis bees present) bee communities. In orchards with non-Apis bees, the foraging behaviour of honey bees changed and the pollination effectiveness of a single honey bee visit was greater than in orchards where non-Apis bees were absent. This change translated to a greater proportion of fruit set in these orchards. Our field experiments show that increased pollinator diversity can synergistically increase pollination service, through species interactions that alter the behaviour and resulting functional quality of a dominant pollinator species. These results of functional synergy between species were supported by an additional controlled cage experiment with Osmia lignaria and Apis mellifera. Our findings highlight a largely unexplored facilitative component of the benefit of biodiversity to ecosystem services, and represent a way to improve pollinator-dependent crop yields in a sustainable manner. PMID:23303545

  1. Why are African honey bees and not European bees invasive? Pollen diet diversity in community experiments

    OpenAIRE

    Rogel Villanueva-G.,; Roubik, David

    2004-01-01

    We studied resource use and competition by varieties of a honey bee, Apis mellifera, through re-introducing European A. m. ligustica in experimental apiaries in a habitat 'saturated' by African (or hybrid African and European) honey bees that naturally colonized forest in the Yucatan Peninsula of Mexico. Over 171 pollen species comprised honey bee diets. The Morisita-Horn similarity index (highest similarity = 1.0) between the two honey bee races was 0.76 for pollen use and, from the average ...

  2. Changes in physical properties and molecular structure of butyl rubber during γ-irradiation

    International Nuclear Information System (INIS)

    Butyl rubber samples have been aged by γ-irradiation at 250C in air. The change in molecular structure due to chain scission and formation of oxygenated groups also change the number-average molecular weight, tensile strength and density of butyl rubber. The rubber predominantly undergoes chain scission upon γ-irradiation up to a dose of 50 Mrad, but there is also substantial chain crosslinking above 50 Mrad. The yield G(x) has been found, which provides an insight into the mechanism of the radiolytic degradation. Hydroperoxide is the major product and unsaturation is incorporated in the polymer back bone. The change in molecular structure due to recombination and chain scission are followed by the formation of a more ordered structure and hence an increase in density. (author)

  3. Theoretical study on molecular packing and electronic structure of bi-1,3,4-oxadiazole derivatives

    KAUST Repository

    Wang, Haitao

    2014-01-01

    The molecular aggregation structure of 5,5′-bis(naphthalen-2-yl)-2,2′-bi(1,3,4-oxadiazole) (BOXD-NP) was studied by computing the intermolecular interaction potential energy surface (PES) at density functional theory level based on a dimer model. All B3LYP, CAM-B3LYP and M062x functionals can yield a reliable isolated molecular geometry. The conformation of BOXD-NP obtained with all methods is perfectly planar, indicating good conjugation ability between oxadiazole and naphthalene rings. The vibrational frequencies of BOXD-NP were also calculated using the B3LYP/6-311+G∗∗ method, which showed great consistency with the experimental observations and makes the assignments of the IR spectra more solid. It was revealed that the lowest excited state of BOXD-NP should be assigned as a highly allowed π-π∗ state by TD-DFT calculation. Considering the non-covalent interactions in molecular aggregates, the M062x functional was applied in the construction of the PES. Besides the packing structure found in the crystals, PES also predicted several stable structures, indicating that PES has great ability in guiding molecular self-assembly. Symmetry Adapted Perturbation Theory (SAPT) analysis on these energy-minimum molecular stacking structures revealed that London dispersion forces are the strongest attractive component in the binding. This journal is

  4. Cocoon orientation in the nests of red mason bees (Osmia bicornis) is affected by cocoon size and available space

    OpenAIRE

    Szentgyörgyi, Hajnalka; Woyciechowski, Michał

    2013-01-01

    Proper orientation of cocoons in linearly structured nests can be crucial for the survival of hatching bees. Nevertheless, misoriented cocoons appear in nature in notable proportions. A detailed analysis of sex, space available for cocoon spinning, cocoon size, and nest diameter in the red mason bee (Osmia bicornis) showed that smaller males are more prone to misorientation than larger females. Generally, smaller individuals of both sexes are more often misoriented because smaller larvae disr...

  5. Molecular Structure of Aggregated Amyloid-β: Insights from Solid-State Nuclear Magnetic Resonance.

    Science.gov (United States)

    Tycko, Robert

    2016-01-01

    Amyloid-β (Aβ) peptides aggregate to form polymorphic amyloid fibrils and a variety of intermediate assemblies, including oligomers and protofibrils, both in vitro and in human brain tissue. Since the beginning of the 21st century, considerable progress has been made to characterize the molecular structures of Aβ aggregates. Full molecular structural models based primarily on data from measurements using solid-state nuclear magnetic resonance (ssNMR) have been developed for several in vitro Aβ fibrils and one metastable protofibril. Partial structural characterization of other aggregation intermediates has been achieved. One full structural model for fibrils derived from brain tissue has also been reported. Future work is likely to focus on additional structures from brain tissue and on further clarification of nonfibrillar Aβ aggregates. PMID:27481836

  6. The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

    Directory of Open Access Journals (Sweden)

    Fei Shi

    2011-01-01

    Full Text Available Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions.

  7. Modification of LDPE molecular structure by gamma irradiation for bioapplications

    International Nuclear Information System (INIS)

    The surface properties of low-density polyethylene (LDPE) can be modified by the grafting of 2-hydroxyethyl methacrylate (HEMA). This was done aiming at the production of new materials suitable for bioapplications. Samples with different monomer concentrations were prepared from LDPE particles by gamma irradiation, following different irradiation protocols, including irradiation in presence and absence of air. The samples were characterized by thermal analysis techniques (DSC and TGA) and by Fourier transform infrared spectroscopy (FTIR). The results obtained show a decrease in the crystallinity of the supporting matrix for copolymers with high yields of grafting. However, the new materials prepared maintain good structural order resulting from the protective effect of polyHEMA grafted onto LDPE backbone. These effects can improve the diffusion of other species deeper inside the matrix and increase the material hydrophilicity. The studies performed made possible the selection of experimental protocols adequate for the production of new copolymeric materials with high grafting yield. These were used in the production of new LDPE films with enhanced hydrophilic properties

  8. Seed coating with a neonicotinoid insecticide negatively affects wild bees.

    Science.gov (United States)

    Rundlöf, Maj; Andersson, Georg K S; Bommarco, Riccardo; Fries, Ingemar; Hederström, Veronica; Herbertsson, Lina; Jonsson, Ove; Klatt, Björn K; Pedersen, Thorsten R; Yourstone, Johanna; Smith, Henrik G

    2015-05-01

    Understanding the effects of neonicotinoid insecticides on bees is vital because of reported declines in bee diversity and distribution and the crucial role bees have as pollinators in ecosystems and agriculture. Neonicotinoids are suspected to pose an unacceptable risk to bees, partly because of their systemic uptake in plants, and the European Union has therefore introduced a moratorium on three neonicotinoids as seed coatings in flowering crops that attract bees. The moratorium has been criticized for being based on weak evidence, particularly because effects have mostly been measured on bees that have been artificially fed neonicotinoids. Thus, the key question is how neonicotinoids influence bees, and wild bees in particular, in real-world agricultural landscapes. Here we show that a commonly used insecticide seed coating in a flowering crop can have serious consequences for wild bees. In a study with replicated and matched landscapes, we found that seed coating with Elado, an insecticide containing a combination of the neonicotinoid clothianidin and the non-systemic pyrethroid β-cyfluthrin, applied to oilseed rape seeds, reduced wild bee density, solitary bee nesting, and bumblebee colony growth and reproduction under field conditions. Hence, such insecticidal use can pose a substantial risk to wild bees in agricultural landscapes, and the contribution of pesticides to the global decline of wild bees may have been underestimated. The lack of a significant response in honeybee colonies suggests that reported pesticide effects on honeybees cannot always be extrapolated to wild bees. PMID:25901681

  9. Study of the molecular structure and dynamics of bakelite with neutron cross section measurements

    International Nuclear Information System (INIS)

    The molecular structure and dynamics of calcined bakelite were studied with neutron transmission and scattering cross section measurements. The total cross sections determined were correlated with data obtained with infra-red spectroscopy, elemental analysis and other techniques to get the probable molecular formulae of bakelite. The total cross section determined showed a deviation smaller than 5% from the literature values. The frequency distribution as well as overall experimental results allowed to suggest a structural model like polycyclic hydrocarbons for bakelite calcined at 8000 C. (F.E.). 65 refs, 31 figs, 5 tabs

  10. Object Recognition in Flight: How Do Bees Distinguish between 3D Shapes?

    Science.gov (United States)

    Werner, Annette; Stürzl, Wolfgang; Zanker, Johannes

    2016-01-01

    Honeybees (Apis mellifera) discriminate multiple object features such as colour, pattern and 2D shape, but it remains unknown whether and how bees recover three-dimensional shape. Here we show that bees can recognize objects by their three-dimensional form, whereby they employ an active strategy to uncover the depth profiles. We trained individual, free flying honeybees to collect sugar water from small three-dimensional objects made of styrofoam (sphere, cylinder, cuboids) or folded paper (convex, concave, planar) and found that bees can easily discriminate between these stimuli. We also tested possible strategies employed by the bees to uncover the depth profiles. For the card stimuli, we excluded overall shape and pictorial features (shading, texture gradients) as cues for discrimination. Lacking sufficient stereo vision, bees are known to use speed gradients in optic flow to detect edges; could the bees apply this strategy also to recover the fine details of a surface depth profile? Analysing the bees’ flight tracks in front of the stimuli revealed specific combinations of flight maneuvers (lateral translations in combination with yaw rotations), which are particularly suitable to extract depth cues from motion parallax. We modelled the generated optic flow and found characteristic patterns of angular displacement corresponding to the depth profiles of our stimuli: optic flow patterns from pure translations successfully recovered depth relations from the magnitude of angular displacements, additional rotation provided robust depth information based on the direction of the displacements; thus, the bees flight maneuvers may reflect an optimized visuo-motor strategy to extract depth structure from motion signals. The robustness and simplicity of this strategy offers an efficient solution for 3D-object-recognition without stereo vision, and could be employed by other flying insects, or mobile robots. PMID:26886006

  11. Screening of environmental contaminants in honey bee wax comb using gas chromatography-high-resolution time-of-flight mass spectrometry.

    Science.gov (United States)

    Gómez-Ramos, M M; García-Valcárcel, A I; Tadeo, J L; Fernández-Alba, A R; Hernando, M D

    2016-03-01

    This study reports an analytical approach intended to be used for investigation of non-targeted environmental contaminants and to characterize the organic pollution pattern of bee wax comb samples. The method comprises a generic extraction followed by detection with gas chromatography coupled to high-resolution time-of-flight mass spectrometry (GC-TOF-MS), operated in electron impact ionization (EI) mode. The screening approach for the investigation of non-targeted contaminants consisted of initial peak detection by deconvolution and matching the first-stage mass spectra EI-MS(1) with a nominal mass spectral library. To gain further confidence in the structural characterization of the contaminants under investigation, the molecular formula of representative ions (molecular ion when present in the EI spectrum) and, for at least other two fragment ions, was provided for those with an accurate mass scoring (mass error < 5 ppm). This methodology was applied for screening environmental contaminants in 50 samples of bee wax comb. This approach has allowed the tentative identification of some GC-amenable contaminants belonging to different chemical groups, among them, phthalates and polycyclic aromatic hydrocarbons (PAHs), along with residues of veterinary treatments used in apiculture. PMID:26527334

  12. Effects of immunostimulation on social behavior, chemical communication and genome-wide gene expression in honey bee workers (Apis mellifera

    Directory of Open Access Journals (Sweden)

    Richard Freddie-Jeanne

    2012-10-01

    Full Text Available Abstract Background Social insects, such as honey bees, use molecular, physiological and behavioral responses to combat pathogens and parasites. The honey bee genome contains all of the canonical insect immune response pathways, and several studies have demonstrated that pathogens can activate expression of immune effectors. Honey bees also use behavioral responses, termed social immunity, to collectively defend their hives from pathogens and parasites. These responses include hygienic behavior (where workers remove diseased brood and allo-grooming (where workers remove ectoparasites from nestmates. We have previously demonstrated that immunostimulation causes changes in the cuticular hydrocarbon profiles of workers, which results in altered worker-worker social interactions. Thus, cuticular hydrocarbons may enable workers to identify sick nestmates, and adjust their behavior in response. Here, we test the specificity of behavioral, chemical and genomic responses to immunostimulation by challenging workers with a panel of different immune stimulants (saline, Sephadex beads and Gram-negative bacteria E. coli. Results While only bacteria-injected bees elicited altered behavioral responses from healthy nestmates compared to controls, all treatments resulted in significant changes in cuticular hydrocarbon profiles. Immunostimulation caused significant changes in expression of hundreds of genes, the majority of which have not been identified as members of the canonical immune response pathways. Furthermore, several new candidate genes that may play a role in cuticular hydrocarbon biosynthesis were identified. Effects of immune challenge expression of several genes involved in immune response, cuticular hydrocarbon biosynthesis, and the Notch signaling pathway were confirmed using quantitative real-time PCR. Finally, we identified common genes regulated by pathogen challenge in honey bees and other insects. Conclusions These results demonstrate that

  13. A molecular dynamics calculation of the fluctuation structure in the diatomic fluids around the critical points

    International Nuclear Information System (INIS)

    The principle of corresponding state on the fluctuation structure, which is the spatial distribution of various clusters of molecules caused by density fluctuations, in supercritical states around the critical points has been investigated. In this paper, we performed Molecular Dynamics (MD) simulation to extract the fluctuation structure around the critical points of 2-Center-Lennard-Jones (2CLJ) fluids, whose characteristics change by their molecular elongations. First, we indentified some critical points of 2CLJ fluids with comparatively shorter elongations applying Lotfi's function, which correctly describes the liquid-vapor coexistence line of Lennard-Jones (LJ) fluid, and successfully defined each critical point. Next, two methods were applied in the estimation of the fluctuation structure: one is the evaluation of the dispersion of the number of molecules at a certain domain, and the other is the calculation of static structure factor. As a result, in 2CLJ fluids which have shorter molecular elongations comparatively, the principle of corresponding state is satisfied because of the small differences in the fluctuation structures extracted in the present two methods. On the other hand, some results imply that the fluctuation may decrease in 2CLJ fluids which have the longer molecular elongations although more accurate evaluation of the critical points in those fluids is necessary for the further investigation. (author)

  14. Molecular and electronic structure of actinide hexa-cyanoferrates

    International Nuclear Information System (INIS)

    The goal of this work is to improve our knowledge on the actinide-ligand bond properties. To this end, the hexacyanoferrate entities have been used as pre-organized ligand. We have synthesized, using mild chemistry, the following series of complexes: AnIV[FeII(CN)6].xH2O (An = Th, U, Np, Pu); AmIII[FeIII(CN)6].xH2O; Pu III[CoIII(CN)6].xH2O and K(H?)AnIII[FeII(CN)6].xH2O (An = Pu, Am). The metal oxidation states have been obtained thanks to the νCN, stretching vibration and to the actinide LIII absorption edge studies. As Prussian Blue, the AnIV[FeII(CN)6].xH2O (An = Np, Pu) are class II of Robin and Day compounds. X-ray Diffraction has shown besides that these complexes crystallize in the P63/m space group, as the isomorphic LaKFe(CN)6.4H2O complex used as structural model. The EXAFS oscillations at the iron K edge and at the An LIII edge allowed to determine the An-N, An-O, Fe-C and Fe-N distances. The display of the multiple scattering paths for both edges explains the actinide contribution absence at the iron edge, whereas the iron signature is present at the actinide edge. We have shown that the actinide coordination sphere in actinides hexa-cyanoferrates is comparable to the one of lanthanides. However, the actinides typical behavior towards the lanthanides is brought to the fore by the AnIV versus LnIII ions presence in this family of complexes. Contrarily to the 4f electrons, the 5f electrons influence the electronic properties of the compounds of this family. However, the gap between the An-N and Ln-N distances towards the corresponding metals ionic radii do not show any covalence bond evolution between the actinide and lanthanide series. (author)

  15. Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins

    Directory of Open Access Journals (Sweden)

    Natalie Heffernan

    2015-01-01

    Full Text Available Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis. Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW phlorotannins were found to have a molecular weight range equivalent to 4–12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs. These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

  16. ZigBee : A Promising Wireless Technology

    Directory of Open Access Journals (Sweden)

    Harleen Kaur Sahota

    2012-12-01

    Full Text Available As a result of high cost of laying the wired networks andincreasing demand for mobility, the wireless network has gainedpopularity in recent times in residential, commercial andindustrial applications. Several wireless technologies haveemerged ranging from short, medium and long distances.Presently, Bluetooth, Infrared and Wireless Local Area Network(WLAN are some of the most widely used wirelesscommunication technologies. These technologies had somelimitations like short battery life, high power dissipation, highdata rate, complex, etc. ZigBee emerges as a powerful wirelessnetwork technology which overcomes these shortcomings ofother wireless technologies. The paper reviews different aspectsof ZigBee network: ZigBee architecture, Devices, RoutingProtocol, Forming and Joining a ZigBee Network.

  17. Gut microbial communities of social bees.

    Science.gov (United States)

    Kwong, Waldan K; Moran, Nancy A

    2016-06-01

    The gut microbiota can have profound effects on hosts, but the study of these relationships in humans is challenging. The specialized gut microbial community of honey bees is similar to the mammalian microbiota, as both are mostly composed of host-adapted, facultatively anaerobic and microaerophilic bacteria. However, the microbial community of the bee gut is far simpler than the mammalian microbiota, being dominated by only nine bacterial species clusters that are specific to bees and that are transmitted through social interactions between individuals. Recent developments, which include the discovery of extensive strain-level variation, evidence of protective and nutritional functions, and reports of eco-physiological or disease-associated perturbations to the microbial community, have drawn attention to the role of the microbiota in bee health and its potential as a model for studying the ecology and evolution of gut symbionts. PMID:27140688

  18. In-depth proteomics characterization of embryogenesis of the honey bee worker (Apis mellifera ligustica).

    Science.gov (United States)

    Fang, Yu; Feng, Mao; Han, Bin; Lu, Xiaoshan; Ramadan, Haitham; Li, Jianke

    2014-09-01

    Identifying proteome changes of honey bee embryogenesis is of prime importance for unraveling the molecular mechanisms that they underlie. However, many proteomic changes during the embryonic period are not well characterized. We analyzed the proteomic alterations over the complete time course of honey bee worker embryogenesis at 24, 48, and 72 h of age, using mass spectrometry-based proteomics, label-free quantitation, and bioinformatics. Of the 1460 proteins identified the embryo of all three ages, the core proteome (proteins shared by the embryos of all three ages, accounting for 40%) was mainly involved in protein synthesis, metabolic energy, development, and molecular transporter, which indicates their centrality in driving embryogenesis. However, embryos at different developmental stages have their own specific proteome and pathway signatures to coordinate and modulate developmental events. The young embryos (honey bee embryogenesis, in which the programmed activation of the proteome matches with the physiological transition observed during embryogenesis. The identified biological pathways and key node proteins allow for further functional analysis and genetic manipulation for both the honey bee embryos and other eusocial insects. PMID:24895377

  19. Field-Level Sublethal Effects of Approved Bee Hive Chemicals on Honey Bees (Apis mellifera L)

    Science.gov (United States)

    Berry, Jennifer A.; Hood, W. Michael; Pietravalle, Stéphane; Delaplane, Keith S.

    2013-01-01

    In a study replicated across two states and two years, we tested the sublethal effects on honey bees of the miticides Apistan (tau fluvalinate) and Check Mite+ (coumaphos) and the wood preservative copper naphthenate applied at label rates in field conditions. A continuous covariate, a colony Varroa mite index, helped us disambiguate the effects of the chemicals on bees while adjusting for a presumed benefit of controlling mites. Mite levels in colonies treated with Apistan or Check Mite+ were not different from levels in non-treated controls. Experimental chemicals significantly decreased 3-day brood survivorship and increased construction of queen supercedure cells compared to non-treated controls. Bees exposed to Check Mite+ as immatures had higher legacy mortality as adults relative to non-treated controls, whereas bees exposed to Apistan had improved legacy mortality relative to non-treated controls. Relative to non-treated controls, Check Mite+ increased adult emergence weight. Although there was a treatment effect on a test of associative learning, it was not possible to statistically separate the treatment means, but bees treated with Apistan performed comparatively well. And finally, there were no detected effects of bee hive chemical on colony bee population, amount of brood, amount of honey, foraging rate, time required for marked released bees to return to their nest, percentage of released bees that return to the nest, and colony Nosema spore loads. To our knowledge, this is the first study to examine sublethal effects of bee hive chemicals applied at label rates under field conditions while disambiguating the results from mite control benefits realized from the chemicals. Given the poor performance of the miticides at reducing mites and their inconsistent effects on the host, these results defend the use of bee health management practices that minimize use of exotic hive chemicals. PMID:24204638

  20. Field-level sublethal effects of approved bee hive chemicals on Honey Bees (Apis mellifera L.

    Directory of Open Access Journals (Sweden)

    Jennifer A Berry

    Full Text Available In a study replicated across two states and two years, we tested the sublethal effects on honey bees of the miticides Apistan (tau fluvalinate and Check Mite+ (coumaphos and the wood preservative copper naphthenate applied at label rates in field conditions. A continuous covariate, a colony Varroa mite index, helped us disambiguate the effects of the chemicals on bees while adjusting for a presumed benefit of controlling mites. Mite levels in colonies treated with Apistan or Check Mite+ were not different from levels in non-treated controls. Experimental chemicals significantly decreased 3-day brood survivorship and increased construction of queen supercedure cells compared to non-treated controls. Bees exposed to Check Mite+ as immatures had higher legacy mortality as adults relative to non-treated controls, whereas bees exposed to Apistan had improved legacy mortality relative to non-treated controls. Relative to non-treated controls, Check Mite+ increased adult emergence weight. Although there was a treatment effect on a test of associative learning, it was not possible to statistically separate the treatment means, but bees treated with Apistan performed comparatively well. And finally, there were no detected effects of bee hive chemical on colony bee population, amount of brood, amount of honey, foraging rate, time required for marked released bees to return to their nest, percentage of released bees that return to the nest, and colony Nosema spore loads. To our knowledge, this is the first study to examine sublethal effects of bee hive chemicals applied at label rates under field conditions while disambiguating the results from mite control benefits realized from the chemicals. Given the poor performance of the miticides at reducing mites and their inconsistent effects on the host, these results defend the use of bee health management practices that minimize use of exotic hive chemicals.

  1. Crystal Structures of Precise Functional Copolymers: Atomistic Molecular Dynamics Simulations and Comparisons with Experiments

    Science.gov (United States)

    Trigg, Edward B.; Stevens, Mark J.; Winey, Karen I.

    Layered crystal structures have been observed in linear poly(ethylene-co-acrylic acid) in which the carboxylic acid groups are placed precisely every 21 carbon atoms along the backbone. The alkane segments form structures resembling orthorhombic polyethylene crystals, while the acid groups form continuous domains that may act as pathways for ion conduction. Further details of the crystal structure have been difficult to elucidate experimentally, but could be important for understanding structure-property relationships. Here, two classes of crystal structures are evaluated via atomistic molecular dynamics: extended chain structures, wherein the polymer backbones are highly extended in near-trans conformations, and adjacent reentry structures, wherein the polymer backbones conform in adjacent reentry loops near the site of each covalently-bonded acid group. Energies of relaxed structures and hydrogen bonding states are compared, and X-ray scattering and other experimental data is compared with the simulation results.

  2. Lithium diffusion in silicon and induced structure disorder: A molecular dynamics study

    Directory of Open Access Journals (Sweden)

    Huanyu Wang

    2013-11-01

    Full Text Available Using molecular dynamics method, we investigate the diffusion property of lithium in different silicon structures and silicon structure's disorder extent during lithium's diffusion process. We find that the pathway and the incident angle between the direction of barrier and diffusion of lithium are also the essential factors to the lithium's diffusion property in silicon anode besides the barrier. Smaller incident angle could decrease the scattering of lithium in silicon structure effectively. Moreover, lithium diffuses easier in the Li-Si alloy structure of higher lithium concentration with deeper injection depth. The silicon's structure will be damaged gradually during the charge and discharge process. However, it will also recover to initial state to a great extent after relaxation. Therefore, the damage of lithium diffusion to silicon anode in the structure of low lithium concentration is reversible to a great degree. In addition, the silicon structure of crystal orientation perform better properties in both lithium's diffusivity and structural stability.

  3. Experimental Study on the comparison of antibacterial and antioxidant effects between the Bee Venom and Sweet Bee Venom

    Directory of Open Access Journals (Sweden)

    Joong chul An

    2006-12-01

    Full Text Available Objectives : This study was conducted to compare antibacterial activities and free radical scavenging activity between the Bee Venom and Sweet Bee Venom in which the allergy-causing enzyme is removed. Methods : To evaluate antibacterial activities of the test samples, gram negative E. coli and gram positive St. aureus were compared using the paper disc method. For comparison of the antioxidant effects, DPPH (1,1-diphenyl-2-picrylhydrazyl free radical scavenging assay and Thiobarbituric Acid Reactive Substances (TBARS assay were conducted. Results : 1. Antibacterial activity against gram negative E. coli was greater in the Sweet Bee Venom group than the Bee Venom group. 2. Antibacterial activity against gram positive St. aureus was similar between the Bee Venom and Sweet Bee Venom groups. 3. DPPH free radical scavenging activity of the Bee Venom group showed 2.8 times stronger than that of the Sweet Bee Venom group. 4. Inhibition of lipid peroxidation of the Bee Venom group showed 782 times greater than that of the Sweet Bee Venom group. Conclusions : The Bee Venom group showed outstanding antibacterial activity against gram positive St. aureus, and allergen-removed Sweet Bee Venom group showed outstanding antibacterial activity against both gram negative E. coli and gram positive St. aureus. For antioxidant effects, the Bee Venom was superior over the Sweet Bee Venom and the superiority was far more apparent for lipid peroxidation.

  4. Molecular structures and metabolic characteristics of protein in brown and yellow flaxseed with altered nutrient traits.

    Science.gov (United States)

    Khan, Nazir Ahmad; Booker, Helen; Yu, Peiqiang

    2014-07-16

    The objectives of this study were to investigate the chemical profiles; crude protein (CP) subfractions; ruminal CP degradation characteristics and intestinal digestibility of rumen undegraded protein (RUP); and protein molecular structures using molecular spectroscopy of newly developed yellow-seeded flax (Linum usitatissimum L.). Seeds from two yellow flaxseed breeding lines and two brown flaxseed varieties were evaluated. The yellow-seeded lines had higher (P < 0.001) contents of oil (44.54 vs 41.42% dry matter (DM)) and CP (24.94 vs 20.91% DM) compared to those of the brown-seeded varieties. The CP in yellow seeds contained lower (P < 0.01) contents of true protein subfraction (81.31 vs 92.71% CP) and more (P < 0.001) extensively degraded (70.8 vs 64.9% CP) in rumen resulting in lower (P < 0.001) content of RUP (29.2 vs 35.1% CP) than that in the brown-seeded varieties. However, the total supply of digestible RUP was not significantly different between the two seed types. Regression equations based on protein molecular structural features gave relatively good estimation for the contents of CP (R(2) = 0.87), soluble CP (R(2) = 0.92), RUP (R(2) = 0.97), and intestinal digestibility of RUP (R(2) = 0.71). In conclusion, molecular spectroscopy can be used to rapidly characterize feed protein molecular structures and predict their nutritive value. PMID:24931851

  5. Structural Changes of a Doubly Spin-Labeled Chemically Driven Molecular Shuttle Probed by PELDOR Spectroscopy.

    Science.gov (United States)

    Franchi, Paola; Bleve, Valentina; Mezzina, Elisabetta; Schäfer, Christian; Ragazzon, Giulio; Albertini, Marco; Carbonera, Donatella; Credi, Alberto; Di Valentin, Marilena; Lucarini, Marco

    2016-06-20

    Gaining detailed information on the structural rearrangements associated with stimuli-induced molecular movements is of utmost importance for understanding the operation of molecular machines. Pulsed electron-electron double resonance (PELDOR) was employed to monitor the geometrical changes arising upon chemical switching of a [2]rotaxane that behaves as an acid-base-controlled molecular shuttle. To this aim, the rotaxane was endowed with stable nitroxide radical units in both the ring and axle components. The combination of PELDOR data and molecular dynamic calculations indicates that in the investigated rotaxane, the ring displacement along the axle, caused by the addition of a base, does not alter significantly the distance between the nitroxide labels, but it is accompanied by a profound change in the geometry adopted by the macrocycle. PMID:27123774

  6. Targeting the untargeted in molecular phenomics with structurally-selective ion mobility-mass spectrometry.

    Science.gov (United States)

    May, Jody Christopher; Gant-Branum, Randi Lee; McLean, John Allen

    2016-06-01

    Systems-wide molecular phenomics is rapidly expanding through technological advances in instrumentation and bioinformatics. Strategies such as structural mass spectrometry, which utilizes size and shape measurements with molecular weight, serve to characterize the sum of molecular expression in biological contexts, where broad-scale measurements are made that are interpreted through big data statistical techniques to reveal underlying patterns corresponding to phenotype. The data density, data dimensionality, data projection, and data interrogation are all critical aspects of these approaches to turn data into salient information. Untargeted molecular phenomics is already having a dramatic impact in discovery science from drug discovery to synthetic biology. It is evident that these emerging techniques will integrate closely in broad efforts aimed at precision medicine. PMID:27132126

  7. Yoghurt enrichment with natural bee farming products

    OpenAIRE

    N. Lomova; S. Narizhnyi; O. Snizhko

    2015-01-01

    Introduction. Bee pollen is a unique and unparalleled natural bioactive substances source. Using it in conjunction with the popular functional fermented milk product -yogurt will expand its product range and increase the biological value. Materials and Methods. Dried bee pollen’s moisture determination was made by gravimetry methods, based on the sample weight loss due to desiccation, until constant weight was reached.Test and control yogurt samples were studi...

  8. Mass envenomations by honey bees and wasps.

    OpenAIRE

    Vetter, R S; Visscher, P.K.; Camazine, S

    1999-01-01

    Stinging events involving honey bees and wasps are rare; most deaths or clinically important incidents involve very few stings (< 10) and anaphylactic shock. However, mass stinging events can prove life-threatening via the toxic action of the venom when injected in large amounts. With the advent of the Africanized honey bee in the southwestern United States and its potential for further spread, mass envenomation incidents will increase. Here we review the literature on mass stinging events in...

  9. Octopamine modulates honey bee dance behavior

    OpenAIRE

    Barron, Andrew B.; Maleszka, Ryszard; Robert K. Vander Meer; Robinson, Gene E.

    2007-01-01

    Honey bees communicate the location and desirability of valuable forage sites to their nestmates through an elaborate, symbolic “dance language.” The dance language is a uniquely complex communication system in invertebrates, and the neural mechanisms that generate dances are largely unknown. Here we show that treatments with controlled doses of the biogenic amine neuromodulator octopamine selectively increased the reporting of resource value in dances by forager bees. Oral and topical octopa...

  10. Large Carpenter Bees as Agricultural Pollinators

    OpenAIRE

    Tamar Keasar

    2010-01-01

    Large carpenter bees (genus Xylocopa) are wood-nesting generalist pollinators of broad geographical distribution that exhibit varying levels of sociality. Their foraging is characterized by a wide range of food plants, long season of activity, tolerance of high temperatures, and activity under low illumination levels. These traits make them attractive candidates for agricultural pollination in hot climates, particularly in greenhouses, and of night-blooming crops. Carpenter bees have demonstr...

  11. Repellent foraging scent recognition across bee families

    OpenAIRE

    Gawleta, Nadine; Zimmermann, Yvonne; Eltz, Thomas

    2005-01-01

    Honeybees and bumblebees avoid probing flowers that have been recently depleted by conspecifics, presumably repelled by odours deposited by the previous visitor (foraging scent marks). Here we show that females of the solitary wool-carder bee Anthidium manicatum (Megachilidae) discriminate against previously visited inflorescences (Stachys officinalis), and that discrimination is equally strong regardless of whether the previous visitor is conspecific or belongs to a different bee family (Bom...

  12. Molecular dynamics simulations of soliton-like structures in a dusty plasma medium

    Energy Technology Data Exchange (ETDEWEB)

    Tiwari, Sanat Kumar, E-mail: sanat-tiwari86@yahoo.co.in; Das, Amita; Sen, Abhijit; Kaw, Predhiman [Institute for Plasma Research, Bhat, Gandhinagar - 382428 (India)

    2015-03-15

    The existence and evolution of soliton-like structures in a dusty plasma medium are investigated in a first principles approach using molecular dynamic (MD) simulations of particles interacting via a Yukawa potential. These localized structures are found to exist in both weakly and strongly coupled regimes with their structures becoming sharper as the correlation effects between the dust particles get stronger. A surprising result, compared to fluid simulations, is the existence of rarefactive soliton-like structures in our non-dissipative system, a feature that arises from the charge conjugation symmetry property of the Yukawa fluid. Our simulation findings closely resemble many diverse experimental results reported in the past.

  13. Molecular Structures and Mechanical Properties of Microbe Rapid Coagulation Natural Rubber

    Institute of Scientific and Technical Information of China (English)

    LIANG Yue; HUANG Mao-Fang; ZENG Zong-Qiang

    2011-01-01

    In this work,molecular structures,dynamic mechanical properties and glass transition temperatures of microbe coagulated natural rubber(NR) samples were analyzed by using pyrolysis gas chromatography-mass spectrometry(py-GC/MS),rubber process analyzer(RPA) and dynamic mechanical thermal analysis(DMA).And the cross-linked network structures and mechanical properties of the corresponding NR vulcanizates were further determined by using nuclear magnetic resonance(NMR) crosslink density spectrometer(XLDS-15) and universal testing machines.The results show that NR raw rubber produced by rapidly coagulated with microorganism exhibits a simple molecular structure composition and good dynamic mechanical properties,and the corresponding NR vulcanizates possess the aggregation structure of high cross-linked density,a high glass transition temperature of-61.5 ℃ and high mechanical properties(tensile strength reaches 25.2 MPa),as compared with that coagulated with acetic acid.

  14. How bees distinguish black from white

    Directory of Open Access Journals (Sweden)

    Horridge A

    2014-10-01

    Full Text Available Adrian Horridge Biological Sciences, Australian National University, Canberra, ACT, AustraliaAbstract: Bee eyes have photoreceptors for ultraviolet, green, and blue wavelengths that are excited by reflected white but not by black. With ultraviolet reflections excluded by the apparatus, bees can learn to distinguish between black, gray, and white, but theories of color vision are clearly of no help in explaining how they succeed. Human vision sidesteps the issue by constructing black and white in the brain. Bees have quite different and accessible mechanisms. As revealed by extensive tests of trained bees, bees learned two strong signals displayed on either target. The first input was the position and a measure of the green receptor modulation at the vertical edges of a black area, which included a measure of the angular width between the edges of black. They also learned the average position and total amount of blue reflected from white areas. These two inputs were sufficient to help decide which of two targets held the reward of sugar solution, but the bees cared nothing for the black or white as colors, or the direction of contrast at black/white edges. These findings provide a small step toward understanding, modeling, and implementing in silicon the anti-intuitive visual system of the honeybee, in feeding behavior. Keywords: vision, detectors, black/white, color, visual processing

  15. NATO Advanced Research Workshop on Vectorization of Advanced Methods for Molecular Electronic Structure

    CERN Document Server

    1984-01-01

    That there have been remarkable advances in the field of molecular electronic structure during the last decade is clear not only to those working in the field but also to anyone else who has used quantum chemical results to guide their own investiga­ tions. The progress in calculating the electronic structures of molecules has occurred through the truly ingenious theoretical and methodological developments that have made computationally tractable the underlying physics of electron distributions around a collection of nuclei. At the same time there has been consider­ able benefit from the great advances in computer technology. The growing sophistication, declining costs and increasing accessibi­ lity of computers have let theorists apply their methods to prob­ lems in virtually all areas of molecular science. Consequently, each year witnesses calculations on larger molecules than in the year before and calculations with greater accuracy and more com­ plete information on molecular properties. We can surel...

  16. Production of antibacterial peptide from bee venom via a new strategy for heterologous expression.

    Science.gov (United States)

    Hou, Chunsheng; Guo, Liqiong; Lin, Junfang; You, Linfeng; Wu, Wuhua

    2014-12-01

    Honey bee is important economic insect that not only pollinates fruits and crops but also provides products with various physiological activities. Bee venom is a functional agent that is widely applied in clinical treatment and pharmacy. Secapin is one of these agents that have a significant role in therapy. The functions of secapin from the bee venom have been documented, but little information is known about its heterologous expression under natural condition. Moreover, few scholars verified experimentally the functions of secapin from bee venom in vitro. In this study, we successfully constructed a heterologous expression vector, which is different from conventional expression system. A transgenic approach was established for transformation of secapin gene from the venom of Apis mellifera carnica (Ac-sec) into the edible fungi, Coprinus cinereus. Ac-sec was encoded by a 234 bp nucleotide that contained a signal peptide domain and two potential phosphorylation sites. The sequence exhibited highly homology with various secapins characterized from honey bee and related species. Southern blot data indicated that Ac-sec was present as single or multiple copy loci in the C. cinereus genome. By co-transformation and double-layer active assay, Ac-sec was expressed successfully in C. cinereus and the antibacterial activity of the recombinants was identified, showing notable antibacterial activities on different bacteria. Although Ac-sec is from the venom of Apidae, phylogenetic analysis demonstrated that Ac-sec was more closely related to that of Vespid than to bee species from Apidae. The molecular characteristics of Ac-sec and the potential roles of small peptides in biology were discussed. PMID:25189650

  17. Molecular dynamics modelling of mechanical properties of polymers for adaptive aerospace structures

    Science.gov (United States)

    Papanikolaou, Michail; Drikakis, Dimitris; Asproulis, Nikolaos

    2015-02-01

    The features of adaptive structures depend on the properties of the supporting materials. For example, morphing wing structures require wing skin materials, such as rubbers that can withstand the forces imposed by the internal mechanism while maintaining the required aerodynamic properties of the aircraft. In this study, Molecular Dynamics and Minimization simulations are being used to establish well-equilibrated models of Ethylene-Propylene-Diene Monomer (EPDM) elastomer systems and investigate their mechanical properties.

  18. Molecular dynamics simulation study on zwitterionic structure to maintain the normal conformations of Glutathione

    Institute of Scientific and Technical Information of China (English)

    YAN; Han; ZHU; HaoMiao; SHEN; Jian

    2007-01-01

    Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The results showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".

  19. One-Dimensional Palladium Wires: Influence of Molecular Changes on Supramolecular Structure

    OpenAIRE

    Campbell, Michael Glenn; Zheng, Shao-Liang; Ritter, Tobias

    2013-01-01

    Nanostructured materials based on one-dimensional (1D) metal wires are of potential utility; however, to date, there is a lack of synthetic methods that allow for variation of structure and therefore properties. Here we report the use of molecular control elements to alter the solid-state structures of 1D palladium wires, including Pd–Pd bond distances and the porosity of the supramolecular framework.

  20. Molecular Dynamics Study on Mechanical Properties in the Structure of Self-Assembled Quantum Dot

    OpenAIRE

    Tatsuya Yamaguchi; Ken-ichi Saitoh

    2012-01-01

    Stress and strain in the structure of self-assembled quantum dots constructed in the Ge/Si(001) system is calculated by using molecular dynamics simulation. Pyramidal hut cluster composed of Ge crystal with {105} facets surfaces observed in the early growth stage are computationally modeled. We calculate atomic stress and strain in relaxed pyramidal structure. Atomic stress for triplet of atoms is approximately defined as an average value of pairwise (virial) quantity inside triplet, which is...

  1. Linear hydrogen adsorbate structures on graphite induced by self-assembled molecular monolayers

    DEFF Research Database (Denmark)

    Nilsson, Louis; Sljivancanin, Zeljko; Balog, Richard; Xu, Wei; Linderoth, Trolle René; Lægsgaard, Erik; Stensgaard, Ivan; Hammer, Bjørk; Besenbacher, Flemming; Hornekær, Liv

    2012-01-01

    Combined scanning tunnelling microscopy measurements and density functional theory calculations reveal a method to induce linear structures of hydrogen adsorbates on graphite by covering the surface with a self-assembled molecular monolayer of cyanuric acid and exposing it to atomic hydrogen. The...... method can in principle be applied to obtain nanopatterned hydrogen structures on free standing graphene and graphene laid down on insulating substrates, hereby opening up for the possibility of substrate independent bandgap engineering of graphene....

  2. Structural and Molecular Characterization of meso-Substituted Zinc Porphyrins: A DFT Supported Study

    OpenAIRE

    Giuseppe Mele; Małgorzata A. Broda; Krzysztof Ejsmont; Gabriela Dyrda; Rudolf Słota

    2011-01-01

    Structural parameters of a range of over 100 meso-substituted zinc porphyrins were reviewed and compared to show how far the nature of the functional group may affect the interatomic distances and bond angles within the porphyrin core. It was proved that even despite evident deformations of the molecular structure, involving twisting of the porphyrin's central plane, the coupled π-bonding system remains flexible and stable. DFT calculations were applied to a number of selected porphyrins repr...

  3. Presentation of thermodynamic functions of isotopic forms using terms of molecular structure

    International Nuclear Information System (INIS)

    Precise mathematical representation of vibration contributions to thermodynamic functions and to their isotopic differences as a matrix of contributions of natural vibration coordinates associated with structural elements of a molecule is developed. The obtained representation permit to unambiguously interpret the given values in terms of molecular structure without using the notion of vibration frquency. It is shown to have essential advantages at interpretation of isotopic effects

  4. Molecular Structure, Function, and Dynamics of Clathrin-Mediated Membrane Traffic

    OpenAIRE

    Kirchhausen, Tom; Owen, David; Harrison, Stephen C.

    2014-01-01

    Clathrin is a molecular scaffold for vesicular uptake of cargo at the plasma membrane, where its assembly into cage-like lattices underlies the clathrin-coated pits of classical endocytosis. This review describes the structures of clathrin, major cargo adaptors, and other proteins that participate in forming a clathrin-coated pit, loading its contents, pinching off the membrane as a lattice-enclosed vesicle, and recycling the components. It integrates as much of the structural information as ...

  5. Molecular dynamics of folding of secondary structures in Go-type models of proteins

    OpenAIRE

    Hoang, Trinh Xuan; Cieplak, Marek

    1999-01-01

    We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and a soft repulsion for the non-native contacts. The interactions are chosen to make the target secondary structure be the native state of the system. We provide a thorough equilibrium and kinetic characterization of the sequences through the molecular dynamic...

  6. EMBEDDED MOLECULAR CLUSTER APPROACH TO THE ELECTRONIC STRUCTURE OF AMORPHOUS AND LIQUID METALS

    OpenAIRE

    Delley, B.; Ellis, D.; Freeman, A

    1980-01-01

    In this approach to the electronic structure of amorphous and liquid metals, we represent the system by molecular clusters which are embedded in an external potential chosen as a suitable representation of the rest of the system. We have determined the electronic structure of a number of Cu, Zr and Cu-Zr clusters using the self-consistent discrete variational-LCAO approach within local density functional theory. Effects due to deviations from perfect crystalline symmetry are analyzed. Total d...

  7. The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

    Science.gov (United States)

    Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

    2016-09-01

    Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. PMID:27235585

  8. Looking beyond Lewis Structures: A General Chemistry Molecular Modeling Experiment Focusing on Physical Properties and Geometry

    Science.gov (United States)

    Linenberger, Kimberly J.; Cole, Renee S.; Sarkar, Somnath

    2011-01-01

    We present a guided-inquiry experiment using Spartan Student Version, ready to be adapted and implemented into a general chemistry laboratory course. The experiment provides students an experience with Spartan Molecular Modeling software while discovering the relationships between the structure and properties of molecules. Topics discussed within…

  9. Structural organization of surfactant aggregates in vacuo: a molecular dynamics and well-tempered metadynamics study.

    Science.gov (United States)

    Longhi, Giovanna; Fornili, Sandro L; Turco Liveri, Vincenzo

    2015-07-01

    Experimental investigations using mass spectrometry have established that surfactant molecules are able to form aggregates in the gas phase. However, there is no general consensus on the organization of these aggregates and how it depends on the aggregation number and surfactant molecular structure. In the present paper we investigate the structural organization of some surfactants in vacuo by molecular dynamics and well-tempered metadynamics simulations to widely explore the space of their possible conformations in vacuo. To study how the specific molecular features of such compounds affect their organization, we have considered as paradigmatic surfactants, the anionic single-chain sodium dodecyl sulfate (SDS), the anionic double-chain sodium bis(2-ethylhexyl) sulfosuccinate (AOT) and the zwitterionic single-chain dodecyl phosphatidyl choline (DPC) within a wide aggregation number range (from 5 to 100). We observe that for low aggregation numbers the aggregates show in vacuo the typical structure of reverse micelles, while for large aggregation numbers a variety of globular aggregates occur that are characterized by the coexistence of interlaced domains formed by the polar or ionic heads and by the alkyl chains of the surfactants. Well-tempered metadynamics simulations allows us to confirm that the structural organizations obtained after 50 ns of molecular dynamics simulations are practically the equilibrium ones. Similarities and differences of surfactant aggregates in vacuo and in apolar media are also discussed. PMID:26050747

  10. Relationship between chemical structure and the occupational asthma hazard of low molecular weight organic compounds

    OpenAIRE

    Jarvis, J; Seed, M; Elton, R; Sawyer, L.; Agius, R.

    2005-01-01

    Aims: To investigate quantitatively, relationships between chemical structure and reported occupational asthma hazard for low molecular weight (LMW) organic compounds; to develop and validate a model linking asthma hazard with chemical substructure; and to generate mechanistic hypotheses that might explain the relationships.

  11. Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Réblová, K.; Štěpánek, Václav

    2015-01-01

    Roč. 35, December 2015 (2015), s. 21-38. ISSN 0031-5850 R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 ; RVO:61388971 Keywords : Barbatosphaeria * molecular systematic * ITS secondary structures Subject RIV: EF - Botanics; EE - Microbiology, Virology (MBU-M) Impact factor: 5.300, year: 2014

  12. Two-dimensional dynamics of a free molecular chain with a secondary structure

    DEFF Research Database (Denmark)

    Zolotaryuk, Alexander; Christiansen, Peter Leth; Savin, A.V.

    1996-01-01

    A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model of an anharmo...

  13. Efficient 3D Kinetic Monte Carlo Method for Modeling of Molecular Structure and Dynamics

    DEFF Research Database (Denmark)

    Panshenskov, Mikhail; Solov'yov, Ilia; Solov'yov, Andrey V.

    2014-01-01

    Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures...

  14. Structure and properties of simple molecular systems at very high density

    International Nuclear Information System (INIS)

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

  15. Revealing structural and dynamical properties of high density lipoproteins through molecular simulations

    DEFF Research Database (Denmark)

    Koivuniemi, A.; Vattulainen, I.

    2012-01-01

    essentially atomistic considerations of HDL particles over microsecond time scales, thereby proving substantial added value to experimental research. In this article, we discuss recent highlights concerning the structure and dynamics of HDL particles as revealed by atomistic and coarse-grained molecular...

  16. Structural investigation of bistrifluron using x-ray crystallography, NMR spectroscopy, and molecular modeling

    CERN Document Server

    Moon, J K; Rhee, S K; Kim, G B; Yun, H S; Chung, B J; Lee, S S; Lim, Y H

    2002-01-01

    A new insecticide, bistrifluron acts as an inhibitor of insect development and interferes with the cuticle formation of insects. Since it shows low acute oral and dermal toxicities, it can be one of potent insecticides. Based on X-ray crystallography, NMR spectroscopy and molecular modeling, the structural studies of bistrifluron have been carried out.

  17. Structure and Function: Insights into Bioinorganic Systems from Molecular Mechanics Calculations

    Science.gov (United States)

    Marques, Helder M.; Egan, Timothy J.; de Villiers, Katherine A.

    The use of empirical force field methods for modeling important systems in bioinorganic chemistry, including the cobalt corrins (derivatives of vitamin B12) and the iron porphyrins, is described. Particular attention is given to the use of molecular dynamics and simulated annealing calculations in exploring the solution structures of corrin, and those of likely complexes between the ferriprotoporphyrin-IX and the arylmethanol antimalarials.

  18. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    International Nuclear Information System (INIS)

    In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample

  19. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    Science.gov (United States)

    Wu, X.; Sha, W.

    2008-12-01

    In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample.

  20. Imidacloprid alters foraging and decreases bee avoidance of predators.

    Directory of Open Access Journals (Sweden)

    Ken Tan

    Full Text Available Concern is growing over the effects of neonicotinoid pesticides, which can impair honey bee cognition. We provide the first demonstration that sublethal concentrations of imidacloprid can harm honey bee decision-making about danger by significantly increasing the probability of a bee visiting a dangerous food source. Apis cerana is a native bee that is an important pollinator of agricultural crops and native plants in Asia. When foraging on nectar containing 40 µg/L (34 ppb imidacloprid, honey bees (Apis cerana showed no aversion to a feeder with a hornet predator, and 1.8 fold more bees chose the dangerous feeder as compared to control bees. Control bees exhibited significant predator avoidance. We also give the first evidence that foraging by A. cerana workers can be inhibited by sublethal concentrations of the pesticide, imidacloprid, which is widely used in Asia. Compared to bees collecting uncontaminated nectar, 23% fewer foragers returned to collect the nectar with 40 µg/L imidacloprid. Bees that did return respectively collected 46% and 63% less nectar containing 20 µg/L and 40 µg/L imidacloprid. These results suggest that the effects of neonicotinoids on honey bee decision-making and other advanced cognitive functions should be explored. Moreover, research should extend beyond the classic model, the European honey bee (A. mellifera, to other important bee species.

  1. Imidacloprid Alters Foraging and Decreases Bee Avoidance of Predators

    Science.gov (United States)

    Tan, Ken; Chen, Weiwen; Dong, Shihao; Liu, Xiwen; Wang, Yuchong; Nieh, James C.

    2014-01-01

    Concern is growing over the effects of neonicotinoid pesticides, which can impair honey bee cognition. We provide the first demonstration that sublethal concentrations of imidacloprid can harm honey bee decision-making about danger by significantly increasing the probability of a bee visiting a dangerous food source. Apis cerana is a native bee that is an important pollinator of agricultural crops and native plants in Asia. When foraging on nectar containing 40 µg/L (34 ppb) imidacloprid, honey bees (Apis cerana) showed no aversion to a feeder with a hornet predator, and 1.8 fold more bees chose the dangerous feeder as compared to control bees. Control bees exhibited significant predator avoidance. We also give the first evidence that foraging by A. cerana workers can be inhibited by sublethal concentrations of the pesticide, imidacloprid, which is widely used in Asia. Compared to bees collecting uncontaminated nectar, 23% fewer foragers returned to collect the nectar with 40 µg/L imidacloprid. Bees that did return respectively collected 46% and 63% less nectar containing 20 µg/L and 40 µg/L imidacloprid. These results suggest that the effects of neonicotinoids on honey bee decision-making and other advanced cognitive functions should be explored. Moreover, research should extend beyond the classic model, the European honey bee (A. mellifera), to other important bee species. PMID:25025334

  2. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: A non-equilibrium molecular dynamics study

    Science.gov (United States)

    Lemarchand, Claire A.; Bailey, Nicholas P.; Todd, Billy D.; Daivis, Peter J.; Hansen, Jesper S.

    2015-06-01

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. At a fixed temperature, the shear-shinning behavior is related not only to the inter- and intramolecular alignments of the solvent molecules but also to the decrease of the average size of the nanoaggregates at high shear rates. The variation of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex systems such as colloidal suspensions, polymer solutions, and associating polymer networks is discussed.

  3. Taxonomic notes on stingless bee Trigona (Tetragonula iridipennis Smith (Hymenoptera: Apidae from India

    Directory of Open Access Journals (Sweden)

    K. Vijayakumar

    2014-10-01

    Full Text Available Stingless Bees are a large and diverse taxon and more than 500 species are recorded worldwide.  Based on the previous reports, totally seven species are reported from India.  The present study reports male and female morphological characteristics of Tetragonula iridipennis belonging to Tetragonula subgenus in Nellithurai Village, Tamil Nadu, India.  The species of Tetragonula group are extremely similar in the external morphology of the workers. The glabrous bands on mesoscutum of female bees and structure and arrangement of gonostylus and the penis valve of male bees are used to separate T. iridipennis from other species in this group.  The identity of T. iridipennis is made based on the male and female key morphological characteristics in the previous literature.

  4. Theoretical Study of Donor - Spacer - Acceptor Structure Molecule for Molecular Rectifier

    Science.gov (United States)

    Mizuseki, Hiroshi; Kenji, Niimura; Belosludov, Rodion; Farajian, Amir; Kawazoe, Yoshiyuki

    2003-03-01

    Recently, the molecular electronics has attracted strong attention as a ``post-silicone technology'' to establish a future nanoscale electronic devices. To realize this molecular device, unimolecular rectifiering function is one of the most important constituents in nanotechnology [C. Majumder, H. Mizuseki, and Y. Kawazoe, Molecular Scale Rectifier: Theoretical Study, J. Phys. Chem. A, 105 (2001) 9454-9459.]. In the present study, the geometric and electronic structure of alkyl derivative C37H50N4O4 (PNX) molecule, (donor - spacer - acceptor), a leading candidate of molecular rectifying device, has been investigated theoretically using ab initio quantum mechanical calculation. The results suggest that in such donor-acceptor molecular complexes, while the lowest unoccupied orbital concentrates on the acceptor subunit, the highest occupied molecular orbital is localized on the donor subunit. The approximate potential differences for optimized PNX molecule have been estimated at the B3PW91/6-311g++(d,p) level of theory, which achieves quite good agreement with experimentally reported results. This study was performed through Special Coordination Funds for Promoting Science and Technology of the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government.

  5. Winter survival of individual honey bees and honey bee colonies depends on level of Varroa destructor infestation.

    Directory of Open Access Journals (Sweden)

    Coby van Dooremalen

    Full Text Available BACKGROUND: Recent elevated winter loss of honey bee colonies is a major concern. The presence of the mite Varroa destructor in colonies places an important pressure on bee health. V. destructor shortens the lifespan of individual bees, while long lifespan during winter is a primary requirement to survive until the next spring. We investigated in two subsequent years the effects of different levels of V. destructor infestation during the transition from short-lived summer bees to long-lived winter bees on the lifespan of individual bees and the survival of bee colonies during winter. Colonies treated earlier in the season to reduce V. destructor infestation during the development of winter bees were expected to have longer bee lifespan and higher colony survival after winter. METHODOLOGY/PRINCIPAL FINDINGS: Mite infestation was reduced using acaricide treatments during different months (July, August, September, or not treated. We found that the number of capped brood cells decreased drastically between August and November, while at the same time, the lifespan of the bees (marked cohorts increased indicating the transition to winter bees. Low V. destructor infestation levels before and during the transition to winter bees resulted in an increase in lifespan of bees and higher colony survival compared to colonies that were not treated and that had higher infestation levels. A variety of stress-related factors could have contributed to the variation in longevity and winter survival that we found between years. CONCLUSIONS/SIGNIFICANCE: This study contributes to theory about the multiple causes for the recent elevated colony losses in honey bees. Our study shows the correlation between long lifespan of winter bees and colony loss in spring. Moreover, we show that colonies treated earlier in the season had reduced V. destructor infestation during the development of winter bees resulting in longer bee lifespan and higher colony survival after winter.

  6. Colonies of Bumble Bees (Bombus impatiens Produce Fewer Workers, Less Bee Biomass, and Have Smaller Mother Queens Following Fungicide Exposure

    Directory of Open Access Journals (Sweden)

    Olivia M. Bernauer

    2015-06-01

    Full Text Available Bees provide vital pollination services to the majority of flowering plants in both natural and agricultural systems. Unfortunately, both native and managed bee populations are experiencing declines, threatening the persistence of these plants and crops. Agricultural chemicals are one possible culprit contributing to bee declines. Even fungicides, generally considered safe for bees, have been shown to disrupt honey bee development and impair bumble bee behavior. Little is known, however, how fungicides may affect bumble bee colony growth. We conducted a controlled cage study to determine the effects of fungicide exposure on colonies of a native bumble bee species (Bombus impatiens. Colonies of B. impatiens were exposed to flowers treated with field-relevant levels of the fungicide chlorothalonil over the course of one month. Colony success was assessed by the number and biomass of larvae, pupae, and adult bumble bees. Bumble bee colonies exposed to fungicide produced fewer workers, lower total bee biomass, and had lighter mother queens than control colonies. Our results suggest that fungicides negatively affect the colony success of a native bumble bee species and that the use of fungicides during bloom has the potential to severely impact the success of native bumble bee populations foraging in agroecosystems.

  7. Colonies of Bumble Bees (Bombus impatiens) Produce Fewer Workers, Less Bee Biomass, and Have Smaller Mother Queens Following Fungicide Exposure.

    Science.gov (United States)

    Bernauer, Olivia M; Gaines-Day, Hannah R; Steffan, Shawn A

    2015-01-01

    Bees provide vital pollination services to the majority of flowering plants in both natural and agricultural systems. Unfortunately, both native and managed bee populations are experiencing declines, threatening the persistence of these plants and crops. Agricultural chemicals are one possible culprit contributing to bee declines. Even fungicides, generally considered safe for bees, have been shown to disrupt honey bee development and impair bumble bee behavior. Little is known, however, how fungicides may affect bumble bee colony growth. We conducted a controlled cage study to determine the effects of fungicide exposure on colonies of a native bumble bee species (Bombus impatiens). Colonies of B. impatiens were exposed to flowers treated with field-relevant levels of the fungicide chlorothalonil over the course of one month. Colony success was assessed by the number and biomass of larvae, pupae, and adult bumble bees. Bumble bee colonies exposed to fungicide produced fewer workers, lower total bee biomass, and had lighter mother queens than control colonies. Our results suggest that fungicides negatively affect the colony success of a native bumble bee species and that the use of fungicides during bloom has the potential to severely impact the success of native bumble bee populations foraging in agroecosystems. PMID:26463198

  8. IR spectrum simulation of molecular structure model of Shendong coal vitrinite by using quantum chemistry method.

    Science.gov (United States)

    Jia, Jian-Bo; Wang, Ying; Li, Feng-Hai; Yi, Gui-Yun; Zeng, Fan-Gui; Guo, Hong-Yu

    2014-01-01

    The structure of coal needs to be understood from a molecular point of view for clean, effective and high value-added utilization of coal. In the literature, molecular structure model of Shendong coal vitrinite (SV) was established by the authors on the basis of experimental results of ultimate analysis and 13C NMR, and the calculated 13C NMR spectrum of SV model was consistent with the experimental spectrum. In order to further verify the accuracy of SV structure model established by the authors, the infrared spectrum of SV structure model was calculated using quantum chemistry semi-empirical VAMP in this thesis. The results showed that the peak shape of calculated IR spectrum of SV structure model was similar to the experiment's, but the wave number of calculated IR spectrum was obviously higher than that of experimental spectrum. According to the calculated results for model compounds by using the same method, calculated vibrational frequency was higher than that of experiment for the same functional groups. Hence, the calculated IR spectrum should be corrected. After correction the calculated IR spectrum of SV structure model matched well with the experimental spectrum. In other words, the SV structure model can truly reflect the structure characteristics of SV. PMID:24783531

  9. SGC method for predicting the standard enthalpy of formation of pure compounds from their molecular structures

    International Nuclear Information System (INIS)

    Highlights: • ΔH°f is predicted from the molecular structure of the compounds alone. • ANN-SGC model predicts ΔH°f with a correlation coefficient of 0.99. • ANN-MNLR model predicts ΔH°f with a correlation coefficient of 0.90. • Better definition of the atom-type molecular groups is presented. • The method is better than others in terms of combined simplicity, accuracy and generality. - Abstract: A theoretical method for predicting the standard enthalpy of formation of pure compounds from various chemical families is presented. Back propagation artificial neural networks were used to investigate several structural group contribution (SGC) methods available in literature. The networks were used to probe the structural groups that have significant contribution to the overall enthalpy of formation property of pure compounds and arrive at the set of groups that can best represent the enthalpy of formation for about 584 substances. The 51 atom-type structural groups listed provide better definitions of group contributions than others in the literature. The proposed method can predict the standard enthalpy of formation of pure compounds with an AAD of 11.38 kJ/mol and a correlation coefficient of 0.9934 from only their molecular structure. The results are further compared with those of the traditional SGC method based on MNLR as well as other methods in the literature

  10. Structure and stability of copper clusters: A tight-binding molecular dynamics study

    International Nuclear Information System (INIS)

    In this paper we propose a tight-binding molecular dynamics with parameters fitted to first-principles calculations on the smaller clusters and with an environment correction, to be a powerful technique for studying large transition-metal/noble-metal clusters. In particular, the structure and stability of Cun clusters for n=3-55 are studied by using this technique. The results for small Cun clusters (n=3-9) show good agreement with ab initio calculations and available experimental results. In the size range 10≤n≤55 most of the clusters adopt icosahedral structure which can be derived from the 13-atom icosahedron, the polyicosahedral 19-, 23-, and 26-atom clusters, and the 55-atom icosahedron, by adding or removing atoms. However, a local geometrical change from icosahedral to decahedral structure is observed for n=40-44 and return to the icosahedral growth pattern is found at n=45 which continues. Electronic 'magic numbers' ( n=2, 8, 20, 34, 40) in this regime are correctly reproduced. Due to electron pairing in highest occupied molecular orbitals (HOMOs), even-odd alternation is found. A sudden loss of even-odd alternation in second difference of cluster binding energy, HOMO-LUMO (LUMO, lowest unoccupied molecular orbital) gap energy and ionization potential is observed in the region n∼40 due to structural change there. Interplay between electronic and geometrical structure is found

  11. SGC method for predicting the standard enthalpy of formation of pure compounds from their molecular structures

    Energy Technology Data Exchange (ETDEWEB)

    Albahri, Tareq A., E-mail: toalbahri@gmail.com; Aljasmi, Abdulla F.

    2013-09-20

    Highlights: • ΔH°{sub f} is predicted from the molecular structure of the compounds alone. • ANN-SGC model predicts ΔH°{sub f} with a correlation coefficient of 0.99. • ANN-MNLR model predicts ΔH°{sub f} with a correlation coefficient of 0.90. • Better definition of the atom-type molecular groups is presented. • The method is better than others in terms of combined simplicity, accuracy and generality. - Abstract: A theoretical method for predicting the standard enthalpy of formation of pure compounds from various chemical families is presented. Back propagation artificial neural networks were used to investigate several structural group contribution (SGC) methods available in literature. The networks were used to probe the structural groups that have significant contribution to the overall enthalpy of formation property of pure compounds and arrive at the set of groups that can best represent the enthalpy of formation for about 584 substances. The 51 atom-type structural groups listed provide better definitions of group contributions than others in the literature. The proposed method can predict the standard enthalpy of formation of pure compounds with an AAD of 11.38 kJ/mol and a correlation coefficient of 0.9934 from only their molecular structure. The results are further compared with those of the traditional SGC method based on MNLR as well as other methods in the literature.

  12. POLLUTION MONITORING OF PUGET SOUND WITH HONEY BEES

    Science.gov (United States)

    To show that honey bees are effective biological monitors of environmental contaminants over large geographic areas, beekeepers of Puget Sound, Washington, collected pollen and bees for chemical analysis. From these data, kriging maps of arsenic, cadmium, and fluoride were genera...

  13. Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

    CERN Document Server

    Singh, Raghvendra Pratap; Cleri, Fabrizio

    2013-01-01

    We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to...

  14. Structure-activity relationship study between baicalein and wogonin by spectrometry, molecular docking and microcalorimetry.

    Science.gov (United States)

    Tu, Bao; Li, Rong-Rong; Liu, Zhi-Juan; Chen, Zhi-Feng; Ouyang, Yu; Hu, Yan-Jun

    2016-10-01

    Flavones (e.g. baicalein and wogonin) extensively used worldwide in food preparation and traditional medicine. In this study, a systematically comparative study of their structure-activity relationships (SAR) on their interaction with BSA, antioxidant activity and antibacterial activity has been carried out by spectrometry, molecular docking and microcalorimetry. Our results show that the skeleton structure of flavones, the number of hydroxyl groups, the type of functional group, conjugated system and the steric hindrance may be responsible for their different biological activity. These findings not only would lay a scientific foundation for discovering and designing flavones-based food and drug, may also help us to understanding the structure-activity relationship between flavones at the molecular level. PMID:27132840

  15. Molecular Dynamics Study of Carbon Nanotubes/Polyamide Reverse Osmosis Membranes: Polymerization, Structure, and Hydration.

    Science.gov (United States)

    Araki, Takumi; Cruz-Silva, Rodolfo; Tejima, Syogo; Takeuchi, Kenji; Hayashi, Takuya; Inukai, Shigeki; Noguchi, Toru; Tanioka, Akihiko; Kawaguchi, Takeyuki; Terrones, Mauricio; Endo, Morinobu

    2015-11-11

    Carbon nanotubes/polyamide (PA) nanocomposite thin films have become very attractive as reverse osmosis (RO) membranes. In this work, we used molecular dynamics to simulate the influence of single walled carbon nanotubes (SWCNTs) in the polyamide molecular structure as a model case of a carbon nanotubes/polyamide nanocomposite RO membrane. It was found that the addition of SWCNTs decreases the pore size of the composite membrane and increases the Na and Cl ion rejection. Analysis of the radial distribution function of water confined in the pores of the membranes shows that SWCNT+PA nanocomposite membranes also exhibit smaller clusters of water molecules within the membrane, thus suggesting a dense membrane structure (SWCNT+PA composite membranes were 3.9% denser than bare PA). The results provide new insights into the fabrication of novel membranes reinforced with tubular structures for enhanced desalination performance. PMID:26505521

  16. Low Cost ZigBee Protocol Based Laboratory Platforms

    Directory of Open Access Journals (Sweden)

    Alvaro Romero-Acero

    2013-11-01

    Full Text Available This paper presents a low cost wireless communication platform, based on the ZigBee protocol. It is designed with the purpose to strengthen the use of information technology in the classroom. Guides laboratory practices are focused on developing undergraduate engineering students to the area of telecommunications. The platform structure is composed of: Labs custom designed, web tools embedded wireless communication system for data acquisition in real time, and the Human Machine Interface (HMI, which records analog data and digital. 

  17. Molecular dynamics simulations of silicate and borate glasses and melts : structure, diffusion dynamics and vibrational properties

    OpenAIRE

    Scherer, Christoph

    2015-01-01

    Molecular dynamics simulations of silicate and borate glasses and melts: Structure, diffusion dynamics and vibrational properties. In this work computer simulations of the model glass formers SiO2 and B2O3 are presented, using the techniques of classical molecular dynamics (MD) simulations and quantum mechanical calculations, based on density functional theory (DFT). The latter limits the system size to about 100−200 atoms. SiO2 and B2O3 are the two most important network formers for industri...

  18. Molecular size distribution and structure investigations of humic substances in groundwater

    International Nuclear Information System (INIS)

    A non-ionic macroporous polymeric sorbent DAX-8 was applied to the isolation of humic and fulvic acids from groundwater. This procedure was able to isolate approximately 40% of the DOC as humic solutes. For the investigation of the structure and molecular size distribution of the isolated humic solutes, the hyphenated SEC-ESIMS system with a quadrupole mass spectrometer and a UV detector were utilized. For the higher-molecular-weight humic acids, the ESI-MS loses sensitivity compared with the parallel UV detection, because of the difficulty in getting the ionized humic compounds to fly efficiently through the mass spectrometer. (orig.)

  19. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity.

    Science.gov (United States)

    Hao, Yajiang; Inhester, Ludger; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-07-01

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging. PMID:26798806

  20. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    CERN Document Server

    Hao, Yajiang; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-01-01

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.