WorldWideScience

Sample records for symbiont function identification

  1. Towards a molecular understanding of symbiont function: identification of a fungal gene for the degradation of xylan in the fungus gardens of leaf-cutting ants

    DEFF Research Database (Denmark)

    Schiøtt, Morten; De Fine Licht, Henrik H; Lange, Lene

    2008-01-01

    -substrate degradation in fungus gardens is a multi-step process comparable to normal biodegradation of organic matter in soil ecosystems, but with the crucial difference that a single fungal symbiont realizes most of the steps that are normally provided by a series of microorganisms that colonize fallen leaves...... in the fungus gardens in order to investigate the dynamics of degradation activities. RESULTS: We cloned a xylanase gene from the mutualistic fungus of Acromyrmex echinatior, determined its protein sequence, and inserted it in a yeast expression vector to confirm its substrate specificity. Our results show...... that the fungus has a functional xylanase gene. We also show by lab experiments in vivo that the activity of fungal xylanase and cellulase is not evenly distributed, but concentrated in the lower layer of fungus gardens, with only modest activity in the middle layer where gongylidia are produced and intermediate...

  2. Pigments Characterization and Molecular Identification of Bacterial Symbionts of Brown Algae Padinasp. Collected from Karimunjawa Island

    Directory of Open Access Journals (Sweden)

    Damar Bayu Murti

    2016-06-01

    Full Text Available The search for carotenoids in nature has been extensively studied because of their applications in foods. One treasure of the biopigment source is symbiotic-microorganisms with marine biota. The advantages of symbiont bacteria are easy to culture and sensitize pigments. The use of symbiont bacteria helps to conserve fish, coral reefs, seagrass, and seaweed. Therefore, the bacteria keeps their existence in their ecosystems. In this study, bacterial symbionts were successfully isolated from brown algae Padina sp. The bacterial symbionts had yellow pigment associated with carotenoids. The pigments were characterized using High Performance Liquid Chromatography (HPLC with a Photo Diode Array (PDA detector. The carotenoid pigments in the bacterial symbionts were identified as dinoxanthin, lutein and neoxanthin. Molecular identification by using a 16S rRNA gene sequence method, reveals that the bacterial symbionts were closely related to Bacillus marisflavi with a homology of 99%. Keywords :carotenoid pigments, brown algae, Padina, bacterial symbionts, 16S rRNA

  3. Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts.

    Science.gov (United States)

    Fan, Lu; Reynolds, David; Liu, Michael; Stark, Manuel; Kjelleberg, Staffan; Webster, Nicole S; Thomas, Torsten

    2012-07-03

    Microorganisms often form symbiotic relationships with eukaryotes, and the complexity of these relationships can range from those with one single dominant symbiont to associations with hundreds of symbiont species. Microbial symbionts occupying equivalent niches in different eukaryotic hosts may share functional aspects, and convergent genome evolution has been reported for simple symbiont systems in insects. However, for complex symbiont communities, it is largely unknown how prevalent functional equivalence is and whether equivalent functions are conducted by evolutionarily convergent mechanisms. Sponges represent an evolutionarily divergent group of species with common physiological and ecological traits. They also host complex communities of microbial symbionts and thus are the ideal model to test whether functional equivalence and evolutionary convergence exist in complex symbiont communities across phylogenetically divergent hosts. Here we use a sampling design to determine the phylogenetic and functional profiles of microbial communities associated with six sponge species. We identify common functions in the six microbiomes, demonstrating the existence of functional equivalence. These core functions are consistent with our current understanding of the biological and ecological roles of sponge-associated microorganisms and also provide insight into symbiont functions. Importantly, core functions also are provided in each sponge species by analogous enzymes and biosynthetic pathways. Moreover, the abundance of elements involved in horizontal gene transfer suggests their key roles in the genomic evolution of symbionts. Our data thus demonstrate evolutionary convergence in complex symbiont communities and reveal the details and mechanisms that underpin the process.

  4. Exploration, Isolation, and Identification of Carotenoid from Bacterial Symbiont of Sponge Callyspongia vaginalis

    Directory of Open Access Journals (Sweden)

    Iqna Kamila Abfa

    2017-06-01

    Full Text Available During the past two decades research on marine bacteria has highlighted the tremendous potential of symbiotic-microorganisms as a source of bioactive secondary. One of the potential of the bacterial symbionts is producing a natural pigment, and these organisms can be used as a sustainable source of natural pigments. Carotenoid is one of the most important pigments that has important roles in physiological and molecular processes of microorganisms, as well as for human health. The objective of this study is to analyze carotenoid pigments from marine bacterial symbionts from sponge and to identify bacterial symbionts that produce carotenoid pigments. Pigment analysis was performed by a UV-VIS spectrophotometer and High Performance Liquid Chromatography (HPLC. Molecular bacterial identification was performed based on 16S rDNA sequence. The isolation of bacterial symbionts from C. vaginalison Zobell 2216E medium resulted in one bacterium, CB-SP5, positively synthesized carotenoids. By reverse phase HPLC analysis, the carotenoid pigments in the bacterial symbionts were identified as diadinoxanthin, fucoxanthin, neoxanthin, dinoxanthin, anddiadinochrome. CB-SP5 shared the highest level of 16S rDNA gene sequence similarity with Psychrobacter celer (99%.   Keywords : carotenoid, sponge, bacterial symbiont, 16S rDNA.

  5. Combined thermal and herbicide stress in functionally diverse coral symbionts.

    Science.gov (United States)

    van Dam, J W; Uthicke, S; Beltran, V H; Mueller, J F; Negri, A P

    2015-09-01

    Most reef building corals rely on symbiotic microalgae (genus Symbiodinium) to supply a substantial proportion of their energy requirements. Functional diversity of different Symbiodinium genotypes, endorsing the host with physiological advantages, has been widely reported. Yet, the influence of genotypic specificity on the symbiont's susceptibility to contaminants or cumulative stressors is unknown. Cultured Symbiodinium of presumed thermal-tolerant clade D tested especially vulnerable to the widespread herbicide diuron, suggesting important free-living populations may be at risk in areas subjected to terrestrial runoff. Co-exposure experiments where cultured Symbiodinium were exposed to diuron over a thermal stress gradient demonstrated how fast-growing clade C1 better maintained photosynthetic capability than clade D. The mixture toxicity model of Independent Action, considering combined thermal stress and herbicide contamination, revealed response additivity for inhibition of photosynthetic yield in both tested cultures, emphasizing the need to account for cumulative stressor impacts in ecological risk assessment and resource management. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  6. Combined thermal and herbicide stress in functionally diverse coral symbionts

    International Nuclear Information System (INIS)

    Dam, J.W. van; Uthicke, S.; Beltran, V.H.; Mueller, J.F.; Negri, A.P.

    2015-01-01

    Most reef building corals rely on symbiotic microalgae (genus Symbiodinium) to supply a substantial proportion of their energy requirements. Functional diversity of different Symbiodinium genotypes, endorsing the host with physiological advantages, has been widely reported. Yet, the influence of genotypic specificity on the symbiont's susceptibility to contaminants or cumulative stressors is unknown. Cultured Symbiodinium of presumed thermal-tolerant clade D tested especially vulnerable to the widespread herbicide diuron, suggesting important free-living populations may be at risk in areas subjected to terrestrial runoff. Co-exposure experiments where cultured Symbiodinium were exposed to diuron over a thermal stress gradient demonstrated how fast-growing clade C1 better maintained photosynthetic capability than clade D. The mixture toxicity model of Independent Action, considering combined thermal stress and herbicide contamination, revealed response additivity for inhibition of photosynthetic yield in both tested cultures, emphasizing the need to account for cumulative stressor impacts in ecological risk assessment and resource management. - Highlights: • Water quality influences thermal stress thresholds in different Symbiodinium types. • Photosystem of clade D tested more sensitive than C1 to a common herbicide. • Increased thermal tolerance quickly countered in presence of herbicide. • Mixture toxicity approach demonstrated response additivity for combined stressors. • Symbiotic partnership may be compromised in areas subjected to terrestrial runoff. - Thermal-tolerant Symbiodinium type D tested especially vulnerable to a common herbicide, emphasizing the significance of cumulative stressors in ecological risk management

  7. Evolution and function of eukaryotic-like proteins from sponge symbionts.

    Science.gov (United States)

    Reynolds, David; Thomas, Torsten

    2016-10-01

    Sponges (Porifera) are ancient metazoans that harbour diverse microorganisms, whose symbiotic interactions are essential for the host's health and function. Although symbiosis between bacteria and sponges are ubiquitous, the molecular mechanisms that control these associations are largely unknown. Recent (meta-) genomic analyses discovered an abundance of genes encoding for eukaryotic-like proteins (ELPs) in bacterial symbionts from different sponge species. ELPs belonging to the ankyrin repeat (AR) class from a bacterial symbiont of the sponge Cymbastela concentrica were subsequently found to modulate amoebal phagocytosis. This might be a molecular mechanism, by which symbionts can control their interaction with the sponge. In this study, we investigated the evolution and function of ELPs from other classes and from symbionts found in other sponges to better understand the importance of ELPs for bacteria-eukaryote interactions. Phylogenetic analyses showed that all of the nine ELPs investigated were most closely related to proteins found either in eukaryotes or in bacteria that can live in association with eukaryotes. ELPs were then recombinantly expressed in Escherichia coli and exposed to the amoeba Acanthamoeba castellanii, which is functionally analogous to phagocytic cells in sponges. Phagocytosis assays with E. coli containing three ELP classes (AR, TPR-SEL1 and NHL) showed a significantly higher percentage of amoeba containing bacteria and average number of intracellular bacteria per amoeba when compared to negative controls. The result that various classes of ELPs found in symbionts of different sponges can modulate phagocytosis indicates that they have a broader function in mediating bacteria-sponge interactions. © 2016 John Wiley & Sons Ltd.

  8. Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution

    OpenAIRE

    McCutcheon, John P.; Moran, Nancy A.

    2010-01-01

    The main genomic changes in the evolution of host-restricted microbial symbionts are ongoing inactivation and loss of genes combined with rapid sequence evolution and extreme structural stability; these changes reflect high levels of genetic drift due to small population sizes and strict clonality. This genomic erosion includes irreversible loss of genes in many functional categories and can include genes that underlie the nutritional contributions to hosts that are the basis of the symbiotic...

  9. Identification of Antipathogenic Bacterial Coral Symbionts Against Porites Ulcerative White Spots Disease

    Science.gov (United States)

    Sa’adah, Nor; Sabdono, Agus; Diah Permata Wijayanti, dan

    2018-02-01

    Coral reef ecosystems are ecosystems that are vulnerable and susceptible to damage due to the exploitation of ocean resources. One of the factors that cause coral damage is the disease that attacks the coral. Porites Ulcerative White Spots (PUWS) is a coral disease found in Indonesia and attacks the coral genera Porites allegedly caused by pathogenic microbial attacks. The purpose of this study was to identify the symbiotic bacteria on healthy coral that have antipatogenic potency against PUWS. The method used in this research was descriptive explorative. Sampling was done in Kemujan Island, Karimunjawa. Bacteria were isolated from healthy coral and coral affected by PUWS disease. Streak method was used to purify coral bacteria, while overlay and agar diffusion were used to test antipathogenic activity. Bacterial identification was carried out based on polyphasic approach. The results of this study showed that coral bacterial symbionts have antipathogenic activity against PUWS disease. The selected bacteria NM 1.2, NM 1.3 and KPSH 5. NM1.2 were closely related to Pseudoalteromonas piscicida, Pseudoalteromonas flavipulchra and Bacillus flexus, respectively.

  10. Molecular identification of symbionts from the pulmonate snail Biomphalaria glabrata in Brazil.

    Science.gov (United States)

    Hertel, Lynn A; Barbosa, Contança S; Santos, Ricardo A A L; Loker, Eric S

    2004-08-01

    The icthyosporean, Capsaspora owczarzaki, a known predator of Schistosoma mansoni sporocysts in vitro, is more prevalent in laboratory-reared strains of the intermediate snail host, Biomphalaria glabrata resistant to S. mansoni, than from the susceptible M line strain. We examined whether B. glabrata resistant to the NIH-PR-1 strain of S. mansoni from 2 regions in Brazil were also host to C. owczarzaki. Symbiont presence was examined using hemolymph culturing and nested polymerase chain reaction of snail genomic DNA with primers designed to specifically amplify sequences from relatives of the Icthyosporea. All B. glabrata of the resistant Salvador strain from the laboratory of Dr. Lobato Paraense in Rio de Janeiro, Brazil (n = 46) tested negative for symbionts. Three of 18 semiresistant 10-R2 B. glabrata from the laboratory of Dr. Barbosa in Recife, Brazil tested positive for C. owczarzaki. Another icthyosporean, Anurofeca sp., was identified from 1, 10-R2 snail and from 2 of 12 field-collected B. glabrata from Praia do Forte Orange, Ilha de Itamaracá. Snails from 2 other sites, Hotel Colibri, Pontezinha and Praia do Sossego, Ilha de Itamaracá, were negative for Anurofeca. Two genera of ciliates were also identified. Paruroleptus sp. was found in 4, 10-R2 snails and Trichodina sp. was identified in 2 field-collected snails from Praia do Forte Orange and Praia do Sossego.

  11. Phosphatidylinositol 3-kinase function at very early symbiont perception: a local nodulation control under stress conditions?

    Science.gov (United States)

    Robert, Germán; Muñoz, Nacira; Alvarado-Affantranger, Xochitl; Saavedra, Laura; Davidenco, Vanina; Rodríguez-Kessler, Margarita; Estrada-Navarrete, Georgina; Sánchez, Federico; Lascano, Ramiro

    2018-04-09

    Root hair curling is an early and essential morphological change required for the success of the symbiotic interaction between legumes and rhizobia. At this stage rhizobia grow as an infection thread within root hairs and are internalized into the plant cells by endocytosis, where the PI3K enzyme plays important roles. Previous observations show that stress conditions affect early stages of the symbiotic interaction, from 2 to 30 min post-inoculation, which we term as very early host responses, and affect symbiosis establishment. Herein, we demonstrated the relevance of the very early host responses for the symbiotic interaction. PI3K and the NADPH oxidase complex are found to have key roles in the microsymbiont recognition response, modulating the apoplastic and intracellular/endosomal ROS induction in root hairs. Interestingly, compared with soybean mutant plants that do not perceive the symbiont, we demonstrated that the very early symbiont perception under sublethal saline stress conditions induced root hair death. Together, these results highlight not only the importance of the very early host-responses on later stages of the symbiont interaction, but also suggest that they act as a mechanism for local control of nodulation capacity, prior to the abortion of the infection thread, preventing the allocation of resources/energy for nodule formation under unfavorable environmental conditions.

  12. Delivery of a functional anti-trypanosome Nanobody in different tsetse fly tissues via a bacterial symbiont, Sodalis glossinidius.

    Science.gov (United States)

    De Vooght, Linda; Caljon, Guy; De Ridder, Karin; Van Den Abbeele, Jan

    2014-11-07

    Sodalis glossinidius, a vertically transmitted microbial symbiont of the tsetse fly, is currently considered as a potential delivery system for anti-trypanosomal components that reduce or eliminate the capability of the tsetse fly host to transmit parasitic trypanosomes, an approach also known as paratransgenesis. An essential step in developing paratransgenic tsetse is the stable colonization of adult flies and their progeny with recombinant Sodalis bacteria, expressing trypanocidal effector molecules in tissues where the parasite resides. In this study, Sodalis was tested for its ability to deliver functional anti-trypanosome nanobodies (Nbs) in Glossina morsitans morsitans. We characterized the in vitro and in vivo stability of recombinant Sodalis (recSodalis) expressing a potent trypanolytic nanobody, i.e. Nb_An46. We show that recSodalis is competitive with WT Sodalis in in vivo conditions and that tsetse flies transiently cleared of their endogenous WT Sodalis population can be successfully repopulated with recSodalis at high densities. In addition, vertical transmission to the offspring was observed. Finally, we demonstrated that recSodalis expressed significant levels (ng range) of functional Nb_An46 in different tsetse fly tissues, including the midgut where an important developmental stage of the trypanosome parasite occurs. We demonstrated the proof-of-concept that the Sodalis symbiont can be genetically engineered to express and release significant amounts of functional anti-trypanosome Nbs in different tissues of the tsetse fly. The application of this innovative concept of using pathogen-targeting nanobodies delivered by insect symbiotic bacteria could be extended to other vector-pathogen systems.

  13. Mesophotic coral depth acclimatization is a function of host-specific symbiont physiology

    KAUST Repository

    Ziegler, Maren

    2015-02-06

    Mesophotic coral ecosystems receive increasing attention owing to their potential as deep coral refuges in times of global environmental change. Here, the mechanisms of coral holobiont photoacclimatization over a 60 m depth gradient in the central Red Sea were examined for the four coral genera Porites, Leptoseris, Pachyseris, and Podabacia. General acclimatization strategies were common to all host-symbiont combinations, e.g., Symbiodinium cell densities and photoprotective (PP) to light-harvesting pigment ratios both significantly decreased with water depth. Porites harbored Symbiodinium type C15 over the whole 60 m depth range, while Pachyseris and Podabacia had limited vertical distributions and hosted mainly Symbiodinium type C1. Symbiodinium type C15 had generally higher xanthophyll de-epoxidation rates and lower maximum quantum yields than C1, and also exhibited a strong photoacclimatory signal over depth that relates to the large distribution range of Porites. Interestingly, the coral host had an effect on Symbiodinium pigment composition. When comparing Symbiodinium type C1 in Podabacia and Pachyseris, the ß-carotene chl a−1, the peridinin chl a−1, and diadinoxanthin chl a−1 ratios were significantly different between host species. Our data support a view that depth acclimatization of corals in the mesophotics is facilitated by Symbiodinium physiology, which in turn is host-specific.

  14. Identification and characterization of a novel porin family highlights a major difference in the outer membrane of chlamydial symbionts and pathogens.

    Directory of Open Access Journals (Sweden)

    Karin Aistleitner

    Full Text Available The Chlamydiae constitute an evolutionary well separated group of intracellular bacteria comprising important pathogens of humans as well as symbionts of protozoa. The amoeba symbiont Protochlamydia amoebophila lacks a homologue of the most abundant outer membrane protein of the Chlamydiaceae, the major outer membrane protein MOMP, highlighting a major difference between environmental chlamydiae and their pathogenic counterparts. We recently identified a novel family of putative porins encoded in the genome of P. amoebophila by in silico analysis. Two of these Protochlamydiaouter membrane proteins, PomS (pc1489 and PomT (pc1077, are highly abundant in outer membrane preparations of this organism. Here we show that all four members of this putative porin family are toxic when expressed in the heterologous host Escherichia coli. Immunofluorescence analysis using antibodies against heterologously expressed PomT and PomS purified directly from elementary bodies, respectively, demonstrated the location of both proteins in the outer membrane of P. amoebophila. The location of the most abundant protein PomS was further confirmed by immuno-transmission electron microscopy. We could show that pomS is transcribed, and the corresponding protein is present in the outer membrane throughout the complete developmental cycle, suggesting an essential role for P. amoebophila. Lipid bilayer measurements demonstrated that PomS functions as a porin with anion-selectivity and a pore size similar to the Chlamydiaceae MOMP. Taken together, our results suggest that PomS, possibly in concert with PomT and other members of this porin family, is the functional equivalent of MOMP in P. amoebophila. This work contributes to our understanding of the adaptations of symbiotic and pathogenic chlamydiae to their different eukaryotic hosts.

  15. Molecular identification of marine symbiont bacteria of gastropods from the waters of the Krakal coast Yogyakarta and its potential as a Multi-Drug Resistant (MDR) antibacterial agent

    Science.gov (United States)

    Bahry, Muhammad Syaifudien; Pringgenies, Delianis; Trianto, Agus

    2017-01-01

    The resistance of pathogenic bacteria may occur to many types of antibiotics, especially in cases of non-compliance use of antibiotics, which likely to allow the evolution of Multi-Drug Resistant (MDR) bacteria. Gastropods seas are marine invertebrates informed capable of production of secondary metabolites as antibacterial MDR. The purpose of the study was the isolation and identification of gastropod symbiont bacteria found in the waters of Krakal, Gunung Kidul, Yogyakarta, which has the ability to produce antibacterial compounds against MDR(Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae, MRSA (methicillin-Resistant Staphylococcus aureus), Staphylococcus aureus, and Staphylococcus homunis) molecular. Stages of this research began with the isolation of bacteria, bacteria screening for anti-MDR compound, mass culture, and extraction, antibacterial activity test, DNA extraction, amplification by PCR 16S rDNA and sequencing. The results of the study showed that 19 isolates of bacteria were isolated from three species of gastropods namely Littorina scabra, Cypraea moneta and Conus ebraeus. Among them, 4 isolates showed activity against MDR test bacteria (E. coli, E. cloacae, K. pneumoniae, S. aureus and S. homunis). The highest activity was displayed by code LS.G1.8 isolate with the largest inhibition zone 15.47±0.45mm on S. humonis at 250 µg/disk concentration. Isolate CM.G2.1 showed largest inhibition zone, with 21.5±0.07mm on MRSA at 1000 µg/disk concentration and isolate the largest inhibition zone CM.G2.5 14.37±0.81mm on MRSA 14.37±0.81mm at concentrations 1000 µg/disk. The molecular identification of isolates LS.G1.8 has 99% homology with Bacillus subtilis and isolates CM.G2.1 has 99% homology with Bacillus pumillus.

  16. Aphid Heritable Symbiont Exploits Defensive Mutualism.

    Science.gov (United States)

    Doremus, Matthew R; Oliver, Kerry M

    2017-04-15

    Insects and other animals commonly form symbioses with heritable bacteria, which can exert large influences on host biology and ecology. The pea aphid, Acyrthosiphon pisum , is a model for studying effects of infection with heritable facultative symbionts (HFS), and each of its seven common HFS species has been reported to provide resistance to biotic or abiotic stresses. However, one common HFS, called X-type, rarely occurs as a single infection in field populations and instead typically superinfects individual aphids with Hamiltonella defensa , another HFS that protects aphids against attack by parasitic wasps. Using experimental aphid lines comprised of all possible infection combinations in a uniform aphid genotype, we investigated whether the most common strain of X-type provides any of the established benefits associated with aphid HFS as a single infection or superinfection with H. defensa We found that X-type does not confer protection to any tested threats, including parasitoid wasps, fungal pathogens, or thermal stress. Instead, component fitness assays identified large costs associated with X-type infection, costs which were ameliorated in superinfected aphids. Together these findings suggest that X-type exploits the aphid/ H. defensa mutualism and is maintained primarily as a superinfection by "hitchhiking" via the mutualistic benefits provided by another HFS. Exploitative symbionts potentially restrict the functions and distributions of mutualistic symbioses with effects that extend to other community members. IMPORTANCE Maternally transmitted bacterial symbionts are widespread and can have major impacts on the biology of arthropods, including insects of medical and agricultural importance. Given that host fitness and symbiont fitness are tightly linked, inherited symbionts can spread within host populations by providing beneficial services. Many insects, however, are frequently infected with multiple heritable symbiont species, providing potential

  17. Metabolomic profiling of 13C-labelled cellulose digestion in a lower termite: insights into gut symbiont function

    Science.gov (United States)

    Tokuda, Gaku; Tsuboi, Yuuri; Kihara, Kumiko; Saitou, Seikou; Moriya, Sigeharu; Lo, Nathan; Kikuchi, Jun

    2014-01-01

    Termites consume an estimated 3–7 billion tonnes of lignocellulose annually, a role in nature which is unique for a single order of invertebrates. Their food is digested with the help of microbial symbionts, a relationship that has been recognized for 200 years and actively researched for at least a century. Although DNA- and RNA-based approaches have greatly refined the details of the process and the identities of the participants, the allocation of roles in space and time remains unclear. To resolve this issue, a pioneer study is reported using metabolomics to chart the in situ catabolism of 13C-cellulose fed to the dampwood species Hodotermopsis sjostedti. The results confirm that the secretion of endogenous cellulases by the host may be significant to the digestive process and indicate that a major contribution by hindgut bacteria is phosphorolysis of cellodextrins or cellobiose. This study provides evidence that essential amino acid acquisition by termites occurs following the lysis of microbial tissue obtained via proctodaeal trophallaxis. PMID:25009054

  18. Differential temporal changes of primary and secondary bacterial symbionts and whitefly host fitness following antibiotic treatments

    Science.gov (United States)

    Zhang, Chang-Rong; Shan, Hong-Wei; Xiao, Na; Zhang, Fan-Di; Wang, Xiao-Wei; Liu, Yin-Quan; Liu, Shu-Sheng

    2015-01-01

    Where multiple symbionts coexist in the same host, the selective elimination of a specific symbiont may enable the roles of a given symbiont to be investigated. We treated the Mediterranean species of the whitefly Bemisia tabaci complex by oral delivery of the antibiotic rifampicin, and then examined the temporal changes of its primary symbiont “Candidatus Portiera aleyrodidarum” and secondary symbiont “Ca. Hamiltonella defensa” as well as host fitness for three generations. In adults treated with rifampicin (F0), the secondary symbiont was rapidly reduced, approaching complete disappearance as adults aged. In contrast, the primary symbiont was little affected until later in the adult life. In the offspring of these adults (F1), both symbionts were significantly reduced and barely detectable when the hosts reached the adult stage. The F1 adults laid few eggs (F2), all of which failed to hatch. Mating experiments illustrated that the negative effects of rifampicin on host fitness were exerted via female hosts but not males. This study provides the first evidence of differential temporal reductions of primary and secondary symbionts in whiteflies following an antibiotic treatment. Studies that disrupt functions of bacterial symbionts must consider their temporal changes. PMID:26510682

  19. Hazard identification based on plant functional modelling

    International Nuclear Information System (INIS)

    Rasmussen, B.; Whetton, C.

    1993-10-01

    A major objective of the present work is to provide means for representing a process plant as a socio-technical system, so as to allow hazard identification at a high level. The method includes technical, human and organisational aspects and is intended to be used for plant level hazard identification so as to identify critical areas and the need for further analysis using existing methods. The first part of the method is the preparation of a plant functional model where a set of plant functions link together hardware, software, operations, work organisation and other safety related aspects of the plant. The basic principle of the functional modelling is that any aspect of the plant can be represented by an object (in the sense that this term is used in computer science) based upon an Intent (or goal); associated with each Intent are Methods, by which the Intent is realized, and Constraints, which limit the Intent. The Methods and Constraints can themselves be treated as objects and decomposed into lower-level Intents (hence the procedure is known as functional decomposition) so giving rise to a hierarchical, object-oriented structure. The plant level hazard identification is carried out on the plant functional model using the Concept Hazard Analysis method. In this, the user will be supported by checklists and keywords and the analysis is structured by pre-defined worksheets. The preparation of the plant functional model and the performance of the hazard identification can be carried out manually or with computer support. (au) (4 tabs., 10 ills., 7 refs.)

  20. Symbiont modulates expression of specific gene categories in Angomonas deanei

    Directory of Open Access Journals (Sweden)

    Luciana Loureiro Penha

    Full Text Available Trypanosomatids are parasites that cause disease in humans, animals, and plants. Most are non-pathogenic and some harbor a symbiotic bacterium. Endosymbiosis is part of the evolutionary process of vital cell functions such as respiration and photosynthesis. Angomonas deanei is an example of a symbiont-containing trypanosomatid. In this paper, we sought to investigate how symbionts influence host cells by characterising and comparing the transcriptomes of the symbiont-containing A. deanei (wild type and the symbiont-free aposymbiotic strains. The comparison revealed that the presence of the symbiont modulates several differentially expressed genes. Empirical analysis of differential gene expression showed that 216 of the 7625 modulated genes were significantly changed. Finally, gene set enrichment analysis revealed that the largest categories of genes that downregulated in the absence of the symbiont were those involved in oxidation-reduction process, ATP hydrolysis coupled proton transport and glycolysis. In contrast, among the upregulated gene categories were those involved in proteolysis, microtubule-based movement, and cellular metabolic process. Our results provide valuable information for dissecting the mechanism of endosymbiosis in A. deanei.

  1. Transfer Function Identification Using Orthogonal Fourier Transform Modeling Functions

    Science.gov (United States)

    Morelli, Eugene A.

    2013-01-01

    A method for transfer function identification, including both model structure determination and parameter estimation, was developed and demonstrated. The approach uses orthogonal modeling functions generated from frequency domain data obtained by Fourier transformation of time series data. The method was applied to simulation data to identify continuous-time transfer function models and unsteady aerodynamic models. Model fit error, estimated model parameters, and the associated uncertainties were used to show the effectiveness of the method for identifying accurate transfer function models from noisy data.

  2. Genomic diversification of giant enteric symbionts reflects host dietary lifestyles.

    Science.gov (United States)

    Ngugi, David Kamanda; Miyake, Sou; Cahill, Matt; Vinu, Manikandan; Hackmann, Timothy J; Blom, Jochen; Tietbohl, Matthew D; Berumen, Michael L; Stingl, Ulrich

    2017-09-05

    Herbivorous surgeonfishes are an ecologically successful group of reef fish that rely on marine algae as their principal food source. Here, we elucidated the significance of giant enteric symbionts colonizing these fishes regarding their roles in the digestive processes of hosts feeding predominantly on polysiphonous red algae and brown Turbinaria algae, which contain different polysaccharide constituents. Using metagenomics, single-cell genomics, and metatranscriptomic analyses, we provide evidence of metabolic diversification of enteric microbiota involved in the degradation of algal biomass in these fishes. The enteric microbiota is also phylogenetically and functionally simple relative to the complex lignocellulose-degrading microbiota of terrestrial herbivores. Over 90% of the enzymes for deconstructing algal polysaccharides emanate from members of a single bacterial lineage, " Candidatus Epulopiscium" and related giant bacteria. These symbionts lack cellulases but encode a distinctive and lineage-specific array of mostly intracellular carbohydrases concurrent with the unique and tractable dietary resources of their hosts. Importantly, enzymes initiating the breakdown of the abundant and complex algal polysaccharides also originate from these symbionts. These are also highly transcribed and peak according to the diel lifestyle of their host, further supporting their importance and host-symbiont cospeciation. Because of their distinctive genomic blueprint, we propose the classification of these giant bacteria into three candidate genera. Collectively, our findings show that the acquisition of metabolically distinct " Epulopiscium " symbionts in hosts feeding on compositionally varied algal diets is a key niche-partitioning driver in the nutritional ecology of herbivorous surgeonfishes.

  3. Evolution: Welcome to Symbiont Prison.

    Science.gov (United States)

    Kiers, E Toby; West, Stuart A

    2016-01-25

    Can egalitarian partnerships exist in nature? A new study demonstrates how protist hosts use and abuse their algal symbionts depending on their needs. While this relationship allows protists to survive in low nutrient conditions, it leaves little room for algal retaliation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Evolution: Welcome to Symbiont Prison

    NARCIS (Netherlands)

    Kiers, E.T.; West, S.A.

    2016-01-01

    Can egalitarian partnerships exist in nature? A new study demonstrates how protist hosts use and abuse their algal symbionts depending on their needs. While this relationship allows protists to survive in low nutrient conditions, it leaves little room for algal retaliation.

  5. Insect symbionts in food webs

    Czech Academy of Sciences Publication Activity Database

    McLean, A. H. C.; Parker, B. J.; Hrček, Jan; Henry, L. M.; Godfray, H. C. J.

    2016-01-01

    Roč. 371, č. 1702 (2016), article number 20150325 ISSN 0962-8436 Institutional support: RVO:60077344 Keywords : food web * symbiont * symbiosis Subject RIV: EE - Microbiology, Virology Impact factor: 5.846, year: 2016 http://rstb.royalsocietypublishing.org/content/371/1702/20150325

  6. Complete Genome Sequence of the Human Gut Symbiont Roseburia hominis

    DEFF Research Database (Denmark)

    Travis, Anthony J.; Kelly, Denise; Flint, Harry J

    2015-01-01

    We report here the complete genome sequence of the human gut symbiont Roseburia hominis A2-183(T) (= DSM 16839(T) = NCIMB 14029(T)), isolated from human feces. The genome is represented by a 3,592,125-bp chromosome with 3,405 coding sequences. A number of potential functions contributing to host...

  7. Temporal changes of symbiont density and host fitness after rifampicin treatment in a whitefly of the Bemisia tabaci species complex.

    Science.gov (United States)

    Shan, Hong-Wei; Zhang, Chang-Rong; Yan, Ting-Ting; Tang, Hai-Qin; Wang, Xiao-Wei; Liu, Shu-Sheng; Liu, Yin-Quan

    2016-04-01

    Microbial symbionts are essential or important partners to phloem-feeding insects. Antibiotics have been used to selectively eliminate symbionts from their host insects and establish host lines with or without certain symbionts for investigating functions of the symbionts. In this study, using the antibiotic rifampicin we attempted to selectively eliminate certain symbionts from a population of the Middle East-Asia Minor 1 whitefly of the Bemisia tabaci species complex, which harbors the primary symbiont "Candidatus Portiera aleyrodidarum" and two secondary symbionts "Candidatus Hamiltonella defensa" and Rickettsia. Neither the primary nor the secondary symbionts were completely depleted in the adults (F0) that fed for 48 h on a diet treated with rifampicin at concentrations of 1-100 μg/mL. However, both the primary and secondary symbionts were nearly completely depleted in the offspring (F1) of the rifampicin-treated adults. Although the F1 adults produced some eggs (F2), most of the eggs failed to hatch and none of them reached the second instar, and consequently the rifampicin-treated whitefly colony vanished at the F2 generation. Interestingly, quantitative polymerase chain reaction assays showed that in the rifampicin-treated whiteflies, the density of the primary symbiont was reduced at an obviously slower pace than the secondary symbionts. Mating experiments between rifampicin-treated and untreated adults demonstrated that the negative effects of rifampicin on host fitness were expressed when the females were treated by the antibiotic, and whether males were treated or not by the antibiotic had little contribution to the negative effects. These observations indicate that with this whitefly population it is not feasible to selectively eliminate the secondary symbionts using rifampicin without affecting the primary symbiont and establish host lines for experimental studies. However, the extinction of the whitefly colony at the second generation after

  8. Comparative metagenomics of Daphnia symbionts

    Directory of Open Access Journals (Sweden)

    Preston James F

    2009-04-01

    Full Text Available Abstract Background Shotgun sequences of DNA extracts from whole organisms allow a comprehensive assessment of possible symbionts. The current project makes use of four shotgun datasets from three species of the planktonic freshwater crustaceans Daphnia: one dataset from clones of D. pulex and D. pulicaria and two datasets from one clone of D. magna. We analyzed these datasets with three aims: First, we search for bacterial symbionts, which are present in all three species. Second, we search for evidence for Cyanobacteria and plastids, which had been suggested to occur as symbionts in a related Daphnia species. Third, we compare the metacommunities revealed by two different 454 pyrosequencing methods (GS 20 and GS FLX. Results In all datasets we found evidence for a large number of bacteria belonging to diverse taxa. The vast majority of these were Proteobacteria. Of those, most sequences were assigned to different genera of the Betaproteobacteria family Comamonadaceae. Other taxa represented in all datasets included the genera Flavobacterium, Rhodobacter, Chromobacterium, Methylibium, Bordetella, Burkholderia and Cupriavidus. A few taxa matched sequences only from the D. pulex and the D. pulicaria datasets: Aeromonas, Pseudomonas and Delftia. Taxa with many hits specific to a single dataset were rare. For most of the identified taxa earlier studies reported the finding of related taxa in aquatic environmental samples. We found no clear evidence for the presence of symbiotic Cyanobacteria or plastids. The apparent similarity of the symbiont communities of the three Daphnia species breaks down on a species and strain level. Communities have a similar composition at a higher taxonomic level, but the actual sequences found are divergent. The two Daphnia magna datasets obtained from two different pyrosequencing platforms revealed rather similar results. Conclusion Three clones from three species of the genus Daphnia were found to harbor a rich

  9. Exploring symbiont management in lichens.

    Science.gov (United States)

    Grube, Martin; Spribille, Toby

    2012-07-01

    Lichens are unique among fungal symbioses in that their mycelial structures are compact and exposed to the light as thallus structures. The myriad intersections of unique fungal species with photosynthetic partner organisms (green algae in 90% of lichens) produce a wide variety of diverse shapes and colours of the fully synthesized lichen thallus when growing in nature. This characteristic complex morphology is, however, not achieved in the fungal axenic state. Even under ideal environmental conditions, the lichen life cycle faces considerable odds: first, meiotic spores are only produced on well-established thalli and often only after achieving considerable age in a stable environment, and second, even then in vivo resynthesis requires the presence of compatible algal strains where fungal spores germinate. Many lichen species have evolved a way around the resynthesis bottleneck by producing asexual propagules for joint propagation of symbionts. These different dispersal strategies ostensibly shape the population genetic structure of lichen symbioses, but the relative contributions of vertical (joint) and horizontal (independent) symbiont transmission have long eluded lichen evolutionary biologists. In this issue of Molecular Ecology, Dal Grande et al. (2012) close in on this question with the lung lichen, Lobaria pulmonaria, a flagship species in the conservation of old growth forests. By capitalizing on available microsatellite markers for both fungal and algal symbionts, they show that while vertical transmission is the predominant mode of reproduction, horizontal transmission is demonstrable and actively shapes population genetic structure. The resulting mixed propagation system is a highly successful balance of safe recruitment of symbiotic clones and endless possibilities for fungal recombination and symbiont shuffling.

  10. Investigations on abundance and activity of microbial sponge symbionts using quantitative real - time PCR

    DEFF Research Database (Denmark)

    Kumala, Lars; Hentschel, Ute; Bayer, Kristina

    Marine sponges are hosts to dense and diverse microbial consortia that are likely to play a key role in the metabolic processes of the host sponge due to their enormous abundance. Common symbioses between nitrogen transforming microorganisms and sponges indicate complex nitrogen cycling within...... the host. Of particular interest is determining the community structure and function of microbial symbionts in order to gain deeper insight into host-symbiont interactions. We investigated the abundance and activity of microbial symbionts in two Mediterranean sponge species using quantitative real-time PCR....... An absolute quantification of functional genes and transcripts in archaeal and bacterial symbionts was conducted to determine their involvement in nitrification and denitrification, comparing the low microbial abundance (LMA) sponge Dysidea avara with the high microbial abundance (HMA) representative Aplysina...

  11. Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes

    Directory of Open Access Journals (Sweden)

    Zhou Xuguo

    2009-10-01

    Full Text Available Abstract Background Termite lignocellulose digestion is achieved through a collaboration of host plus prokaryotic and eukaryotic symbionts. In the present work, we took a combined host and symbiont metatranscriptomic approach for investigating the digestive contributions of host and symbiont in the lower termite Reticulitermes flavipes. Our approach consisted of parallel high-throughput sequencing from (i a host gut cDNA library and (ii a hindgut symbiont cDNA library. Subsequently, we undertook functional analyses of newly identified phenoloxidases with potential importance as pretreatment enzymes in industrial lignocellulose processing. Results Over 10,000 expressed sequence tags (ESTs were sequenced from the 2 libraries that aligned into 6,555 putative transcripts, including 171 putative lignocellulase genes. Sequence analyses provided insights in two areas. First, a non-overlapping complement of host and symbiont (prokaryotic plus protist glycohydrolase gene families known to participate in cellulose, hemicellulose, alpha carbohydrate, and chitin degradation were identified. Of these, cellulases are contributed by host plus symbiont genomes, whereas hemicellulases are contributed exclusively by symbiont genomes. Second, a diverse complement of previously unknown genes that encode proteins with homology to lignase, antioxidant, and detoxification enzymes were identified exclusively from the host library (laccase, catalase, peroxidase, superoxide dismutase, carboxylesterase, cytochrome P450. Subsequently, functional analyses of phenoloxidase activity provided results that were strongly consistent with patterns of laccase gene expression. In particular, phenoloxidase activity and laccase gene expression are mostly restricted to symbiont-free foregut plus salivary gland tissues, and phenoloxidase activity is inducible by lignin feeding. Conclusion To our knowledge, this is the first time that a dual host-symbiont transcriptome sequencing effort

  12. Biometric identification using local iterated function

    Science.gov (United States)

    Al-Saidi, N. M. G.; Said, M. R. M.

    2014-06-01

    Biometric identification protocol has been received an increasing interest recently. It is a process that determines person identity by making use of their biometric features. A new biometric identification method is presented in this paper based on partial self-similarity that used to identify features within fingerprint images. This approach is already used in Fractal Image Compression (FIC) due to their ability to represent the images by a limited number of affine transformations, and its variation of scale, translation or rotation. These features give the recognition process high impact and good performance. To process data in a fingerprint image, it first converted into digital format using Optical Fingerprint Reader (OFR). The verification process is done by comparing these data with the server data. The system analysis shows that the proposed method is efficient in terms of memory and time complexity.

  13. Novel bacteriocyte-associated pleomorphic symbiont of the grain pest beetleRhyzopertha dominica(Coleoptera: Bostrichidae).

    Science.gov (United States)

    Okude, Genta; Koga, Ryuichi; Hayashi, Toshinari; Nishide, Yudai; Meng, Xian-Ying; Nikoh, Naruo; Miyanoshita, Akihiro; Fukatsu, Takema

    2017-01-01

    The lesser grain borer Rhyzopertha dominica (Coleoptera: Bostrichidae) is a stored-product pest beetle. Early histological studies dating back to 1930s have reported that R. dominica and other bostrichid species possess a pair of oval symbiotic organs, called the bacteriomes, in which the cytoplasm is densely populated by pleomorphic symbiotic bacteria of peculiar rosette-like shape. However, the microbiological nature of the symbiont has remained elusive. Here we investigated the bacterial symbiont of R. dominica using modern molecular, histological, and microscopic techniques. Whole-mount fluorescence in situ hybridization specifically targeting symbiotic bacteria consistently detected paired bacteriomes, in which the cytoplasm was full of pleomorphic bacterial cells, in the abdomen of adults, pupae and larvae, confirming previous histological descriptions. Molecular phylogenetic analysis identified the symbiont as a member of the Bacteroidetes, in which the symbiont constituted a distinct bacterial lineage allied to a variety of insect-associated endosymbiont clades, including Uzinura of diaspidid scales, Walczuchella of giant scales, Brownia of root mealybugs, Sulcia of diverse hemipterans, and Blattabacterium of roaches. The symbiont gene exhibited markedly AT-biased nucleotide composition and significantly accelerated molecular evolution, suggesting degenerative evolution of the symbiont genome. The symbiotic bacteria were detected in oocytes and embryos, confirming continuous host-symbiont association and vertical symbiont transmission in the host life cycle. We demonstrate that the symbiont of R. dominica constitutes a novel bacterial lineage in the Bacteroidetes. We propose that reductive evolution of the symbiont genome may be relevant to the amorphous morphology of the bacterial cells via disruption of genes involved in cell wall synthesis and cell division. Genomic and functional aspects of the host-symbiont relationship deserve future studies.

  14. Smell Identification Function in Children with Attention Deficit Hyperactivity Disorder

    OpenAIRE

    Ghanizadeh, Ahmad; Bahrani, Maryam; Miri, Ramin; Sahraian, Ali

    2012-01-01

    Objective Deficits in olfactory function are common features in neurodegenerative and neuropsychiatric disorders. Olfactory processing is related to dopamine metabolism and orbitofrontal cortex functioning, both known to be involved in the neurobiology of ADHD. Some investigations suggested alterations in olfactory processing (identification and detection threshold) in patients with ADHD. Despite increasing knowledge, controversy about this topic still exists regarding children with ADHD. Thi...

  15. Wolbachia symbiont infections induce strong cytoplasmic incompatibility in the tsetse fly Glossina morsitans.

    Directory of Open Access Journals (Sweden)

    Uzma Alam

    2011-12-01

    Full Text Available Tsetse flies are vectors of the protozoan parasite African trypanosomes, which cause sleeping sickness disease in humans and nagana in livestock. Although there are no effective vaccines and efficacious drugs against this parasite, vector reduction methods have been successful in curbing the disease, especially for nagana. Potential vector control methods that do not involve use of chemicals is a genetic modification approach where flies engineered to be parasite resistant are allowed to replace their susceptible natural counterparts, and Sterile Insect technique (SIT where males sterilized by chemical means are released to suppress female fecundity. The success of genetic modification approaches requires identification of strong drive systems to spread the desirable traits and the efficacy of SIT can be enhanced by identification of natural mating incompatibility. One such drive mechanism results from the cytoplasmic incompatibility (CI phenomenon induced by the symbiont Wolbachia. CI can also be used to induce natural mating incompatibility between release males and natural populations. Although Wolbachia infections have been reported in tsetse, it has been a challenge to understand their functional biology as attempts to cure tsetse of Wolbachia infections by antibiotic treatment damages the obligate mutualistic symbiont (Wigglesworthia, without which the flies are sterile. Here, we developed aposymbiotic (symbiont-free and fertile tsetse lines by dietary provisioning of tetracycline supplemented blood meals with yeast extract, which rescues Wigglesworthia-induced sterility. Our results reveal that Wolbachia infections confer strong CI during embryogenesis in Wolbachia-free (Gmm(Apo females when mated with Wolbachia-infected (Gmm(Wt males. These results are the first demonstration of the biological significance of Wolbachia infections in tsetse. Furthermore, when incorporated into a mathematical model, our results confirm that Wolbachia can

  16. Fungal proteomics: from identification to function.

    Science.gov (United States)

    Doyle, Sean

    2011-08-01

    Some fungi cause disease in humans and plants, while others have demonstrable potential for the control of insect pests. In addition, fungi are also a rich reservoir of therapeutic metabolites and industrially useful enzymes. Detailed analysis of fungal biochemistry is now enabled by multiple technologies including protein mass spectrometry, genome and transcriptome sequencing and advances in bioinformatics. Yet, the assignment of function to fungal proteins, encoded either by in silico annotated, or unannotated genes, remains problematic. The purpose of this review is to describe the strategies used by many researchers to reveal protein function in fungi, and more importantly, to consolidate the nomenclature of 'unknown function protein' as opposed to 'hypothetical protein' - once any protein has been identified by protein mass spectrometry. A combination of approaches including comparative proteomics, pathogen-induced protein expression and immunoproteomics are outlined, which, when used in combination with a variety of other techniques (e.g. functional genomics, microarray analysis, immunochemical and infection model systems), appear to yield comprehensive and definitive information on protein function in fungi. The relative advantages of proteomic, as opposed to transcriptomic-only, analyses are also described. In the future, combined high-throughput, quantitative proteomics, allied to transcriptomic sequencing, are set to reveal much about protein function in fungi. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  17. Symbiont shuffling linked to differential photochemical dynamics of Symbiodinium in three Caribbean reef corals

    Science.gov (United States)

    Cunning, Ross; Silverstein, Rachel N.; Baker, Andrew C.

    2018-03-01

    Dynamic symbioses with functionally diverse dinoflagellate algae in the genus Symbiodinium may allow some reef corals to alter their phenotypes through `symbiont shuffling', or changes in symbiont community composition. In particular, corals may become more bleaching resistant by increasing the relative abundance of thermally tolerant Symbiodinium in clade D after bleaching. Despite the immediate relevance of this phenomenon to corals living in warming oceans—and to interventions aimed at boosting coral resilience—the mechanisms governing how, why, and when symbiont shuffling occurs are still poorly understood. Here, we performed controlled thermal bleaching and recovery experiments on three species of Caribbean corals hosting mixtures of D1a ( S. trenchii) and other symbionts in clades B or C. We show that the degree of symbiont shuffling is related to (1) the duration of stress exposure and (2) the difference in photochemical efficiency ( F v /F m) of co-occurring symbionts under stress (i.e., the `photochemical advantage' of one symbiont over the other). The advantage of D1a under stress was greatest in Montastraea cavernosa, intermediate in Siderastrea siderea, and lowest in Orbicella faveolata and correlated positively with the magnitude of shuffling toward D1a. In holobionts where D1a had less of an advantage over co-occurring symbionts (i.e., only slightly higher F v /F m under stress), a longer stress duration was required to elicit commensurate increases in D1a abundance. In fact, across these three coral species, 92.9% of variation in the degree of symbiont shuffling could be explained by the time-integrated photochemical advantage of D1a under heat stress. Although F v /F m is governed by numerous factors that this study is unable to resolve mechanistically, its strong empirical relationship with symbiont shuffling helps elucidate general features that govern this process in reef corals, which will help refine predictions of coral responses to

  18. The evolution of host-symbiont dependence

    NARCIS (Netherlands)

    Fisher, Roberta M.; Henry, Lee M.; Cornwallis, Charlie K.; Kiers, E. Toby; West, Stuart A.

    2017-01-01

    Organisms across the tree of life form symbiotic partnerships with microbes for metabolism, protection and resources. While some hosts evolve extreme dependence on their symbionts, others maintain facultative associations. Explaining this variation is fundamental to understanding when symbiosis can

  19. Justification identification criterion cellular structures state functions

    Directory of Open Access Journals (Sweden)

    Владимир Георгиевич Куликов

    2017-02-01

    Full Text Available The paper considers the possibility of presenting situations the state of cellular structures functions of the state in the form of regression equations. This allows you to create a replica of an information storage medium on the system status at a given time. The process of system transition from the initial to the final state are invited to formalize a coherent set of regression equations. The regression equations as state functions allow the verbal process of representing the states to replace the system - model. This, in turn, allows the development of parametric methods of management structure formation.

  20. Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

    KAUST Repository

    Ziegler, Maren

    2017-01-02

    Aim: Coral reefs rely on the symbiosis between scleractinian corals and intracellular, photosynthetic dinoflagellates of the genus Symbiodinium making the assessment of symbiont diversity critical to our understanding of ecological resilience of these ecosystems. This study characterizes Symbiodinium diversity around the Arabian Peninsula, which contains some of the most thermally diverse and understudied reefs on Earth. Location: Shallow water coral reefs throughout the Red Sea (RS), Sea of Oman (SO), and Persian/Arabian Gulf (PAG). Methods: Next-generation sequencing of the ITS2 marker gene was used to assess Symbiodinium community composition and diversity comprising 892 samples from 46 hard and soft coral genera. Results: Corals were associated with a large diversity of Symbiodinium, which usually consisted of one or two prevalent symbiont types and many types at low abundance. Symbiodinium communities were strongly structured according to geographical region and to a lesser extent by coral host identity. Overall symbiont communities were composed primarily of species from clade A and C in the RS, clade A, C, and D in the SO, and clade C and D in the PAG, representing a gradual shift from C- to D-dominated coral hosts. The analysis of symbiont diversity in an Operational Taxonomic Unit (OTU)-based framework allowed the identification of differences in symbiont taxon richness over geographical regions and host genera. Main conclusions: Our study represents a comprehensive overview over biogeography and molecular diversity of Symbiodinium in the Arabian Seas, where coral reefs thrive in one of the most extreme environmental settings on the planet. As such our data will serve as a baseline for further exploration into the effects of environmental change on host-symbiont pairings and the identification and ecological significance of Symbiodinium types from regions already experiencing \\'Future Ocean\\' conditions.

  1. Complete functional characterization of sensory neurons by system identification.

    Science.gov (United States)

    Wu, Michael C-K; David, Stephen V; Gallant, Jack L

    2006-01-01

    System identification is a growing approach to sensory neurophysiology that facilitates the development of quantitative functional models of sensory processing. This approach provides a clear set of guidelines for combining experimental data with other knowledge about sensory function to obtain a description that optimally predicts the way that neurons process sensory information. This prediction paradigm provides an objective method for evaluating and comparing computational models. In this chapter we review many of the system identification algorithms that have been used in sensory neurophysiology, and we show how they can be viewed as variants of a single statistical inference problem. We then review many of the practical issues that arise when applying these methods to neurophysiological experiments: stimulus selection, behavioral control, model visualization, and validation. Finally we discuss several problems to which system identification has been applied recently, including one important long-term goal of sensory neuroscience: developing models of sensory systems that accurately predict neuronal responses under completely natural conditions.

  2. Expression and extracellular release of a functional anti-trypanosome Nanobody® in Sodalis glossinidius, a bacterial symbiont of the tsetse fly

    Directory of Open Access Journals (Sweden)

    De Vooght Linda

    2012-02-01

    Full Text Available Abstract Background Sodalis glossinidius, a gram-negative bacterial endosymbiont of the tsetse fly, has been proposed as a potential in vivo drug delivery vehicle to control trypanosome parasite development in the fly, an approach known as paratransgenesis. Despite this interest of S. glossinidius as a paratransgenic platform organism in tsetse flies, few potential effector molecules have been identified so far and to date none of these molecules have been successfully expressed in this bacterium. Results In this study, S. glossinidius was transformed to express a single domain antibody, (Nanobody® Nb_An33, that efficiently targets conserved cryptic epitopes of the variant surface glycoprotein (VSG of the parasite Trypanosoma brucei. Next, we analyzed the capability of two predicted secretion signals to direct the extracellular delivery of significant levels of active Nb_An33. We show that the pelB leader peptide was successful in directing the export of fully functional Nb_An33 to the periplasm of S. glossinidius resulting in significant levels of extracellular release. Finally, S. glossinidius expressing pelBNb_An33 exhibited no significant reduction in terms of fitness, determined by in vitro growth kinetics, compared to the wild-type strain. Conclusions These data are the first demonstration of the expression and extracellular release of functional trypanosome-interfering Nanobodies® in S. glossinidius. Furthermore, Sodalis strains that efficiently released the effector protein were not affected in their growth, suggesting that they may be competitive with endogenous microbiota in the midgut environment of the tsetse fly. Collectively, these data reinforce the notion for the potential of S. glossinidius to be developed into a paratransgenic platform organism.

  3. Smell identification function in children with attention deficit hyperactivity disorder.

    Science.gov (United States)

    Ghanizadeh, Ahmad; Bahrani, Maryam; Miri, Ramin; Sahraian, Ali

    2012-06-01

    Deficits in olfactory function are common features in neurodegenerative and neuropsychiatric disorders. Olfactory processing is related to dopamine metabolism and orbitofrontal cortex functioning, both known to be involved in the neurobiology of ADHD. Some investigations suggested alterations in olfactory processing (identification and detection threshold) in patients with ADHD. Despite increasing knowledge, controversy about this topic still exists regarding children with ADHD. This study was conducted to help elucidate some of this controversy. 50 participants (8-15 years, mean=10.70±1.77) with ADHD were compared to 50 controls. The two groups were well matched for age, gender and Mean School Scores (MSS). We assessed odor identification and threshold through a smell test composed of two tests of identification and detection threshold. Odor detection threshold was assessed with the odorant phenyl ethyl alcohol solved in propylene glycol using a single staircase method. Odor identification was assessed with chemical essences of five common odorants. The mean Sensory Identification Score for children with ADHD and the control groups were 3.76 (1.06) and 4.46 (0.76), respectively (pSensory Threshold Score for ADHD and control group was 6.4 (3.35) and 9.75 (2.16), respectively (p<0.001). This study replicated altered olfactory performance in ADHD. Substantial olfactory deficits across the two domains of identification and detection threshold are observed in children with ADHD. These deficits do not seem to be a result of olfactory task difficulty and are not influenced by age, gender and MSS. Further studies are required to investigate whether olfactory function can be used as a biological marker for early diagnosis, treatment and prognosis of ADHD.

  4. Co-niche construction between hosts and symbionts

    Indian Academy of Sciences (India)

    Symbiosis is a process that can generate evolutionary novelties and can extend the phenotypic niche space of organisms. Symbionts can act together with their hosts to co-construct host organs, within which symbionts are housed. Once established within hosts, symbionts can also influence various aspects of host ...

  5. Co-niche construction between hosts and symbionts: ideas and ...

    Indian Academy of Sciences (India)

    2017-07-05

    Jul 5, 2017 ... Symbiosis is a process that can generate evolutionary novelties and can extend the phenotypic niche space of organisms. Symbionts can act together with their hosts to co-construct host organs, within which symbionts are housed. Once established within hosts, symbionts can also influence various ...

  6. Functional module identification in protein interaction networks by interaction patterns

    Science.gov (United States)

    Wang, Yijie; Qian, Xiaoning

    2014-01-01

    Motivation: Identifying functional modules in protein–protein interaction (PPI) networks may shed light on cellular functional organization and thereafter underlying cellular mechanisms. Many existing module identification algorithms aim to detect densely connected groups of proteins as potential modules. However, based on this simple topological criterion of ‘higher than expected connectivity’, those algorithms may miss biologically meaningful modules of functional significance, in which proteins have similar interaction patterns to other proteins in networks but may not be densely connected to each other. A few blockmodel module identification algorithms have been proposed to address the problem but the lack of global optimum guarantee and the prohibitive computational complexity have been the bottleneck of their applications in real-world large-scale PPI networks. Results: In this article, we propose a novel optimization formulation LCP2 (low two-hop conductance sets) using the concept of Markov random walk on graphs, which enables simultaneous identification of both dense and sparse modules based on protein interaction patterns in given networks through searching for LCP2 by random walk. A spectral approximate algorithm SLCP2 is derived to identify non-overlapping functional modules. Based on a bottom-up greedy strategy, we further extend LCP2 to a new algorithm (greedy algorithm for LCP2) GLCP2 to identify overlapping functional modules. We compare SLCP2 and GLCP2 with a range of state-of-the-art algorithms on synthetic networks and real-world PPI networks. The performance evaluation based on several criteria with respect to protein complex prediction, high level Gene Ontology term prediction and especially sparse module detection, has demonstrated that our algorithms based on searching for LCP2 outperform all other compared algorithms. Availability and implementation: All data and code are available at http://www.cse.usf.edu/∼xqian/fmi/slcp2hop

  7. Functional Identification of Putrescine C- and N-Hydroxylases.

    Science.gov (United States)

    Li, Bin; Lowe-Power, Tiffany; Kurihara, Shin; Gonzales, Stephen; Naidoo, Jacinth; MacMillan, John B; Allen, Caitilyn; Michael, Anthony J

    2016-10-21

    The small polyamine putrescine (1,4-diaminobutane) is ubiquitously and abundantly found in all three domains of life. It is a precursor, through N-aminopropylation or N-aminobutylation, for biosynthesis of the longer polyamines spermidine, sym-homospermidine, spermine, and thermospermine and longer and branched chain polyamines. Putrescine is also biochemically modified for purposes of metabolic regulation and catabolism, e.g. N-acetylation and N-glutamylation, and for incorporation into specialized metabolites, e.g. N-methylation, N-citrylation, N-palmitoylation, N-hydroxylation, and N-hydroxycinnamoylation. Only one example is known where putrescine is modified on a methylene carbon: the formation of 2-hydroxyputrescine by an unknown C-hydroxylase. Here, we report the functional identification of a previously undescribed putrescine 2-hydroxylase, a Rieske-type nonheme iron sulfur protein from the β-proteobacteria Bordetella bronchiseptica and Ralstonia solanacearum. Identification of the putrescine 2-hydroxylase will facilitate investigation of the physiological functions of 2-hydroxyputrescine. One known role of 2-hydroxyputrescine has direct biomedical relevance: its role in the biosynthesis of the cyclic hydroxamate siderophore alcaligin, a potential virulence factor of the causative agent of whooping cough, Bordetella pertussis. We also report the functional identification of a putrescine N-hydroxylase from the γ-proteobacterium Shewanella oneidensis, which is homologous to FAD- and NADPH-dependent ornithine and lysine N-monooxygenases involved in siderophore biosynthesis. Heterologous expression of the putrescine N-hydroxylase in E. coli produced free N-hydroxyputrescine, never detected previously in a biological system. Furthermore, the putrescine C- and N-hydroxylases identified here could contribute new functionality to polyamine structural scaffolds, including C-H bond functionalization in synthetic biology strategies.

  8. Social insect symbionts: evolution in homeostatic fortresses

    DEFF Research Database (Denmark)

    Hughes, David P; Pierce, Naomi E; Boomsma, Jacobus J

    2008-01-01

    The massive environmentally buffered nests of some social insects can contain millions of individuals and a wide variety of parasites, commensals and mutualists. We suggest that the ways in which these homeostatic fortress environments affect the evolution of social insect symbionts are relevant ...

  9. Influence of microbial symbionts on insect pheromones.

    Science.gov (United States)

    Engl, Tobias; Kaltenpoth, Martin

    2018-03-22

    Covering: up to 2018Pheromones serve as chemical signals between individuals of the same species and play important roles for mate localization and mate choice as well as other social interactions in insects. A growing body of literature indicates that microbial symbionts can modulate their hosts' chemical profiles, mate choice decisions and social behavior. This modulation can occur by the direct biosynthesis of pheromone components or the provisioning of precursors, or through general changes in the metabolite pool of the host and its resource allocation into pheromone production. Here we review and discuss the contexts in which microbial modulation of intraspecific communication in insects occurs and emphasize cases in which microbes are known to affect the involved chemistry. The described examples for a symbiotic influence on mate attraction and mate choice, aggregation, nestmate and kin recognition highlight the context-dependent costs and benefits of these symbiotic interactions and the potential for conflict and manipulation among the interacting partners. However, despite the increasing number of studies reporting on symbiont-mediated effects on insect chemical communication, experimentally validated connections between the presence of specific symbionts, changes in the host's chemistry, and behavioral effects thereof, remain limited to very few systems, highlighting the need for increased collaborative efforts between symbiosis researchers and chemical ecologists to gain more comprehensive insights into the influence of microbial symbionts on insect pheromones.

  10. Potential applications of insect symbionts in biotechnology.

    Science.gov (United States)

    Berasategui, Aileen; Shukla, Shantanu; Salem, Hassan; Kaltenpoth, Martin

    2016-02-01

    Symbiotic interactions between insects and microorganisms are widespread in nature and are often the source of ecological innovations. In addition to supplementing their host with essential nutrients, microbial symbionts can produce enzymes that help degrade their food source as well as small molecules that defend against pathogens, parasites, and predators. As such, the study of insect ecology and symbiosis represents an important source of chemical compounds and enzymes with potential biotechnological value. In addition, the knowledge on insect symbiosis can provide novel avenues for the control of agricultural pest insects and vectors of human diseases, through targeted manipulation of the symbionts or the host-symbiont associations. Here, we discuss different insect-microbe interactions that can be exploited for insect pest and human disease control, as well as in human medicine and industrial processes. Our aim is to raise awareness that insect symbionts can be interesting sources of biotechnological applications and that knowledge on insect ecology can guide targeted efforts to discover microorganisms of applied value.

  11. Advances in Marine Microbial Symbionts in the China Sea and Related Pharmaceutical Metabolites

    Directory of Open Access Journals (Sweden)

    Zhiyong Li

    2009-04-01

    Full Text Available Marine animals and plants such as sponges, sea squirts, corals, worms and algae host diverse and abundant symbiotic microorganisms. Marine microbial symbionts are possible the true producers or take part in the biosynthesis of some bioactive marine natural products isolated from the marine organism hosts. Investigation of the pharmaceutical metabolites may reveal the biosynthesis mechanisms of related natural products and solve the current problem of supply limitation in marine drug development. This paper reviews the advances in diversity revelation, biological activity and related pharmaceutical metabolites, and functional genes of marine microbial symbionts from the China Sea.

  12. Detecting Symbioses in Complex Communities: the Fungal Symbionts of Bark and Ambrosia Beetles Within Asian Pines.

    Science.gov (United States)

    Skelton, James; Jusino, Michelle A; Li, You; Bateman, Craig; Thai, Pham Hong; Wu, Chengxu; Lindner, Daniel L; Hulcr, Jiri

    2018-02-24

    Separating symbioses from incidental associations is a major obstacle in symbiosis research. In this survey of fungi associated with Asian bark and ambrosia beetles, we used quantitative culture and DNA barcode identification to characterize fungal communities associated with co-infesting beetle species in pines (Pinus) of China and Vietnam. To quantitatively discern likely symbioses from coincidental associations, we used multivariate analysis and multilevel pattern analysis (a type of indicator species analysis). Nearly half of the variation in fungal community composition in beetle galleries and on beetle bodies was explained by beetle species. We inferred a spectrum of ecological strategies among beetle-associated fungi: from generalist multispecies associates to highly specialized single-host symbionts that were consistently dominant within the mycangia of their hosts. Statistically significant fungal associates of ambrosia beetles were typically only found with one beetle species. In contrast, bark beetle-associated fungi were often associated with multiple beetle species. Ambrosia beetles and their galleries were frequently colonized by low-prevalence ambrosia fungi, suggesting that facultative ambrosial associations are commonplace, and ecological mechanisms such as specialization and competition may be important in these dynamic associations. The approach used here could effectively delimit symbiotic interactions in any system where symbioses are obscured by frequent incidental associations. It has multiple advantages including (1) powerful statistical tests for non-random associations among potential symbionts, (2) simultaneous evaluation of multiple co-occurring host and symbiont associations, and (3) identifying symbionts that are significantly associated with multiple host species.

  13. Identification of fractional order systems using modulating functions method

    KAUST Repository

    Liu, Dayan

    2013-06-01

    The modulating functions method has been used for the identification of linear and nonlinear systems. In this paper, we generalize this method to the on-line identification of fractional order systems based on the Riemann-Liouville fractional derivatives. First, a new fractional integration by parts formula involving the fractional derivative of a modulating function is given. Then, we apply this formula to a fractional order system, for which the fractional derivatives of the input and the output can be transferred into the ones of the modulating functions. By choosing a set of modulating functions, a linear system of algebraic equations is obtained. Hence, the unknown parameters of a fractional order system can be estimated by solving a linear system. Using this method, we do not need any initial values which are usually unknown and not equal to zero. Also we do not need to estimate the fractional derivatives of noisy output. Moreover, it is shown that the proposed estimators are robust against high frequency sinusoidal noises and the ones due to a class of stochastic processes. Finally, the efficiency and the stability of the proposed method is confirmed by some numerical simulations.

  14. Protein kinase substrate identification on functional protein arrays

    Directory of Open Access Journals (Sweden)

    Zhou Fang

    2008-02-01

    Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

  15. Identification of MIMO systems with sparse transfer function coefficients

    Science.gov (United States)

    Qiu, Wanzhi; Saleem, Syed Khusro; Skafidas, Efstratios

    2012-12-01

    We study the problem of estimating transfer functions of multivariable (multiple-input multiple-output--MIMO) systems with sparse coefficients. We note that subspace identification methods are powerful and convenient tools in dealing with MIMO systems since they neither require nonlinear optimization nor impose any canonical form on the systems. However, subspace-based methods are inefficient for systems with sparse transfer function coefficients since they work on state space models. We propose a two-step algorithm where the first step identifies the system order using the subspace principle in a state space format, while the second step estimates coefficients of the transfer functions via L1-norm convex optimization. The proposed algorithm retains good features of subspace methods with improved noise-robustness for sparse systems.

  16. The Calyptogena magnifica chemoautotrophic symbiont genome

    Energy Technology Data Exchange (ETDEWEB)

    Newton, I.L.; Woyke, T.; Auchtung, T.A.; Dilly, G.F.; Dutton,R.J.; Fisher, M.C.; Fontanez, K.M.; Lau, E.; Stewart, F.J.; Richardson,P.M.; Barry, K.W.; Saunders, E.; Detter, J.C.; Wu, D.; Eisen, J.A.; Cavanaugh, C.M.

    2007-03-01

    Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.

  17. Potential applications of insect symbionts in biotechnology

    OpenAIRE

    Berasategui, A.; Shukla, S.; Salem, H.; Kaltenpoth, M.

    2016-01-01

    Symbiotic interactions between insects and microorganisms are widespread in nature and are often the source of ecological innovations. In addition to supplementing their host with essential nutrients, microbial symbionts can produce enzymes that help degrade their food source as well as small molecules that defend against pathogens, parasites, and predators. As such, the study of insect ecology and symbiosis represents an important source of chemical compounds and enzymes with potential biote...

  18. Interactions among symbionts operate across scales to influence parasite epidemics.

    Science.gov (United States)

    Halliday, Fletcher W; Umbanhowar, James; Mitchell, Charles E

    2017-10-01

    Parasite epidemics may be influenced by interactions among symbionts, which can depend on past events at multiple spatial scales. Within host individuals, interactions can depend on the sequence in which symbionts infect a host, generating priority effects. Across host individuals, interactions can depend on parasite phenology. To test the roles of parasite interactions and phenology in epidemics, we embedded multiple cohorts of sentinel plants, grown from seeds with and without a vertically transmitted symbiont, into a wild host population, and tracked foliar infections caused by three common fungal parasites. Within hosts, parasite growth was influenced by coinfections, but coinfections were often prevented by priority effects among symbionts. Across hosts, parasite phenology altered host susceptibility to secondary infections, symbiont interactions and ultimately the magnitude of parasite epidemics. Together, these results indicate that parasite phenology can influence parasite epidemics by altering the sequence of infection and interactions among symbionts within host individuals. © 2017 John Wiley & Sons Ltd/CNRS.

  19. Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont "Candidatus Synechococcus pongiarum"

    KAUST Repository

    Gao, Zhao-Ming

    2014-04-01

    "Candidatus Synechococcus spongiarum" is a cyanobacterial symbiont widely distributed in sponges, but its functions at the genome level remain unknown. Here, we obtained the draft genome (1.66 Mbp, 90% estimated genome recovery) of "Ca. Synechococcus spongiarum" strain SH4 inhabiting the Red Sea sponge Carteriospongia foliascens. Phylogenomic analysis revealed a high dissimilarity between SH4 and free-living cyanobacterial strains. Essential functions, such as photosynthesis, the citric acid cycle, and DNA replication, were detected in SH4. Eukaryoticlike domains that play important roles in sponge-symbiont interactions were identified exclusively in the symbiont. However, SH4 could not biosynthesize methionine and polyamines and had lost partial genes encoding low-molecular-weight peptides of the photosynthesis complex, antioxidant enzymes, DNA repair enzymes, and proteins involved in resistance to environmental toxins and in biosynthesis of capsular and extracellular polysaccharides. These genetic modifications imply that "Ca. Synechococcus spongiarum" SH4 represents a low-light-adapted cyanobacterial symbiont and has undergone genome streamlining to adapt to the sponge\\'s mild intercellular environment. 2014 Gao et al.

  20. The MicroRNA Repertoire of Symbiodinium, the Dinoflagellate Symbiont of Reef-Building Corals

    KAUST Repository

    Baumgarten, Sebastian

    2013-07-01

    Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3’UTRs of 12,858 mRNAs and 53 plantlike target sites in 51,917 genes. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.

  1. Atlas-based identification of targets for functional radiosurgery

    International Nuclear Information System (INIS)

    Stancanello, Joseph; Romanelli, Pantaleo; Modugno, Nicola; Cerveri, Pietro; Ferrigno, Giancarlo; Uggeri, Fulvio; Cantore, Giampaolo

    2006-01-01

    Functional disorders of the brain, such as Parkinson's disease, dystonia, epilepsy, and neuropathic pain, may exhibit poor response to medical therapy. In such cases, surgical intervention may become necessary. Modern surgical approaches to such disorders include radio-frequency lesioning and deep brain stimulation (DBS). The subthalamic nucleus (STN) is one of the most useful stereotactic targets available: STN DBS is known to induce substantial improvement in patients with end-stage Parkinson's disease. Other targets include the Globus Pallidus pars interna (GPi) for dystonia and Parkinson's disease, and the centromedian nucleus of the thalamus (CMN) for neuropathic pain. Radiosurgery is an attractive noninvasive alternative to treat some functional brain disorders. The main technical limitation to radiosurgery is that the target can be selected only on the basis of magnetic resonance anatomy without electrophysiological confirmation. The aim of this work is to provide a method for the correct atlas-based identification of the target to be used in functional neurosurgery treatment planning. The coordinates of STN, CMN, and GPi were identified in the Talairach and Tournoux atlas and transformed to the corresponding regions of the Montreal Neurological Institute (MNI) electronic atlas. Binary masks describing the target nuclei were created. The MNI electronic atlas was deformed onto the patient magnetic resonance imaging-T1 scan by applying an affine transformation followed by a local nonrigid registration. The first transformation was based on normalized cross correlation and the second on optimization of a two-part objective function consisting of similarity criteria and weighted regularization. The obtained deformation field was then applied to the target masks. The minimum distance between the surface of an implanted electrode and the surface of the deformed mask was calculated. The validation of the method consisted of comparing the electrode-mask distance to

  2. Horizontal Transmission of Intracellular Insect Symbionts via Plants

    Directory of Open Access Journals (Sweden)

    Ewa Chrostek

    2017-11-01

    Full Text Available Experimental evidence is accumulating that endosymbionts of phytophagous insects may transmit horizontally via plants. Intracellular symbionts known for manipulating insect reproduction and altering fitness (Rickettsia, Cardinium, Wolbachia, and bacterial parasite of the leafhopper Euscelidius variegatus have been found to travel from infected insects into plants. Other insects, either of the same or different species can acquire the symbiont from the plant through feeding, and in some cases transfer it to their progeny. These reports prompt many questions regarding how intracellular insect symbionts are delivered to plants and how they affect them. Are symbionts passively transported along the insect-plant-insect path, or do they actively participate in the process? How widespread are these interactions? How does symbiont presence influence the plant? And what conditions are required for the new infection to establish in an insect? From an ecological, evolutionary, and applied perspective, this mode of horizontal transmission could have profound implications if occurring frequently enough or if new stable symbiont infections are established. Transmission of symbionts through plants likely represents an underappreciated means of infection, both in terms of symbiont epidemiology and the movement of symbionts to new host species.

  3. Horizontal Transmission of Intracellular Insect Symbionts via Plants.

    Science.gov (United States)

    Chrostek, Ewa; Pelz-Stelinski, Kirsten; Hurst, Gregory D D; Hughes, Grant L

    2017-01-01

    Experimental evidence is accumulating that endosymbionts of phytophagous insects may transmit horizontally via plants. Intracellular symbionts known for manipulating insect reproduction and altering fitness ( Rickettsia, Cardinium, Wolbachia , and bacterial parasite of the leafhopper Euscelidius variegatus ) have been found to travel from infected insects into plants. Other insects, either of the same or different species can acquire the symbiont from the plant through feeding, and in some cases transfer it to their progeny. These reports prompt many questions regarding how intracellular insect symbionts are delivered to plants and how they affect them. Are symbionts passively transported along the insect-plant-insect path, or do they actively participate in the process? How widespread are these interactions? How does symbiont presence influence the plant? And what conditions are required for the new infection to establish in an insect? From an ecological, evolutionary, and applied perspective, this mode of horizontal transmission could have profound implications if occurring frequently enough or if new stable symbiont infections are established. Transmission of symbionts through plants likely represents an underappreciated means of infection, both in terms of symbiont epidemiology and the movement of symbionts to new host species.

  4. Sphingolipid Metabolism of a Sea Anemone Is Altered by the Presence of Dinoflagellate Symbionts.

    Science.gov (United States)

    Kitchen, Sheila A; Poole, Angela Z; Weis, Virginia M

    2017-12-01

    In host-microbe interactions, signaling lipids function in interpartner communication during both the establishment and maintenance of associations. Previous evidence suggests that sphingolipids play a role in the mutualistic cnidarian-Symbiodinium symbiosis. Exogenously applied sphingolipids have been shown to alter this partnership, though endogenous host regulation of sphingolipids by the sphingosine rheostat under different symbiotic conditions has not been characterized. The rheostat regulates levels of pro-survival sphingosine-1-phosphate (S1P) and pro-apoptotic sphingosine (Sph) through catalytic activities of sphingosine kinase (SPHK) and S1P phosphatase (SGPP). The role of the rheostat in recognition and establishment of cnidarian-Symbiodinium symbiosis was investigated in the sea anemone Aiptasia pallida by measuring gene expression, protein levels, and sphingolipid metabolites in symbiotic, aposymbiotic, and newly recolonized anemones. Comparison of two host populations showed that symbiotic animals from one population had lower SGPP gene expression and Sph lipid concentrations compared to aposymbiotic animals, while the other population had higher S1P concentrations than their aposymbiotic counterparts. In both populations, the host rheostat trended toward host cell survival in the presence of symbionts. Furthermore, upregulation of both rheostat enzymes on the first day of host recolonization by symbionts suggests a role for the rheostat in host-symbiont recognition during symbiosis onset. Collectively, these data suggest a regulatory role of sphingolipid signaling in cnidarian-Symbiodinium symbiosis and symbiont uptake.

  5. Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians

    KAUST Repository

    Wolfowicz, Iliona

    2016-09-01

    Symbiosis, defined as the persistent association between two distinct species, is an evolutionary and ecologically critical phenomenon facilitating survival of both partners in diverse habitats. The biodiversity of coral reef ecosystems depends on a functional symbiosis with photosynthetic dinoflagellates of the highly diverse genus Symbiodinium, which reside in coral host cells and continuously support their nutrition. The mechanisms underlying symbiont selection to establish a stable endosymbiosis in non-symbiotic juvenile corals are unclear. Here we show for the first time that symbiont selection patterns for larvae of two Acropora coral species and the model anemone Aiptasia are similar under controlled conditions. We find that Aiptasia larvae distinguish between compatible and incompatible symbionts during uptake into the gastric cavity and phagocytosis. Using RNA-Seq, we identify a set of candidate genes potentially involved in symbiosis establishment. Together, our data complement existing molecular resources to mechanistically dissect symbiont phagocytosis in cnidarians under controlled conditions, thereby strengthening the role of Aiptasia larvae as a powerful model for cnidarian endosymbiosis establishment.

  6. Advances in methods for identification and characterization of plant transporter function

    DEFF Research Database (Denmark)

    Larsen, Bo; Xu, Deyang; Halkier, Barbara Ann

    2017-01-01

    Transport proteins are crucial for cellular function at all levels. Numerous importers and exporters facilitate transport of a diverse array of metabolites and ions intra- and intercellularly. Identification of transporter function is essential for understanding biological processes at both......-based approaches. In this review, we highlight examples that illustrate how new technology and tools have advanced identification and characterization of plant transporter functions....

  7. Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri.

    Directory of Open Access Journals (Sweden)

    Tyler R Schleicher

    Full Text Available The beneficial symbiosis between the Hawaiian bobtail squid, Euprymna scolopes, and the bioluminescent bacterium, Vibrio fischeri, provides a unique opportunity to study host/microbe interactions within a natural microenvironment. Colonization of the squid light organ by V. fischeri begins a lifelong association with a regulated daily rhythm. Each morning the host expels an exudate from the light organ consisting of 95% of the symbiont population in addition to host hemocytes and shed epithelial cells. We analyzed the host and symbiont proteomes of adult squid exudate and surrounding light organ epithelial tissue using 1D- and 2D-polyacrylamide gel electrophoresis and multidimensional protein identification technology (MudPIT in an effort to understand the contribution of both partners to the maintenance of this association. These proteomic analyses putatively identified 1581 unique proteins, 870 proteins originating from the symbiont and 711 from the host. Identified host proteins indicate a role of the innate immune system and reactive oxygen species (ROS in regulating the symbiosis. Symbiont proteins detected enhance our understanding of the role of quorum sensing, two-component signaling, motility, and detoxification of ROS and reactive nitrogen species (RNS inside the light organ. This study offers the first proteomic analysis of the symbiotic microenvironment of the adult light organ and provides the identification of proteins important to the regulation of this beneficial association.

  8. Frequency Response Function Based Damage Identification for Aerospace Structures

    Science.gov (United States)

    Oliver, Joseph Acton

    Structural health monitoring technologies continue to be pursued for aerospace structures in the interests of increased safety and, when combined with health prognosis, efficiency in life-cycle management. The current dissertation develops and validates damage identification technology as a critical component for structural health monitoring of aerospace structures and, in particular, composite unmanned aerial vehicles. The primary innovation is a statistical least-squares damage identification algorithm based in concepts of parameter estimation and model update. The algorithm uses frequency response function based residual force vectors derived from distributed vibration measurements to update a structural finite element model through statistically weighted least-squares minimization producing location and quantification of the damage, estimation uncertainty, and an updated model. Advantages compared to other approaches include robust applicability to systems which are heavily damped, large, and noisy, with a relatively low number of distributed measurement points compared to the number of analytical degrees-of-freedom of an associated analytical structural model (e.g., modal finite element model). Motivation, research objectives, and a dissertation summary are discussed in Chapter 1 followed by a literature review in Chapter 2. Chapter 3 gives background theory and the damage identification algorithm derivation followed by a study of fundamental algorithm behavior on a two degree-of-freedom mass-spring system with generalized damping. Chapter 4 investigates the impact of noise then successfully proves the algorithm against competing methods using an analytical eight degree-of-freedom mass-spring system with non-proportional structural damping. Chapter 5 extends use of the algorithm to finite element models, including solutions for numerical issues, approaches for modeling damping approximately in reduced coordinates, and analytical validation using a composite

  9. Genomic diversification of giant enteric symbionts reflects host dietary lifestyles

    KAUST Repository

    Ngugi, David

    2017-08-24

    Herbivorous surgeonfishes are an ecologically successful group of reef fish that rely on marine algae as their principal food source. Here, we elucidated the significance of giant enteric symbionts colonizing these fishes regarding their roles in the digestive processes of hosts feeding predominantly on polysiphonous red algae and brown Turbinaria algae, which contain different polysaccharide constituents. Using metagenomics, single-cell genomics, and metatranscriptomic analyses, we provide evidence of metabolic diversification of enteric microbiota involved in the degradation of algal biomass in these fishes. The enteric microbiota is also phylogenetically and functionally simple relative to the complex lignocellulose-degrading microbiota of terrestrial herbivores. Over 90% of the enzymes for deconstructing algal polysaccharides emanate from members of a single bacterial lineage,

  10. Symbiont diversity in Reticulitermes santonensis (Isoptera: Rhinotermitidae): investigation strategy through proteomics.

    Science.gov (United States)

    Bauwens, Julien; Millet, Catherine; Tarayre, Cedric; Brasseur, Catherine; Destain, Jacqueline; Vandenbol, Micheline; Thonart, Philippe; Portetelle, Daniel; De Pauw, Edwin; Haubruge, Eric; Francis, Frederic

    2013-10-01

    The complex microbial community living in the hindgut of lower termites includes prokaryotes, flagellates, yeasts, and filamentous fungi. Many microorganisms are found in the termite gut, but only a few are thought to be involved in symbiotic association to participate in cellulose digestion. Proteomics provides analyses from both taxonomical and functional perspectives. We aimed to identify symbiont diversity in the gut of Reticulitermes santonensis (Feytaud), via complementary electrospray ionization associated to ion trap tandem mass spectrometry (LC-MS/MS) and two-dimensional gel electrophoresis associated to matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry analysis. One specific challenge to the study of lower termites is the relatively few data available on abundant symbiotic flagellates. Analysis based on LC-MS/MS revealed few protein families showing assignments to eukaryotes and the taxonomic origin of highly represented actins could not be established. Tubulins proved to be the most suitable protein family with which to identify flagellate populations from hindgut samples using LC-MS/MS, compared with other protein families, although this method targeted few prokaryotes in our assay. Similarly, two-dimensional gel electrophoresis associated to matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry did not succeed in identifying flagellate populations, but did permit the identification of most of the prokaryotic components of the symbiotic system. Finally, fungi and yeasts were identified by both methods. Owing to the lack of sequenced genes in flagellates, targeting tubulins for LC-MS/MS could allow fingerprints of flagellate populations to be established. Experimental and technical improvements might increase the efficiency of identification of prokaryotic populations in the near future, based on metaproteomic development.

  11. Comparative genomics of vesicomyid clam (Bivalvia: Mollusca chemosynthetic symbionts

    Directory of Open Access Journals (Sweden)

    Girguis Peter R

    2008-12-01

    Full Text Available Abstract Background The Vesicomyidae (Bivalvia: Mollusca are a family of clams that form symbioses with chemosynthetic gamma-proteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a reduced gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. Recently, two vesicomyid symbiont genomes were sequenced, illuminating the possible nutritional contributions of the symbiont to the host and making genome-wide evolutionary analyses possible. Results To examine the genomic evolution of the vesicomyid symbionts, a comparative genomics framework, including the existing genomic data combined with heterologous microarray hybridization results, was used to analyze conserved gene content in four vesicomyid symbiont genomes. These four symbionts were chosen to include a broad phylogenetic sampling of the vesicomyid symbionts and represent distinct chemosynthetic environments: cold seeps and hydrothermal vents. Conclusion The results of this comparative genomics analysis emphasize the importance of the symbionts' chemoautotrophic metabolism within their hosts. The fact that these symbionts appear to be metabolically capable autotrophs underscores the extent to which the host depends on them for nutrition and reveals the key to invertebrate colonization of these challenging environments.

  12. Standard methods for research on apis mellifera gut symbionts

    Science.gov (United States)

    Gut microbes can play an important role in digestion, disease resistance, and the general health of animals, but little is known about the biology of gut symbionts in Apis mellifera. This paper is part of a series on honey bee research methods, providing protocols for studying gut symbionts. We desc...

  13. Standard methods for research on Apis mellifera gut symbionts

    Science.gov (United States)

    Gut microbes can play an important role in digestion, disease resistance, and the general health of animals, but little is known about the biology of gut symbionts in Apis mellifera. This paper is part of a series on honey bee research methods, providing protocols for studying gut symbionts. We desc...

  14. Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: diversity and seasonal variability.

    Directory of Open Access Journals (Sweden)

    James R White

    Full Text Available BACKGROUND: Marine sponge species are of significant interest to many scientific fields including marine ecology, conservation biology, genetics, host-microbe symbiosis and pharmacology. One of the most intriguing aspects of the sponge "holobiont" system is the unique physiology, interaction with microbes from the marine environment and the development of a complex commensal microbial community. However, intraspecific variability and temporal stability of sponge-associated bacterial symbionts remain relatively unknown. METHODOLOGY/PRINCIPAL FINDINGS: We have characterized the bacterial symbiont community biodiversity of seven different individuals of the Caribbean reef sponge Axinella corrugata, from two different Florida reef locations during variable seasons using multiplex 454 pyrosequencing of 16 S rRNA amplicons. Over 265,512 high-quality 16 S rRNA sequences were generated and analyzed. Utilizing versatile bioinformatics methods and analytical software such as the QIIME and CloVR packages, we have identified 9,444 distinct bacterial operational taxonomic units (OTUs. Approximately 65,550 rRNA sequences (24% could not be matched to bacteria at the class level, and may therefore represent novel taxa. Differentially abundant classes between seasonal Axinella communities included Gammaproteobacteria, Flavobacteria, Alphaproteobacteria, Cyanobacteria, Acidobacter and Nitrospira. Comparisons with a proximal outgroup sponge species (Amphimedon compressa, and the growing sponge symbiont literature, indicate that this study has identified approximately 330 A. corrugata-specific symbiotic OTUs, many of which are related to the sulfur-oxidizing Ectothiorhodospiraceae. This family appeared exclusively within A. corrugata, comprising >34.5% of all sequenced amplicons. Other A. corrugata symbionts such as Deltaproteobacteria, Bdellovibrio, and Thiocystis among many others are described. CONCLUSIONS/SIGNIFICANCE: Slight shifts in several bacterial taxa

  15. A biologically inspired psychometric function for accuracy of visual identification as a function of exposure duration

    DEFF Research Database (Denmark)

    Petersen, Anders; Andersen, Tobias

    in modelling human performance in whole and partial report tasks in which multiple simultaneously presented letters are to be reported (Shibuya & Bundesen, 1988). Therefore, we investigated visual letter identification as a function of exposure duration. On each trial, a single randomly chosen letter (A...... rising from zero, then peaking, and finally decaying to a somewhat sustained plateau, mimicking closely observed instantaneous firing rates of monkey visual cortex neurons. The new psychometric function fits well to experimental data in both the present study and in a previous study of single...... into Bundesen’s Theory of Visual Attention (Bundesen, 1990), the new psychometric function enables closer fits to data from a previous whole and partial report experiment....

  16. Regional-scale identification of forest stands with protective functionality

    Science.gov (United States)

    Huber, Andreas; Kofler, Andreas; Fischer, Jan-Thomas

    2017-04-01

    In avalanche practice physical-based dynamical models are commonly utilized to estimate expected avalanche characteristics, such as runout lengths, velocities or impact pressures. These are of major interest for hazard zoning or planning and construction of mitigation measures and infrastructure in avalanche prone terrain. Physical-based models are commonly applied on a local scale for single avalanche tracks, where required model inputs are estimated based on local expertise and calculation times are not a limiting criterion. For regional scale studies on geophysical mass flows the area-wide availability of input parameters and required computational times present constraints on model applicability. Consequently, for studies encompassing larger areas, spatially distributed models with limited input parameter requirements have been developed and successfully applied in recent years. Published approaches often apply a combination of a one-dimensional physical or empirical runout model with different algorithms for flow propagation and spreading. Here, we describe a model for snow avalanche runout estimation based on an empirical runout criterion coupled with a simple propagation model. Avalanche runout lengths are obtained by a travel-angle and flow propagation is calculated based on hydrological flow directions derived from a raster digital elevation model. We compare model results to observed avalanche events and subsequently employ the model for a regional-scale identification of forest stands, which potentially provide direct protection for infrastructure objects. This comprises forested areas which are located in potential avalanche release areas and/or modeled avalanche tracks upslope of infrastructure objects. These are identified by back-tracing modeled flow paths from affected infrastructure objects to the respective release areas, which are delineated based on a combined thresholds for slope-angle and a proxy for seasonal snow cover. Results indicate that

  17. Acetic Acid Bacteria as Symbionts of Insects

    KAUST Repository

    Crotti, Elena

    2016-06-14

    Acetic acid bacteria (AAB) are being increasingly described as associating with different insect species that rely on sugar-based diets. AAB have been found in several insect orders, among them Diptera, Hemiptera, and Hymenoptera, including several vectors of plant, animal, and human diseases. AAB have been shown to associate with the epithelia of different organs of the host, they are able to move within the insect’s body and to be transmitted horizontally and vertically. Here, we review the ecology of AAB and examine their relationships with different insect models including mosquitoes, leafhoppers, and honey bees. We also discuss the potential use of AAB in symbiont-based control strategies, such as “Trojan-horse” agents, to block the transmission of vector-borne diseases.

  18. Saprotrophic fungal mycorrhizal symbionts in achlorophyllous orchids

    Science.gov (United States)

    Martos, Florent; Perry, Brian A; Padamsee, Mahajabeen; Roy, Mélanie; Pailler, Thierry

    2010-01-01

    Mycoheterotrophic plants are achlorophyllous plants that obtain carbon from their mycorrhizal fungi. They are usually considered to associate with fungi that are (1) specific of each mycoheterotrophic species and (2) mycorrhizal on surrounding green plants, which are the ultimate carbon source of the entire system. Here we review recent works revealing that some mycoheterotrophic plants are not fungal-specific, and that some mycoheterotrophic orchids associate with saprophytic fungi. A re-examination of earlier data suggests that lower specificity may be less rare than supposed in mycoheterotrophic plants. Association between mycoheterotrophic orchids and saprophytic fungi arose several times in the evolution of the two partners. We speculate that this indirectly illustrates why transition from saprotrophy to mycorrhizal status is common in fungal evolution. Moreover, some unexpected fungi occasionally encountered in plant roots should not be discounted as ‘molecular scraps’, since these facultatively biotrophic encounters may evolve into mycorrhizal symbionts in some other plants. PMID:20061806

  19. Symbiont-mediated RNA interference in insects

    Science.gov (United States)

    Whitten, Miranda M. A.; Facey, Paul D.; Del Sol, Ricardo; Fernández-Martínez, Lorena T.; Evans, Meirwyn C.; Mitchell, Jacob J.; Bodger, Owen G.

    2016-01-01

    RNA interference (RNAi) methods for insects are often limited by problems with double-stranded (ds) RNA delivery, which restricts reverse genetics studies and the development of RNAi-based biocides. We therefore delegated to insect symbiotic bacteria the task of: (i) constitutive dsRNA synthesis and (ii) trauma-free delivery. RNaseIII-deficient, dsRNA-expressing bacterial strains were created from the symbionts of two very diverse pest species: a long-lived blood-sucking bug, Rhodnius prolixus, and a short-lived globally invasive polyphagous agricultural pest, western flower thrips (Frankliniella occidentalis). When ingested, the manipulated bacteria colonized the insects, successfully competed with the wild-type microflora, and sustainably mediated systemic knockdown phenotypes that were horizontally transmissible. This represents a significant advance in the ability to deliver RNAi, potentially to a large range of non-model insects. PMID:26911963

  20. Rare symbionts may contribute to the resilience of coral-algal assemblages.

    Science.gov (United States)

    Ziegler, Maren; Eguíluz, Víctor M; Duarte, Carlos M; Voolstra, Christian R

    2018-01-01

    The association between corals and photosynthetic dinoflagellates (Symbiodinium spp.) is the key to the success of reef ecosystems in highly oligotrophic environments, but it is also their Achilles' heel due to its vulnerability to local stressors and the effects of climate change. Research during the last two decades has shaped a view that coral host-Symbiodinium pairings are diverse, but largely exclusive. Deep sequencing has now revealed the existence of a rare diversity of cryptic Symbiodinium assemblages within the coral holobiont, in addition to one or a few abundant algal members. While the contribution of the most abundant resident Symbiodinium species to coral physiology is widely recognized, the significance of the rare and low abundant background Symbiodinium remains a matter of debate. In this study, we assessed how coral-Symbiodinium communities assemble and how rare and abundant components together constitute the Symbiodinium community by analyzing 892 coral samples comprising >110 000 unique Symbiodinium ITS2 marker gene sequences. Using network modeling, we show that host-Symbiodinium communities assemble in non-random 'clusters' of abundant and rare symbionts. Symbiodinium community structure follows the same principles as bacterial communities, for which the functional significance of rare members (the 'rare bacterial biosphere') has long been recognized. Importantly, the inclusion of rare Symbiodinium taxa in robustness analyses revealed a significant contribution to the stability of the host-symbiont community overall. As such, it highlights the potential functions rare symbionts may provide to environmental resilience of the coral holobiont.

  1. Rare symbionts may contribute to the resilience of coral–algal assemblages

    KAUST Repository

    Ziegler, Maren

    2017-12-01

    The association between corals and photosynthetic dinoflagellates (Symbiodinium spp.) is the key to the success of reef ecosystems in highly oligotrophic environments, but it is also their Achilles‘ heel due to its vulnerability to local stressors and the effects of climate change. Research during the last two decades has shaped a view that coral host–Symbiodinium pairings are diverse, but largely exclusive. Deep sequencing has now revealed the existence of a rare diversity of cryptic Symbiodinium assemblages within the coral holobiont, in addition to one or a few abundant algal members. While the contribution of the most abundant resident Symbiodinium species to coral physiology is widely recognized, the significance of the rare and low abundant background Symbiodinium remains a matter of debate. In this study, we assessed how coral–Symbiodinium communities assemble and how rare and abundant components together constitute the Symbiodinium community by analyzing 892 coral samples comprising >110 000 unique Symbiodinium ITS2 marker gene sequences. Using network modeling, we show that host–Symbiodinium communities assemble in non-random ‘clusters‘ of abundant and rare symbionts. Symbiodinium community structure follows the same principles as bacterial communities, for which the functional significance of rare members (the ‘rare bacterial biosphere’) has long been recognized. Importantly, the inclusion of rare Symbiodinium taxa in robustness analyses revealed a significant contribution to the stability of the host–symbiont community overall. As such, it highlights the potential functions rare symbionts may provide to environmental resilience of the coral holobiont.

  2. Nonlinear System Identification via Basis Functions Based Time Domain Volterra Model

    Directory of Open Access Journals (Sweden)

    Yazid Edwar

    2014-07-01

    Full Text Available This paper proposes basis functions based time domain Volterra model for nonlinear system identification. The Volterra kernels are expanded by using complex exponential basis functions and estimated via genetic algorithm (GA. The accuracy and practicability of the proposed method are then assessed experimentally from a scaled 1:100 model of a prototype truss spar platform. Identification results in time and frequency domain are presented and coherent functions are performed to check the quality of the identification results. It is shown that results between experimental data and proposed method are in good agreement.

  3. Earthworm ecology affects the population structure of their Verminephrobacter symbionts

    DEFF Research Database (Denmark)

    Macedo Viana, Flavia Daniela; Jensen, Christopher Erik; Macey, Michael

    2016-01-01

    . Although several studies have addressed the Verminephrobacter diversity between worm species, the intra-species diversity of the symbiont population has never been investigated. To address symbiont population structure, we used a multi-locus sequence typing (MLST) approach on Verminephrobacter isolated...... from two contrasting ecological types of earthworm hosts: the high population density, fast reproducing compost worms, Eisenia andrei and E. fetida, and the low-density, slow reproducing Aporrectodea tuberculata, commonly found in garden soils; for both types, three distinct populations were...... across host individuals from the same population. Thus, host ecology shapes the population structure of the Verminephrobacter symbionts. The homogeneous symbiont populations in the compost worms indicate that Verminephrobacter can be transferred bi-parentally or via leaky horizontal transmission in high...

  4. Parasitic wasp responses to symbiont-based defense in aphids

    Directory of Open Access Journals (Sweden)

    Oliver Kerry M

    2012-02-01

    Full Text Available Abstract Background Recent findings indicate that several insect lineages receive protection against particular natural enemies through infection with heritable symbionts, but little is yet known about whether enemies are able to discriminate and respond to symbiont-based defense. The pea aphid, Acyrthosiphon pisum, receives protection against the parasitic wasp, Aphidius ervi, when infected with the bacterial symbiont Hamiltonella defensa and its associated bacteriophage APSE (Acyrthosiphon pisum secondary endosymbiont. Internally developing parasitoid wasps, such as A. ervi, use maternal and embryonic factors to create an environment suitable for developing wasps. If more than one parasitoid egg is deposited into a single aphid host (superparasitism, then additional complements of these factors may contribute to the successful development of the single parasitoid that emerges. Results We performed experiments to determine if superparasitism is a tactic allowing wasps to overcome symbiont-mediated defense. We found that the deposition of two eggs into symbiont-protected aphids significantly increased rates of successful parasitism relative to singly parasitized aphids. We then conducted behavioral assays to determine whether A. ervi selectively superparasitizes H. defensa-infected aphids. In choice tests, we found that A. ervi tends to deposit a single egg in uninfected aphids, but two or more eggs in H. defensa-infected aphids, indicating that oviposition choices may be largely determined by infection status. Finally, we identified differences in the quantity of the trans-β-farnesene, the major component of aphid alarm pheromone, between H. defensa-infected and uninfected aphids, which may form the basis for discrimination. Conclusions Here we show that the parasitic wasp A. ervi discriminates among symbiont-infected and uninfected aphids, and changes its oviposition behavior in a way that increases the likelihood of overcoming symbiont

  5. Tracking transmission of apicomplexan symbionts in diverse Caribbean corals.

    Directory of Open Access Journals (Sweden)

    Nathan L Kirk

    Full Text Available Symbionts in each generation are transmitted to new host individuals either vertically (parent to offspring, horizontally (from exogenous sources, or a combination of both. Scleractinian corals make an excellent study system for understanding patterns of symbiont transmission since they harbor diverse symbionts and possess distinct reproductive modes of either internal brooding or external broadcast spawning that generally correlate with vertical or horizontal transmission, respectively. Here, we focused on the under-recognized, but apparently widespread, coral-associated apicomplexans (Protista: Alveolata to determine if symbiont transmission depends on host reproductive mode. Specifically, a PCR-based assay was utilized towards identifying whether planula larvae and reproductive adults from brooding and broadcast spawning scleractinian coral species in Florida and Belize harbored apicomplexan DNA. Nearly all (85.5%; n = 85/89 examined planulae of five brooding species (Porites astreoides, Agaricia tenuifolia, Agaricia agaricites, Favia fragum, Mycetophyllia ferox and adults of P. astreoides were positive for apicomplexan DNA. In contrast, no (n = 0/10 apicomplexan DNA was detected from planulae of four broadcast spawning species (Acropora cervicornis, Acropora palmata, Pseudodiploria strigosa, and Orbicella faveolata and rarely in gametes (8.9%; n = 5/56 of these species sampled from the same geographical range as the brooding species. In contrast, tissue samples from nearly all (92.0%; n = 81/88 adults of the broadcast spawning species A. cervicornis, A. palmata and O. faveolata harbored apicomplexan DNA, including colonies whose gametes and planulae tested negative for these symbionts. Taken together, these data suggest apicomplexans are transmitted vertically in these brooding scleractinian coral species while the broadcast spawning scleractinian species examined here acquire these symbionts horizontally. Notably, these transmission

  6. Tracking transmission of apicomplexan symbionts in diverse Caribbean corals.

    Science.gov (United States)

    Kirk, Nathan L; Ritson-Williams, Raphael; Coffroth, Mary Alice; Miller, Margaret W; Fogarty, Nicole D; Santos, Scott R

    2013-01-01

    Symbionts in each generation are transmitted to new host individuals either vertically (parent to offspring), horizontally (from exogenous sources), or a combination of both. Scleractinian corals make an excellent study system for understanding patterns of symbiont transmission since they harbor diverse symbionts and possess distinct reproductive modes of either internal brooding or external broadcast spawning that generally correlate with vertical or horizontal transmission, respectively. Here, we focused on the under-recognized, but apparently widespread, coral-associated apicomplexans (Protista: Alveolata) to determine if symbiont transmission depends on host reproductive mode. Specifically, a PCR-based assay was utilized towards identifying whether planula larvae and reproductive adults from brooding and broadcast spawning scleractinian coral species in Florida and Belize harbored apicomplexan DNA. Nearly all (85.5%; n = 85/89) examined planulae of five brooding species (Porites astreoides, Agaricia tenuifolia, Agaricia agaricites, Favia fragum, Mycetophyllia ferox) and adults of P. astreoides were positive for apicomplexan DNA. In contrast, no (n = 0/10) apicomplexan DNA was detected from planulae of four broadcast spawning species (Acropora cervicornis, Acropora palmata, Pseudodiploria strigosa, and Orbicella faveolata) and rarely in gametes (8.9%; n = 5/56) of these species sampled from the same geographical range as the brooding species. In contrast, tissue samples from nearly all (92.0%; n = 81/88) adults of the broadcast spawning species A. cervicornis, A. palmata and O. faveolata harbored apicomplexan DNA, including colonies whose gametes and planulae tested negative for these symbionts. Taken together, these data suggest apicomplexans are transmitted vertically in these brooding scleractinian coral species while the broadcast spawning scleractinian species examined here acquire these symbionts horizontally. Notably, these transmission patterns are

  7. Marine sponges and their microbial symbionts: love and other relationships.

    Science.gov (United States)

    Webster, Nicole S; Taylor, Michael W

    2012-02-01

    Many marine sponges harbour dense and diverse microbial communities of considerable ecological and biotechnological importance. While the past decade has seen tremendous advances in our understanding of the phylogenetic diversity of sponge-associated microorganisms (more than 25 bacterial phyla have now been reported from sponges), it is only in the past 3-4 years that the in situ activity and function of these microbes has become a major research focus. Already the rewards of this new emphasis are evident, with genomics and experimental approaches yielding novel insights into symbiont function. Key steps in the nitrogen cycle [denitrification, anaerobic ammonium oxidation (Anammox)] have recently been demonstrated in sponges for the first time, with diverse bacteria - including the sponge-associated candidate phylum 'Poribacteria'- being implicated in these processes. In this minireview we examine recent major developments in the microbiology of sponges, and identify several research areas (e.g. biology of viruses in sponges, effects of environmental stress) that we believe are deserving of increased attention. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  8. Experimental evolution of a plant pathogen into a legume symbiont.

    Directory of Open Access Journals (Sweden)

    Marta Marchetti

    2010-01-01

    Full Text Available Rhizobia are phylogenetically disparate alpha- and beta-proteobacteria that have achieved the environmentally essential function of fixing atmospheric nitrogen in symbiosis with legumes. Ample evidence indicates that horizontal transfer of symbiotic plasmids/islands has played a crucial role in rhizobia evolution. However, adaptive mechanisms that allow the recipient genomes to express symbiotic traits are unknown. Here, we report on the experimental evolution of a pathogenic Ralstonia solanacearum chimera carrying the symbiotic plasmid of the rhizobium Cupriavidus taiwanensis into Mimosa nodulating and infecting symbionts. Two types of adaptive mutations in the hrpG-controlled virulence pathway of R. solanacearum were identified that are crucial for the transition from pathogenicity towards mutualism. Inactivation of the hrcV structural gene of the type III secretion system allowed nodulation and early infection to take place, whereas inactivation of the master virulence regulator hrpG allowed intracellular infection of nodule cells. Our findings predict that natural selection of adaptive changes in the legume environment following horizontal transfer has been a major driving force in rhizobia evolution and diversification and show the potential of experimental evolution to decipher the mechanisms leading to symbiosis.

  9. Helping hippocrates: a cross-functional approach to patient identification.

    Science.gov (United States)

    Greenly, Margaret A

    2006-08-01

    The Joint Commission on Accreditation of Healthcare Organizations National Patient Safety Goal 1, which requires the use of at least two patient identifiers, is the foundation for other patient safety goals. St. Francis Hospital involved staff and patients in the "Helping Hippocrates" Project, which used a "game" with staff and patients to ensure the accuracy of information on patients' identification (ID) bands. Members of all hospital departments assigned to a specific day were to compare the ID band with the patient census report and identify patients who had no ID band on their wrist and patients who had a band with inaccuracies. They were to also ask patients if the staff had checked the ID band before treatments or procedures. Also, the nurse manager was to select a patient to add to his or her own ID band a special band bearing the name Hippocrates. The department conducting the survey had to find Hippocrates. Internal data showed that patient identification errors declined from 8.2% to a sustained zero. Patient satisfaction data showed that since the inception of Helping Hippocrates, patients' perceptions of staffs compliance with ID verification showed steady improvement. Helping Hippocrates demonstrates the value of using an innovative problem-solving strategy that engages the entire organization.

  10. Quality or quantity: is nutrient transfer driven more by symbiont identity and productivity than by symbiont abundance?

    Science.gov (United States)

    Freeman, Christopher J; Thacker, Robert W; Baker, David M; Fogel, Marilyn L

    2013-06-01

    By forming symbiotic interactions with microbes, many animals and plants gain access to the products of novel metabolic pathways. We investigated the transfer of symbiont-derived carbon and nitrogen to the sponges Aplysina cauliformis, Aplysina fulva, Chondrilla caribensis, Neopetrosia subtriangularis and Xestospongia bocatorensis, all of which host abundant microbial populations, and Niphates erecta, which hosts a sparse symbiont community. We incubated sponges in light and dark bottles containing seawater spiked with (13)C- and (15)N-enriched inorganic compounds and then measured (13)C and (15)N enrichment in the microbial (nutrient assimilation) and sponge (nutrient transfer) fractions. Surprisingly, although most sponges hosting abundant microbial communities were more enriched in (13)C than N. erecta, only N. subtriangularis was more enriched in (15)N than N. erecta. Although photosymbiont abundance varied substantially across species, (13)C and (15)N enrichment was not significantly correlated with photosymbiont abundance. Enrichment was significantly correlated with the ratio of gross productivity to respiration (P:R), which varied across host species and symbiont phylotype. Because irradiance impacts P:R ratios, we also incubated A. cauliformis in (13)C-enriched seawater under different irradiances to determine whether symbiont carbon fixation and transfer are dependent on irradiance. Carbon fixation and transfer to the sponge host occurred in all treatments, but was greatest at higher irradiances and was significantly correlated with P:R ratios. Taken together, these results demonstrate that nutrient transfer from microbial symbionts to host sponges is influenced more by host-symbiont identities and P:R ratios than by symbiont abundance.

  11. Host-Symbiont Interactions for Potentially Managing Heteropteran Pests

    Directory of Open Access Journals (Sweden)

    Simone Souza Prado

    2012-01-01

    Full Text Available Insects in the suborder Heteroptera, the so-called true bugs, include over 40,000 species worldwide. This insect group includes many important agricultural pests and disease vectors, which often have bacterial symbionts associated with them. Some symbionts have coevolved with their hosts to the extent that host fitness is compromised with the removal or alteration of their symbiont. The first bug/microbial interactions were discovered over 50 years ago. Only recently, mainly due to advances in molecular techniques, has the nature of these associations become clearer. Some researchers have pursued the genetic modification (paratransgenesis of symbionts for disease control or pest management. With the increasing interest and understanding of the bug/symbiont associations and their ecological and physiological features, it will only be a matter of time before pest/vector control programs utilize this information and technique. This paper will focus on recent discoveries of the major symbiotic systems in Heteroptera, highlighting how the understanding of the evolutionary and biological aspects of these relationships may lead to the development of alternative techniques for efficient heteropteran pest control and suppression of diseases vectored by Heteroptera.

  12. A journey into the wild of the cnidarian model system Aiptasia and its symbionts

    KAUST Repository

    Voolstra, Christian R.

    2013-08-27

    The existence of coral reef ecosystems relies critically on the mutualistic relationship between calcifying cnidarians and photosynthetic, dinoflagellate endosymbionts in the genus Symbiodinium. Reef-corals have declined globally due to anthropogenic stressors, for example, rising sea-surface temperatures and pollution that often disrupt these symbiotic relationships (known as coral bleaching), exacerbating mass mortality and the spread of disease. This threatens one of the most biodiverse marine ecosystems providing habitats to millions of species and supporting an estimated 500 million people globally (Hoegh-Guldberg et al. 2007). Our understanding of cnidarian-dinoflagellate symbioses has improved notably with the recent application of genomic and transcriptomic tools (e.g. Voolstra et al. 2009; Bayer et al. 2012; Davy et al. 2012), but a model system that allows for easy manipulation in a laboratory environment is needed to decipher underlying cellular mechanisms important to the functioning of these symbioses. To this end, the sea anemone Aiptasia, otherwise known as a \\'pest\\' to aquarium hobbyists, is emerging as such a model system (Schoenberg & Trench 1980; Sunagawa et al. 2009; Lehnert et al. 2012). Aiptasia is easy to grow in culture and, in contrast to its stony relatives, can be maintained aposymbiotically (i.e. dinoflagellate free) with regular feeding. However, we lack basic information on the natural distribution and genetic diversity of these anemones and their endosymbiotic dinoflagellates. These data are essential for placing the significance of this model system into an ecological context. In this issue of Molecular Ecology, Thornhill et al. (2013) are the first to present genetic evidence on the global distribution, diversity and population structure of Aiptasia and its associated Symbiodinium spp. By integrating analyses of the host and symbiont, this research concludes that the current Aitpasia taxonomy probably needs revision and that two

  13. Identification of Novel Functional Inhibitors of Acid Sphingomyelinase

    DEFF Research Database (Denmark)

    Kornhuber, Johannes; Muehlbacher, Markus; Trapp, Stefan

    2011-01-01

    We describe a hitherto unknown feature for 27 small drug-like molecules, namely functional inhibition of acid sphingomyelinase (ASM). These entities named FIASMAs (Functional Inhibitors of Acid SphingoMyelinAse), therefore, can be potentially used to treat diseases associated with enhanced activi...

  14. Functional recognition imaging using artificial neural networks: applications to rapid cellular identification via broadband electromechanical response

    Energy Technology Data Exchange (ETDEWEB)

    Nikiforov, M P; Guo, S; Kalinin, S V; Jesse, S [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831 (United States); Reukov, V V; Thompson, G L; Vertegel, A A, E-mail: sergei2@ornl.go [Department of Bioengineering, Clemson University, Clemson, SC 29634 (United States)

    2009-10-07

    Functional recognition imaging in scanning probe microscopy (SPM) using artificial neural network identification is demonstrated. This approach utilizes statistical analysis of complex SPM responses at a single spatial location to identify the target behavior, which is reminiscent of associative thinking in the human brain, obviating the need for analytical models. We demonstrate, as an example of recognition imaging, rapid identification of cellular organisms using the difference in electromechanical activity over a broad frequency range. Single-pixel identification of model Micrococcus lysodeikticus and Pseudomonas fluorescens bacteria is achieved, demonstrating the viability of the method.

  15. Metagenomic Analysis of Microbial Symbionts in a Gutless Worm

    Energy Technology Data Exchange (ETDEWEB)

    Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N.; Hunteman, Marcel; Richter, Michael; Gloeckner, Frank Oliver; Boeffelli, Dario; Barry, Kerrie W.; Shapiro, Harris J.; Anderson, Iain J.; Szeto, Ernest; Kyrpides, Nikos C.; Mussmann, Marc; Amann, Rudolf; Bergin, Claudia; Ruehland, Caroline; Rubin, Edward M.; Dubilier, Nicole

    2006-05-01

    Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulphur-oxidizing and sulphate-reducing bacteria, all of which are capable of carbon fixation, thus providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits.

  16. Almost there: transmission routes of bacterial symbionts between trophic levels.

    Directory of Open Access Journals (Sweden)

    Elad Chiel

    Full Text Available Many intracellular microbial symbionts of arthropods are strictly vertically transmitted and manipulate their host's reproduction in ways that enhance their own transmission. Rare horizontal transmission events are nonetheless necessary for symbiont spread to novel host lineages. Horizontal transmission has been mostly inferred from phylogenetic studies but the mechanisms of spread are still largely a mystery. Here, we investigated transmission of two distantly related bacterial symbionts--Rickettsia and Hamiltonella--from their host, the sweet potato whitefly, Bemisia tabaci, to three species of whitefly parasitoids: Eretmocerus emiratus, Eretmocerus eremicus and Encarsia pergandiella. We also examined the potential for vertical transmission of these whitefly symbionts between parasitoid generations. Using florescence in situ hybridization (FISH and transmission electron microscopy we found that Rickettsia invades Eretmocerus larvae during development in a Rickettsia-infected host, persists in adults and in females, reaches the ovaries. However, Rickettsia does not appear to penetrate the oocytes, but instead is localized in the follicular epithelial cells only. Consequently, Rickettsia is not vertically transmitted in Eretmocerus wasps, a result supported by diagnostic polymerase chain reaction (PCR. In contrast, Rickettsia proved to be merely transient in the digestive tract of Encarsia and was excreted with the meconia before wasp pupation. Adults of all three parasitoid species frequently acquired Rickettsia via contact with infected whiteflies, most likely by feeding on the host hemolymph (host feeding, but the rate of infection declined sharply within a few days of wasps being removed from infected whiteflies. In contrast with Rickettsia, Hamiltonella did not establish in any of the parasitoids tested, and none of the parasitoids acquired Hamiltonella by host feeding. This study demonstrates potential routes and barriers to horizontal

  17. Identification based on fusion of cardiovascular function measurements

    Science.gov (United States)

    Israel, Steven A.; Irvine, John M.; Wiederhold, Brenda K.; Wiederhold, Mark D.

    2008-03-01

    Recent investigations indicate cardiovascular function is a viable biometric. This paper explores biometric techniques based on multiple modalities for sensing cardiovascular function. Analysis of data acquired with an electrocardiogram (ECG) combined with corresponding data from pulse oximetry and blood pressure indicates that features can be extracted from the signals, which correspond to individuals. While a person's heart rate can vary with mental and emotional state, certain features corresponding to the heartbeat appear to be unique to the individual. Our protocol induced a range of mental and emotional states in the subject and the analysis identifies features of the cardiovascular signals that are invariant to mental and emotional state. Furthermore, the three measures of cardiovascular function provide independent information, which can be fused to achieve robust performance compared to a single modality.

  18. Long‑term ungulate exclusion reduces fungal symbiont prevalence in native grasslands

    Science.gov (United States)

    Jennifer A. Rudgers; Rebecca A. Fletcher; Eric Olivas; Carolyn A. Young; Nikki D. Charlton; Dean E. Pearson; John L. Maron

    2016-01-01

    When symbionts are inherited by offspring, they can have substantial ecological and evolutionary consequences because they occur in all host life stages. Although natural frequencies of inherited symbionts are commonly <100 %, few studies investigate the ecological drivers of variation in symbiont prevalence. In plants, inherited fungal endophytes can...

  19. Wave mode identification via wave distribution function analysis

    Czech Academy of Sciences Publication Activity Database

    Oscarsson, T.; Sternberg, G.; Santolík, Ondřej

    2001-01-01

    Roč. 26, 6, Part C (2001), s. 229-235 ISSN 1464-1917 R&D Projects: GA ČR GA205/99/1712 Institutional research plan: CEZ:AV0Z3042911 Keywords : auroral magnetosphere * wave propagation * wave distribution function Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 0.399, year: 2001

  20. Complexity of Identification and Dualization of Positive Boolean Functions

    NARCIS (Netherlands)

    J.C. Bioch (Cor); T. Ibaraki

    1995-01-01

    textabstractWe consider in this paper the problem of identifying min T(f{hook}) and max F(f{hook}) of a positive (i.e., monotone) Boolean function f{hook}, by using membership queries only, where min T(f{hook}) (max F(f{hook})) denotes the set of minimal true vectors (maximal false vectors) of

  1. Identification of older hospitalized patients at risk for functional decline

    NARCIS (Netherlands)

    Hoogerduijn, J.G.

    2011-01-01

    Between 30% and 60% of older patients experience functional decline after hospitalization, resulting in a decline in health-related quality of life and autonomy. This is associated with increased risk of readmission, nursing home placement and mortality, increased length of hospital stay and

  2. Identification of a supplier network through Quality Function Deployment

    DEFF Research Database (Denmark)

    Kristensen, Preben Sander; Holmen, Elsebeth

    1994-01-01

    During 1993-94 the authors followed a product development process in a Danish Butter Cookie company. The process was structured according to the Quality Function Deployment technique House of Quality. Customer attributes were derived from a discus a diabetics end-user focus group. During a series...

  3. Numerical study on identification of transfer functions in a feedback system and model reduction

    International Nuclear Information System (INIS)

    Kishida, Kuniharu

    1997-01-01

    Identification of transfer function matrices in a feedback system is discussed by using the singular value decomposition of Hankel matrix from the viewpoint of inverse problems. A method of model reduction is considered, and selection criteria are proposed for identification of them. Transformation formula between open loop and closed loop transfer function matrices are determined from the feedback loop structure, and they are needed for identification of open loop transfer function matrices under such a condition where the feedback system is in a minimum phase. Though the identifiability of open loop transfer function matrices can be examined in the framework of innovation model equivalent to the feedback system, there are pole-zero cancellations in the identification of them. The method to reduce a model order of an open loop transfer function is discussed by using the singular value decomposition of a gramian given by the open loop transfer function with higher degree. To check reliability of the present algorithm, a simulation study is performed for an example. (author)

  4. Identification of Functional Information Subgraphs in Complex Networks

    International Nuclear Information System (INIS)

    Bettencourt, Luis M. A.; Gintautas, Vadas; Ham, Michael I.

    2008-01-01

    We present a general information theoretic approach for identifying functional subgraphs in complex networks. We show that the uncertainty in a variable can be written as a sum of information quantities, where each term is generated by successively conditioning mutual informations on new measured variables in a way analogous to a discrete differential calculus. The analogy to a Taylor series suggests efficient optimization algorithms for determining the state of a target variable in terms of functional groups of other nodes. We apply this methodology to electrophysiological recordings of cortical neuronal networks grown in vitro. Each cell's firing is generally explained by the activity of a few neurons. We identify these neuronal subgraphs in terms of their redundant or synergetic character and reconstruct neuronal circuits that account for the state of target cells

  5. Transfer Function Identification of an Electro-Rheological Actuator

    Science.gov (United States)

    Brookfield, D. J.; Dlodlo, Z. B.

    A fluid clutch utilising an Electro-Rheological (ER) suspension provides a controlled torque coupling between input and output through the control of the applied electric field. If the input is driven at constant speed the device can be considered as an ER torque actuator and thus be used to drive robot links or other mechanisms requiring precise positioning. Such an ER torque actuator can replace a DC servo-motor in robotic applications with the benefits of low time constant and smooth output torque unaffected by cogging (i.e. variation in torque of a DC motor as the magnetic reluctance of the armature-stator path changes with rotation). Although the ER actuator has many benefits, it suffers from a non-linear and time varying relationship between input voltage and output torque. These undesirable characteristics can be mitigated by providing a local closed loop controller around the system. The design of such a controller requires a knowledge of the relationship between the applied voltage and output torque; i.e. the transfer function of the actuator. This transfer function has been determined by observing the response of an ER torque actuator in the frequency domain. It is shown that a linear transfer function model reasonable represents the actuator behaviour, that the actuator is a stable second order system and that the time constant of the clutch studied is sufficiently short to hold considerable promise for robotic applications. Furthermore, the maximum torque capability is shown to be sufficient for many medium scale industrial robots.

  6. Strict Host-Symbiont Cospeciation and Reductive Genome Evolution in Insect Gut Bacteria

    Science.gov (United States)

    Hosokawa, Takahiro; Kikuchi, Yoshitomo; Nikoh, Naruo; Shimada, Masakazu; Fukatsu, Takema

    2006-01-01

    Host-symbiont cospeciation and reductive genome evolution have been identified in obligate endocellular insect symbionts, but no such example has been identified from extracellular ones. Here we first report such a case in stinkbugs of the family Plataspidae, wherein a specific gut bacterium is vertically transmitted via “symbiont capsule.” In all of the plataspid species, females produced symbiont capsules upon oviposition and their gut exhibited specialized traits for capsule production. Phylogenetic analysis showed that the plataspid symbionts constituted a distinct group in the γ-Proteobacteria, whose sister group was the aphid obligate endocellular symbionts Buchnera. Removal of the symbionts resulted in retarded growth, mortality, and sterility of the insects. The host phylogeny perfectly agreed with the symbiont phylogeny, indicating strict host-symbiont cospeciation despite the extracellular association. The symbionts exhibited AT-biased nucleotide composition, accelerated molecular evolution, and reduced genome size, as has been observed in obligate endocellular insect symbionts. These findings suggest that not the endocellular conditions themselves but the population genetic attributes of the vertically transmitted symbionts are probably responsible for the peculiar genetic traits of these insect symbionts. We proposed the designation “Candidatus Ishikawaella capsulata” for the plataspid symbionts. The plataspid stinkbugs, wherein the host-symbiont associations can be easily manipulated, provide a novel system that enables experimental approaches to previously untouched aspects of the insect-microbe mutualism. Furthermore, comparative analyses of the sister groups, the endocellular Buchnera and the extracellular Ishikawaella, would lead to insights into how the different symbiotic lifestyles have affected their genomic evolution. PMID:17032065

  7. Sodium chloride accumulation in glycophyte plants with cyanobacterial symbionts.

    Science.gov (United States)

    Green, Thomas George Allan; Sancho, Leopoldo G; Pintado, Ana; Saco, Dolores; Martín, Soledad; Arróniz-Crespo, María; Angel Casermeiro, Miguel; de la Cruz Caravaca, Maria Teresa; Cameron, Steven; Rozzi, Ricardo

    2017-11-01

    The majority of plant species are glycophytes and are not salt-tolerant and maintain low sodium levels within their tissues; if . high tissue sodium concentrations do occur, it is in response to elevated environmental salt levels. Here we report an apparently novel and taxonomically diverse grouping of plants that continuously maintain high tissue sodium contents and share the rare feature of possessing symbiotic cyanobacteria. Leaves of Gunnera magellanica in Tierra del Fuego always had sodium contents (dry weight basis) of around 4.26 g kg -1 , about 20 times greater than measured in other higher plants in the community (0.29 g kg -1 ). Potassium and chloride levels were also elevated. This was not a response to soil sodium and chloride levels as these were low at all sites. High sodium contents were also confirmed in G. magellanica from several other sites in Tierra del Fuego, in plants taken to, and cultivated in Madrid for 2 years at low soil salt conditions, and also in other free living or cultivated species of Gunnera from the UK and New Zealand. Gunnera species are the only angiosperms that possess cyanobacterial symbionts so we analysed other plants that have this rather rare symbiosis, all being glycophytes. Samples of Azolla , a floating aquatic fern, from Europe and New Zealand all had even higher sodium levels than Gunnera . Roots of the gymnosperm Cycas revoluta had lower sodium contents (2.52 ± 0.34 g kg -1 ) but still higher than the non-symbiotic glycophytes. The overaccumulation of salt even when it is at low levels in the environment appears to be linked to the possession of a cyanobacterial symbiosis although the actual functional basis is unclear.

  8. Antibiotics, primary symbionts and wing polyphenism in three aphid species.

    Science.gov (United States)

    Hardie, Jim; Leckstein, Peter

    2007-08-01

    The possible role of the primary Buchnera symbionts in wing polyphenism is examined in three aphid species. Presumptive winged aphids were fed on antibiotic-treated beans to destroy these symbionts. As previously reported, this leads to inhibited growth and low/zero fecundity. When such treatment is applied to the short-day-induced gynoparae (the winged autumn migrant) of the black bean aphid, Aphis fabae, it also causes many insects to develop as wingless or winged/wingless intermediate adult forms (apterisation). However, whilst antibiotic treatment of crowd-induced, long-day winged forms of the pea aphid, Acyrthosiphon pisum (a green and a pink clone) and the vetch aphid, Megoura viciae has similar effects on size and fecundity, it does not affect wing development. Food deprivation also promotes apterisation in A. fabae gynoparae but not in the crowd-induced winged morphs of the other two species. Thus, it appears that apterisation in A. fabae is not a direct effect of antibiotic treatment or a novel role for symbionts but is most likely related to impaired nutrition induced by the loss of the symbiont population.

  9. A nuptially transmitted Ichthyosproean symbiont of Tenebrio molitor (Coleoptera: Tenebrionidae)

    Science.gov (United States)

    The yellow mealworm, Tenebrio molitor, harbors a symbiont that has spores with a thick, laminated wall and infects the fat body and ventral nerve chord of adult and larval beetles. In adult males, there is heavy infection of the epithelial cells of the testes and between testes lobes with occasional...

  10. Symbiont Dependent Thermal Bleaching Susceptiblity in Two Reef ...

    African Journals Online (AJOL)

    Symbiont Dependent Thermal Bleaching Susceptiblity in Two Reef-building Corals, Stylophora pistillata and Platygyra ryukyuensis . ... Symbiodinium ITS2 types exhibit diverse photo-physiological responses to thermal stress, and may partially explain the variable bleaching susceptibilities of some hermatypic coral species.

  11. Identification and functional characterization of cardiac pacemaker cells in zebrafish.

    Directory of Open Access Journals (Sweden)

    Federico Tessadori

    Full Text Available In the mammalian heart a conduction system of nodes and conducting cells generates and transduces the electrical signals evoking myocardial contractions. Specialized pacemaker cells initiating and controlling cardiac contraction rhythmicity are localized in an anatomically identifiable structure of myocardial origin, the sinus node. We previously showed that in mammalian embryos sinus node cells originate from cardiac progenitors expressing the transcription factors T-box transcription factor 3 (Tbx3 and Islet-1 (Isl1. Although cardiac development and function are strikingly conserved amongst animal classes, in lower vertebrates neither structural nor molecular distinguishable components of a conduction system have been identified, questioning its evolutionary origin. Here we show that zebrafish embryos lacking the LIM/homeodomain-containing transcription factor Isl1 display heart rate defects related to pacemaker dysfunction. Moreover, 3D reconstructions of gene expression patterns in the embryonic and adult zebrafish heart led us to uncover a previously unidentified, Isl1-positive and Tbx2b-positive region in the myocardium at the junction of the sinus venosus and atrium. Through their long interconnecting cellular protrusions the identified Isl1-positive cells form a ring-shaped structure. In vivo labeling of the Isl1-positive cells by transgenic technology allowed their isolation and electrophysiological characterization, revealing their unique pacemaker activity. In conclusion we demonstrate that Isl1-expressing cells, organized as a ring-shaped structure around the venous pole, hold the pacemaker function in the adult zebrafish heart. We have thereby identified an evolutionary conserved, structural and molecular distinguishable component of the cardiac conduction system in a lower vertebrate.

  12. Communication with your packaging: possibilities for intelligent functions and identification methods in packaging

    NARCIS (Netherlands)

    Schilthuizen, S.F.

    1999-01-01

    Intelligent functions in packaging can have all kinds of forms. This paper focuses on methods of identifying a packaging and other important tasks which can be performed after identification: tracing, tracking, monitoring and sensing of conditions. The recent developments in ID-technology and sensor

  13. Identification of differential item functioning in multiple-group settings: a multivariate outlier detection approach

    NARCIS (Netherlands)

    Magis, D.; de Boeck, P.

    2011-01-01

    We focus on the identification of differential item functioning (DIF) when more than two groups of examinees are considered. We propose to consider items as elements of a multivariate space, where DIF items are outlying elements. Following this approach, the situation of multiple groups is a quite

  14. CONFAC Decomposition Approach to Blind Identification of Underdetermined Mixtures Based on Generating Function Derivatives

    NARCIS (Netherlands)

    de Almeida, Andre L. F.; Luciani, Xavier; Stegeman, Alwin; Comon, Pierre

    2012-01-01

    This work proposes a new tensor-based approach to solve the problem of blind identification of underdetermined mixtures of complex-valued sources exploiting the cumulant generating function (CGF) of the observations. We show that a collection of second-order derivatives of the CGF of the

  15. Functional fractional calculus for system identification and controls

    CERN Document Server

    Das, Shantanu

    2008-01-01

    This work is inspired by thought to have an overall fuel-ef?cient nuclear plant control system. I picked up the topic in 2002 while deriving the reactor control laws, which aimed at fuel ef?ciency. Controlling the nuclear reactor close to its natural behavior by concept of exponent shape governor, ratio control and use of logarithmic logic, aims at the fuel ef?ciency. The power-maneuvering trajectory is obtained by shaped-normalized-period function, and this de?nes the road map on which the reactor should be governed. The experience of this concept governing the Atomic Power Plant of Tarapur Atomic Power Station gives lesser overall gains compared to the older plants, where conventional proportional integral and deri- tive type (PID) scheme is employed. Therefore, this motivation led to design the scheme for control system than the conventional schemes to aim at overall plant ef?ciency. Thus, I felt the need to look beyondPID and obtained the answer in fr- tional order control system, requiring fractional cal...

  16. Identification and Immune Functional Characterization of Pigeon TLR7

    Science.gov (United States)

    Xiong, Dan; Song, Li; Pan, Zhiming; Chen, Xiang; Geng, Shizhong; Jiao, Xinan

    2015-01-01

    Toll-like receptor 7 (TLR7) is activated by single-stranded RNA and synthetic imidazoquinoline components, and induces interferon production. In this study, we cloned the TLR7 gene from King pigeon (Columba livia). The TLR7 open reading frame is 3144 bp and encodes a 1047-amino acid protein, consisting of a canonical TLR composition with 15 leucine-rich repeats (LRRs). Amino acid-inserting modifications were found at position 15 of LRR2, LRR11, LRR13, and LRR14 and position 10 of LRR10. The tissue distribution of pigeon TLR7 suggests that immune-associated tissues, especially the spleen and liver, have high TLR7 expression. HEK293T cells transfected with pigeon TLR7 plasmid responded to the agonist R848, indicating a functional TLR7 homolog. Following R848 stimulation of pigeon peripheral blood mononuclear cells, the levels of IFN-γ, IL-6, IL-8, CCL5, and IL-10 mRNA, assessed using quantitative real-time PCR, were significantly up-regulated. After Newcastle disease virus vaccine strain LaSota inoculation and agonist R848 injection, the level of TLR7 mRNA in the spleen of pigeons increased significantly in the R848-injected group, but decreased in the LaSota-inoculated group at three day post-infection (d.p.i.). The mRNA levels of inflammatory cytokines and chemokines were significantly upregulated in both LaSota-inoculated and R848-injected groups. Triggering pigeon TLR7 leads to robust up-regulation of inflammatory cytokines and chemokines, suggesting an important role in the innate immune response. PMID:25874762

  17. Dark production of extracellular superoxide by the coral Porites astreoides and representative symbionts

    Directory of Open Access Journals (Sweden)

    Tong Zhang

    2016-11-01

    Full Text Available The reactive oxygen species (ROS superoxide has been implicated in both beneficial and detrimental processes in coral biology, ranging from pathogenic disease resistance to coral bleaching. Despite the critical role of ROS in coral health, there is a distinct lack of ROS measurements and thus an incomplete understanding of underpinning ROS sources and production mechanisms within coral systems. Here, we quantified in situ extracellular superoxide concentrations at the surfaces of aquaria-hosted Porites astreoides during a diel cycle. High concentrations of superoxide (~10’s of nM were present at coral surfaces, and these levels did not change significantly as a function of time of day. These results indicate that the coral holobiont produces extracellular superoxide in the dark, independent of photosynthesis. As a short-lived anion at physiological pH, superoxide has a limited ability to cross intact biological membranes. Further, removing surface mucus layers from the P. astreoides colonies did not impact external superoxide concentrations. We therefore attribute external superoxide derived from the coral holobiont under these conditions to the activity of the coral host epithelium, rather than mucus-derived epibionts or internal sources such as endosymbionts (e.g., Symbiodinium. However, endosymbionts likely contribute to internal ROS levels via extracellular superoxide production. Indeed, common coral symbionts, including multiple strains of Symbiodinium (clades A to D and the bacterium Endozoicomonas montiporae LMG 24815, produced extracellular superoxide in the dark and at low light levels. Further, representative P. astreoides symbionts, Symbiodinium CCMP2456 (clade A and E. montiporae, produced similar concentrations of superoxide alone and in combination with each other, in the dark and low light, and regardless of time of day. Overall, these results indicate that healthy, non-stressed P. astreoides and representative symbionts produce

  18. The dominant detritus-feeding invertebrate in Arctic peat soils derives its essential amino acids from gut symbionts

    DEFF Research Database (Denmark)

    Larsen, Thomas; Ventura, Marc; Maraldo, Kristine

    2016-01-01

    insufficiencies of macronutrients such as essential amino acids (EAA). Documenting whether gut symbionts also function as partners for symbiotic EAA supplementation is important because the question of how some detritivores are able to subsist on nutritionally insufficient diets has remained unresolved. 3....... To answer this poorly understood nutritional aspect of symbiont-host interactions, we studied the enchytraeid worm, a bulk soil feeder that thrives in Arctic peatlands. In a combined field and laboratory study, we employed stable isotope fingerprinting of amino acids to identify the biosynthetic origins...... of amino acids to bacteria, fungi and plants in enchytraeids. 4. Enchytraeids collected from Arctic peatlands derived more than 80% of their EAA from bacteria. In a controlled feeding study with the enchytraeid Enchytraeus crypticus, EAA derived almost exclusively from gut bacteria when the worms fed...

  19. Identification of hidden failures in process control systems through function-oriented system analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jalashgar, A.

    1997-05-01

    The main subject of this thesis is to identify hidden failures in process control systems by developing and using a function-oriented system analysis method. Qualitative failure analysis and the characteristics of the classical failure analysis methods and function-oriented modelling methods are covered. The general limitations of the methods in connection with the identification and representation of hidden failures are discussed. The discussion has led to the justification of developing and using a function-oriented system analysis method to identify and represent the capabilities of the system components, which realize different sets of functions in connection with different sets of goals that the system must achieve. A terminology is introduced to define the basic aspects of technical systems including goals, functions, capabilities and physical structure. A function-oriented system analysis method using this terminology and a tailored combination of the two function-oriented modelling approaches, is also introduced. It is then explained how the method can be applied in the identification and representation of hidden failures. The building blocks of a knowledge-oriented system to perform the diagnosis on the basis of the developed method are equally described. A prototype of the knowledge-based system is developed to demonstrate the applicability of the function-oriented system analysis method and the knowledge-based system. The prototype is implemented within the object-oriented software environment G2. (au) 65 ills., 32 refs.

  20. Individual Identification Using Functional Brain Fingerprint Detected by Recurrent Neural Network.

    Science.gov (United States)

    Chen, Shiyang; Hu, Xiaoping P

    2018-03-20

    Individual identification based on brain function has gained traction in literature. Investigating individual differences in brain function can provide additional insights into the brain. In this work, we introduce a recurrent neural network based model for identifying individuals based on only a short segment of resting state functional MRI data. In addition, we demonstrate how the global signal and differences in atlases affect the individual identifiability. Furthermore, we investigate neural network features that exhibit the uniqueness of each individual. The results indicate that our model is able to identify individuals based on neural features and provides additional information regarding brain dynamics.

  1. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance.

    Science.gov (United States)

    Coleman-Derr, Devin; Tringe, Susannah G

    2014-01-01

    The exponential growth in world population is feeding a steadily increasing global need for arable farmland, a resource that is already in high demand. This trend has led to increased farming on subprime arid and semi-arid lands, where limited availability of water and a host of environmental stresses often severely reduce crop productivity. The conventional approach to mitigating the abiotic stresses associated with arid climes is to breed for stress-tolerant cultivars, a time and labor intensive venture that often neglects the complex ecological context of the soil environment in which the crop is grown. In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. Here, we highlight many of the advantages of these symbiont-based approaches and argue in favor of the broader recognition of crop species as ecological niches for a diverse community of microorganisms that function in concert with their plant hosts and each other to thrive under fluctuating environmental conditions.

  2. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance

    Directory of Open Access Journals (Sweden)

    Devin eColeman-Derr

    2014-06-01

    Full Text Available The exponential growth in world population is feeding a steadily increasing global need for arable farmland, a resource that is already in high demand. This trend has led to increased farming on subprime arid and semi-arid lands, where limited availability of water and a host of environmental stresses often severely reduce crop productivity. The conventional approach to mitigating the abiotic stresses associated with arid climes is to breed for stress-tolerant cultivars, a time and labor intensive venture that often neglects the complex ecological context of the soil environment in which the crop is grown. In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. Here, we highlight many of the advantages of these symbiont-based approaches and argue in favor of the broader recognition of crop species as ecological niches for a diverse community of microorganisms that function in concert with their plant hosts and each other to thrive under fluctuating environmental conditions.

  3. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance

    Energy Technology Data Exchange (ETDEWEB)

    Coleman-Derr, Devin [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Tringe, Susannah G. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

    2014-06-06

    The exponential growth in world population is feeding a steadily increasing global need for arable farmland, a resource that is already in high demand. This trend has led to increased farming on subprime arid and semi-arid lands, where limited availability of water and a host of environmental stresses often severely reduce crop productivity. The conventional approach to mitigating the abiotic stresses associated with arid climes is to breed for stress-tolerant cultivars, a time and labor intensive venture that often neglects the complex ecological context of the soil environment in which the crop is grown. In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. Here in this paper, we highlight many of the advantages of these symbiont-based approaches and argue in favor of the broader recognition of crop species as ecological niches for a diverse community of microorganisms that function in concert with their plant hosts and each other to thrive under fluctuating environmental conditions

  4. Symbiont acquisition as neoseme: origin of species and higher taxa

    Science.gov (United States)

    Bermudes, D.; Margulis, L.

    1987-01-01

    We examine the hypothesis that, in the origin of species and higher taxa of eukaryotes, symbiont acquisition followed by partner integration has been equivalent to neoseme appearance leading to speciation. The formation of stable symbiotic associations involves partner-surface recognition, behavioral and metabolic interaction, and, in some cases, gene product (RNA, protein) and genic (RNA, DNA) integration. This analysis is applied here to examples of neosemes that define specific taxa and to neosemes in plants, fungi, and animals that involve the appearance of new types of tissue. If this hypothesis is correct--if the origin of major genetic variation leading to speciation and even higher taxa may occur through symbiont acquisition and integration--then the analysis of "origins of species and higher taxa" becomes analogous to the study of microbial community ecology.

  5. Comparative Genomic Analysis of Holospora spp., Intranuclear Symbionts of Paramecia

    Directory of Open Access Journals (Sweden)

    Sofya K. Garushyants

    2018-04-01

    Full Text Available While most endosymbiotic bacteria are transmitted only vertically, Holospora spp., an alphaproteobacterium from the Rickettsiales order, can desert its host and invade a new one. All bacteria from the genus Holospora are intranuclear symbionts of ciliates Paramecium spp. with strict species and nuclear specificity. Comparative metabolic reconstruction based on the newly sequenced genome of Holospora curviuscula, a macronuclear symbiont of Paramecium bursaria, and known genomes of other Holospora species shows that even though all Holospora spp. can persist outside the host, they cannot synthesize most of the essential small molecules, such as amino acids, and lack some central energy metabolic pathways, including glycolysis and the citric acid cycle. As the main energy source, Holospora spp. likely rely on nucleotides pirated from the host. Holospora-specific genes absent from other Rickettsiales are possibly involved in the lifestyle switch from the infectious to the reproductive form and in cell invasion.

  6. A nuptially transmitted ichthyosporean symbiont of Tenebrio molitor (Coleoptera: Tenebrionidae).

    Science.gov (United States)

    Lord, Jeffrey C; Hartzer, Kris L; Kambhampati, Srinivas

    2012-01-01

    The yellow mealworm, Tenebrio molitor, harbors a symbiont that has spores with a thick, laminated wall and infects the fat body and ventral nerve chord of adult and larval beetles. In adult males, there is heavy infection of the epithelial cells of the testes and between testes lobes with occasional penetration of the lobes. Spores are enveloped in the spermatophores when they are formed at the time of mating and transferred to the female's bursa copulatrix. Infection has not been found in the ovaries. The sequence of the nuclear small subunit rDNA indicates that the symbiont is a member of the Ichthyosporea, a class of protists near the animal-fungi divergence. © 2012 The Author(s) Journal of Eukaryotic Microbiology © 2012 International Society of Protistologists.

  7. Genomics of "Candidatus Synechococcus spongiarium", a Cyanobacterial Sponge Symbiont

    Energy Technology Data Exchange (ETDEWEB)

    Slaby, Beate M. [Univ. of Wuerzburg (Germany); Copeland, Alex [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Woyke, Tanja [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Hentschel, Ute [Univ. of Wuerzburg (Germany)

    2014-03-21

    Marine sponges (Porifera): ancient metazoans of ecological importance, that produce bioactive secondary metabolites and interact with various microorganisms including cyanobacteria1: Marine Synechococcus spp.: cyanobacteria, important contributors to the global carbon cycle and major primary producers in the oceans2 Ca. S. spongiarum: an ecotype of this genus, widespread and abundant symbiont of various marine sponges around the world3, e.g. Aplysina aerophoba

  8. Vertically and horizontally transmitted microbial symbionts shape the gut microbiota ontogenesis of a skin-mucus feeding discus fish progeny.

    Science.gov (United States)

    Sylvain, François-Étienne; Derome, Nicolas

    2017-07-12

    Fish gut microbial communities play key functions for their hosts, but their ontogenesis is poorly understood. Recent studies on the zebrafish suggest that gut symbionts are recruited naturally through horizontal transmission from environmental water. We used an alternative fish model, the discus (Symphysodon aequifasciata), to identify the main factors driving fish gut microbiota ontogenesis. The discus exhibits a unique parenting behavior: both discus parents vertically feed their fry with a cutaneous mucus secretion during three weeks post-hatching. We hypothesized that vertical microbial transmission via parental mucus feeding, along with horizontal transmission of environmental microbial symbionts, helps to shape the taxonomic structure of the discus fry gut microbiota. To assess this premise, we thoroughly documented the gut microbiota ontogenesis of a discus progeny during 100 days post-hatching. The V4 16S rRNA gene was sequenced to assess taxonomic structure of fry gut, parent mucus, and water samples. Our main results suggest that specific microbial symbionts both from the parents skin mucus and environmental water play important roles in shaping the structure of the fry gut microbiota.

  9. Phylogenetic affinity of arbuscular mycorrhizal symbionts in Psilotum nudum.

    Science.gov (United States)

    Winther, Jennifer L; Friedman, William E

    2009-09-01

    Many lineages of land plants (from lycopsids to angiosperms) have non-photosynthetic life cycle phases that involve obligate mycoheterotrophic arbuscular mycorrhizal (AM) associations where the plant host gains organic carbon through glomalean symbionts. Our goal was to isolate and phylogenetically identify the AM fungi associated with both the autotrophic and underground mycoheterotrophic life cycle phases of Psilotum nudum. Phylogenetic analyses recovered 11 fungal phylotypes in four diverse clades of Glomus A that form AM associations with P. nudum mycoheterotrophic gametophytes and autotrophic sporophytes, and angiosperm roots found in the same greenhouse pots. The correspondence of identities of AM symbionts in P. nudum sporophytes, gametophytes and neighboring angiosperms provides compelling evidence that photosynthetic heterospecific and conspecific plants can serve as the ultimate sources of fixed carbon for mycoheterotrophic gametophytes of P. nudum, and that the transfer of carbon occurs via shared fungal networks. Moreover, broader phylogenetic analyses suggest greenhouse Psilotum populations, like field-surveyed populations of mycoheterotrophic plants, form AM associations with restricted clades of Glomus A. The phylogenetic affinities and distribution of Glomus A symbionts indicate that P. nudum greenhouse populations have the potential to be exploited as an experimental system to further study the physiology, ecology and evolution of mycoheterotrophic AM associations.

  10. Bacterial and fungal symbionts of parasitic Dendroctonus bark beetles.

    Science.gov (United States)

    Dohet, Loïc; Grégoire, Jean-Claude; Berasategui, Aileen; Kaltenpoth, Martin; Biedermann, Peter H W

    2016-09-01

    Bark beetles (Curculionidae: Scolytinae) are one of the most species-rich herbivorous insect groups with many shifts in ecology and host-plant use, which may be mediated by their bacterial and fungal symbionts. While symbionts are well studied in economically important, tree-killing species, little is known about parasitic species whose broods develop in living trees. Here, using culture-dependent and independent methods, we provide a comprehensive overview of the associated bacteria, yeasts and filamentous fungi of the parasitic Dendroctonus micans, D. punctatus and D. valens, and compare them to those of other tree-inhabiting insects. Despite inhabiting different geographical regions and/or host trees, the three species showed similar microbial communities. Enterobacteria were the most prevalent bacteria, in particular Rahnella, Pantoea and Ewingella, in addition to Streptomyces Likewise, the yeasts Candida/Cyberlindnera were the most prominent fungi. All these microorganisms are widespread among tree-inhabiting insects with various ecologies, but their high prevalence overall might indicate a beneficial role such as detoxification of tree defenses, diet supplementation or protection against pathogens. As such, our results enable comparisons of symbiont communities of parasitic bark beetles with those of other beetles, and will contribute to our understanding of how microbial symbioses facilitate dietary shifts in insects. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. On the accumulation of radionuclids by lichen symbionts

    International Nuclear Information System (INIS)

    Nifontova, M.G.; Kulikov, N.V.

    1983-01-01

    The aim of investigation is the quantitative estimation of ability and role of separate symbionts in the accumulation of radionuclides. As investigation volumes, dUrably cUltivated green lichen alga Trebouxia erici and lichen fungi extracted from Cladonia rangiferina, Parmelia caperata and Acarospora fuscata are used. The accumulation of radioactive isotopes with fUngi and seaweeds is estimated according to accUmulation coefficients (AC) which are the ratio of radiation concentration in plants and agarized medium. Radionuclide content ( 90 Sr and 137 Cs) is determined radiometrically. A special series of eXperiments is done to investigate radionuclide accumulation dependences with lichen seaweed and fungi on light conditions. It is shown that both symbionts of lichen-seaweek and fungus take part in the accumulation of radionuclide from outer medium (atmospheric fall-out and soil). However fungus component constituting the base of structural organization of thallus provides the greater part of radionuclides accumulated by the plant. Along with this the violation of viability of seaweed symbionts particularly in the case of light deficiency brings about the reduction of 137 Cs sorption by seaweeds and tells on the total content of radiocesium in plant thallus

  12. Use of Medical Metered Dose Inhalers for Functionality Testing of Bioaerosol Detection and Identification Systems

    Science.gov (United States)

    2012-05-01

    testing of two near-real-time UV bioaerosol detectors. Aerosol generated from one actuation of a bioMDD containing 1 µm fluorescently tagged PSLs...resulted in complete alarming. 26 5. RECOMMENDATIONS In general , bioMDDs should be suitable for testing functionality of bioaerosol ... BIOAEROSOL DETECTION AND IDENTIFICATION SYSTEMS ECBC-TR-964 Jana Kesavan Deborah R. Schepers Jerold R. Bottiger RESEARCH AND TECHNOLOGY

  13. Studying the Complex Communities of Ants and Their Symbionts Using Ecological Network Analysis.

    Science.gov (United States)

    Ivens, Aniek B F; von Beeren, Christoph; Blüthgen, Nico; Kronauer, Daniel J C

    2016-01-01

    Ant colonies provide well-protected and resource-rich environments for a plethora of symbionts. Historically, most studies of ants and their symbionts have had a narrow taxonomic scope, often focusing on a single ant or symbiont species. Here we discuss the prospects of studying these assemblies in a community ecology context using the framework of ecological network analysis. We introduce three basic network metrics that we consider particularly relevant for improving our knowledge of ant-symbiont communities: interaction specificity, network modularity, and phylogenetic signal. We then discuss army ant symbionts as examples of large and primarily parasitic communities, and symbiotic sternorrhynchans as examples of generally smaller and primarily mutualistic communities in the context of these network analyses. We argue that this approach will provide new and complementary insights into the evolutionary and ecological dynamics between ants and their many associates, and will facilitate comparisons across different ant-symbiont assemblages as well as across different types of ecological networks.

  14. Cellular tropism, population dynamics, host range and taxonomic status of an aphid secondary symbiont, SMLS (Sitobion miscanthi L type symbiont.

    Directory of Open Access Journals (Sweden)

    Tong Li

    Full Text Available SMLS (Sitobion miscanthi L type symbiont is a newly reported aphid secondary symbiont. Phylogenetic evidence from molecular markers indicates that SMLS belongs to the Rickettsiaceae and has a sibling relationship with Orientia tsutsugamushi. A comparative analysis of coxA nucleotide sequences further supports recognition of SMLS as a new genus in the Rickettsiaceae. In situ hybridization reveals that SMLS is housed in both sheath cells and secondary bacteriocytes and it is also detected in aphid hemolymph. The population dynamics of SMLS differ from those of Buchnera aphidicola and titer levels of SMLS increase in older aphids. A survey of 13 other aphids reveals that SMLS only occurs in wheat-associated species.

  15. Cellular Tropism, Population Dynamics, Host Range and Taxonomic Status of an Aphid Secondary Symbiont, SMLS (Sitobion miscanthi L Type Symbiont)

    Science.gov (United States)

    Li, Tong; Xiao, Jin-Hua; Xu, Zhao-Huan; Murphy, Robert W.; Huang, Da-Wei

    2011-01-01

    SMLS (Sitobion miscanthi L type symbiont) is a newly reported aphid secondary symbiont. Phylogenetic evidence from molecular markers indicates that SMLS belongs to the Rickettsiaceae and has a sibling relationship with Orientia tsutsugamushi. A comparative analysis of coxA nucleotide sequences further supports recognition of SMLS as a new genus in the Rickettsiaceae. In situ hybridization reveals that SMLS is housed in both sheath cells and secondary bacteriocytes and it is also detected in aphid hemolymph. The population dynamics of SMLS differ from those of Buchnera aphidicola and titer levels of SMLS increase in older aphids. A survey of 13 other aphids reveals that SMLS only occurs in wheat-associated species. PMID:21789197

  16. Aphid secondary symbionts do not affect prey attractiveness to two species of predatory lady beetles

    OpenAIRE

    Kovacs, Jennifer L.; Wolf, Candice; Voisin, Den?; Wolf, Seth

    2017-01-01

    Heritable symbionts have been found to mediate interactions between host species and their natural enemies in a variety of organisms. Aphids, their facultative symbionts, and their potential fitness effects have been particularly well-studied. For example, the aphid facultative symbiont Regiella can protect its host from infection from a fungal pathogen, and aphids with Hamiltonella are less likely to be parasitized by parasitic wasps. Recent work has also found there to be negative fitness e...

  17. ChIP-seq for the Identification of Functional Elements in the Human Genome.

    Science.gov (United States)

    Marinov, Georgi K

    2017-01-01

    Functional elements in the genome express their function through physical association with particular proteins: transcription factors, components of the transcription machinery, specific histone modifications, and others. The genome-wide characterization of the protein-DNA interaction landscape of these proteins is thus a key approach toward the identification of candidate genomic regulatory regions. ChIP-seq (Chromatin Immunoprecipitation coupled with high-throughput sequencing) has emerged as the primary experimental methods for carrying out this task. Here, the ChIP-seq protocol is described together with some of the most important considerations for applying it in practice.

  18. Aphid secondary symbionts do not affect prey attractiveness to two species of predatory lady beetles.

    Directory of Open Access Journals (Sweden)

    Jennifer L Kovacs

    Full Text Available Heritable symbionts have been found to mediate interactions between host species and their natural enemies in a variety of organisms. Aphids, their facultative symbionts, and their potential fitness effects have been particularly well-studied. For example, the aphid facultative symbiont Regiella can protect its host from infection from a fungal pathogen, and aphids with Hamiltonella are less likely to be parasitized by parasitic wasps. Recent work has also found there to be negative fitness effects for the larvae of two species of aphidophagous lady beetles that consumed aphids with facultative symbionts. In both species, larvae that consumed aphids with secondary symbionts were significantly less likely to survive to adulthood. In this study we tested whether adult Harmonia axyridis and Hippodamia convergens lady beetles avoided aphids with symbionts in a series of choice experiments. Adults of both lady beetle species were as likely to choose aphids with symbionts as those without, despite the potential negative fitness effects associated with consuming aphids with facultative symbionts. This may suggest that under natural conditions aphid secondary symbionts are not a significant source of selection for predatory lady beetles.

  19. Aphid secondary symbionts do not affect prey attractiveness to two species of predatory lady beetles

    Science.gov (United States)

    Wolf, Candice; Voisin, Dené; Wolf, Seth

    2017-01-01

    Heritable symbionts have been found to mediate interactions between host species and their natural enemies in a variety of organisms. Aphids, their facultative symbionts, and their potential fitness effects have been particularly well-studied. For example, the aphid facultative symbiont Regiella can protect its host from infection from a fungal pathogen, and aphids with Hamiltonella are less likely to be parasitized by parasitic wasps. Recent work has also found there to be negative fitness effects for the larvae of two species of aphidophagous lady beetles that consumed aphids with facultative symbionts. In both species, larvae that consumed aphids with secondary symbionts were significantly less likely to survive to adulthood. In this study we tested whether adult Harmonia axyridis and Hippodamia convergens lady beetles avoided aphids with symbionts in a series of choice experiments. Adults of both lady beetle species were as likely to choose aphids with symbionts as those without, despite the potential negative fitness effects associated with consuming aphids with facultative symbionts. This may suggest that under natural conditions aphid secondary symbionts are not a significant source of selection for predatory lady beetles. PMID:28880922

  20. Ephemeral windows of opportunity for horizontal transmission of fungal symbionts in leaf-cutting ants

    DEFF Research Database (Denmark)

    Poulsen, Michael; Fernández-Marín, Hermógenes; Currie, Cameron R.

    2009-01-01

    Evolutionary theory predicts that hosts are selected to prevent mixing of genetically different symbionts when competition among lineages reduces the productivity of a mutualism. The symbionts themselves may also defend their interests: recent studies of Acromyrmex leaf-cutting ants showed...... and the original symbiont, and by the ant species the novel symbiont came from. The colony founding stage may thus provide an efficient but transient window for horizontal transmission, in which the fungus is unable to actively defend its partnership position before the host feeds on it, so that host fecal...

  1. Aphid secondary symbionts do not affect prey attractiveness to two species of predatory lady beetles.

    Science.gov (United States)

    Kovacs, Jennifer L; Wolf, Candice; Voisin, Dené; Wolf, Seth

    2017-01-01

    Heritable symbionts have been found to mediate interactions between host species and their natural enemies in a variety of organisms. Aphids, their facultative symbionts, and their potential fitness effects have been particularly well-studied. For example, the aphid facultative symbiont Regiella can protect its host from infection from a fungal pathogen, and aphids with Hamiltonella are less likely to be parasitized by parasitic wasps. Recent work has also found there to be negative fitness effects for the larvae of two species of aphidophagous lady beetles that consumed aphids with facultative symbionts. In both species, larvae that consumed aphids with secondary symbionts were significantly less likely to survive to adulthood. In this study we tested whether adult Harmonia axyridis and Hippodamia convergens lady beetles avoided aphids with symbionts in a series of choice experiments. Adults of both lady beetle species were as likely to choose aphids with symbionts as those without, despite the potential negative fitness effects associated with consuming aphids with facultative symbionts. This may suggest that under natural conditions aphid secondary symbionts are not a significant source of selection for predatory lady beetles.

  2. Biparental transmission of Verminephrobacter symbionts in the earthworm Aporrectodea tuberculata (Lumbricidae).

    Science.gov (United States)

    Paz, Laura-Carlota; Schramm, Andreas; Lund, Marie Braad

    2017-05-01

    Most lumbricid earthworms harbor species-specific Verminephrobacter symbionts in their excretory organs (nephridia). These symbionts are vertically transmitted via the cocoon, where they colonize the embryos. Despite cospeciation for >100 million years with their hosts, Verminephrobacter lack genome reduction and AT bias typical of evolutionary old, vertically transmitted symbionts, caused by recurring bottlenecks. We hypothesized that biparental symbiont transmission into the cocoon enabled genetic mixing and relieved the bottleneck, and tested biparental transmission experimentally for V. aporrectodeae subsp. tuberculata, the specific symbiont of the earthworm Aporrectodea tuberculata, for which aposymbiotic worm lines are available. Virgin symbiotic and aposymbiotic adult worms were tagged, mated in pairs, separated before the start of cocoon production and their offspring assessed for Verminephrobacter. Specific PCR detected the symbionts in 41.5% of 188 juveniles produced by 20 aposymbiotic worms; fluorescence in situ hybridization showed a patchy but successful colonization of their nephridia. Symbionts were present in the mucus but absent in feed, soil, and spermatophora/nephridia of the aposymbiotic partner, suggesting symbiont transfer via mucus during mating. These results are consistent with the hypothesis that genome evolution in Verminephrobacter is distinct from other vertical-ly transmitted symbionts due to genetic mixing during transmission, partially facilitated by biparental transmission. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. A Novel, Extremely Elongated, and Endocellular Bacterial Symbiont Supports Cuticle Formation of a Grain Pest Beetle.

    Science.gov (United States)

    Hirota, Bin; Okude, Genta; Anbutsu, Hisashi; Futahashi, Ryo; Moriyama, Minoru; Meng, Xian-Ying; Nikoh, Naruo; Koga, Ryuichi; Fukatsu, Takema

    2017-09-26

    The saw-toothed grain beetle, Oryzaephilus surinamensis (Silvanidae), is a cosmopolitan stored-product pest. Early studies on O. surinamensis in the 1930s described the presence of peculiar bacteriomes harboring endosymbiotic bacteria in the abdomen. Since then, however, the microbiological nature of the symbiont has been elusive. Here we investigated the endosymbiotic system of O. surinamensis in detail. In the abdomen of adults, pupae, and larvae, four oval bacteriomes were consistently identified, whose cytoplasm was full of extremely elongated tubular bacterial cells several micrometers wide and several hundred micrometers long. Molecular phylogenetic analysis identified the symbiont as a member of the Bacteroidetes , in which the symbiont was the most closely related to the endosymbiont of a grain pest beetle, Rhyzopertha dominica (Bostrichidae). The symbiont was detected in developing embryos, corroborating vertical symbiont transmission through host generations. The symbiont gene showed AT-biased nucleotide composition and accelerated molecular evolution, plausibly reflecting degenerative evolution of the symbiont genome. When the symbiont infection was experimentally removed, the aposymbiotic insects grew and reproduced normally, but exhibited a slightly but significantly more reddish cuticle and lighter body mass. These results indicate that the symbiont of O. surinamensis is not essential for the host's growth and reproduction but contributes to the host's cuticle formation. Symbiont genome sequencing and detailed comparison of fitness parameters between symbiotic and aposymbiotic insects under various environmental conditions will provide further insights into the symbiont's biological roles for the stored-product pest. IMPORTANCE Some beetles notorious as stored-product pests possess well-developed symbiotic organs called bacteriomes for harboring specific symbiotic bacteria, although their biological roles have been poorly understood. Here we report

  4. Identification and functional analysis of ‘hypothetical’ genes expressed in Haemophilus influenzae

    Science.gov (United States)

    Kolker, Eugene; Makarova, Kira S.; Shabalina, Svetlana; Picone, Alex F.; Purvine, Samuel; Holzman, Ted; Cherny, Tim; Armbruster, David; Munson, Robert S.; Kolesov, Grigory; Frishman, Dmitrij; Galperin, Michael Y.

    2004-01-01

    The progress in genome sequencing has led to a rapid accumulation in GenBank submissions of uncharacterized ‘hypothetical’ genes. These genes, which have not been experimentally characterized and whose functions cannot be deduced from simple sequence comparisons alone, now comprise a significant fraction of the public databases. Expression analyses of Haemophilus influenzae cells using a combination of transcriptomic and proteomic approaches resulted in confident identification of 54 ‘hypothetical’ genes that were expressed in cells under normal growth conditions. In an attempt to understand the functions of these proteins, we used a variety of publicly available analysis tools. Close homologs in other species were detected for each of the 54 ‘hypothetical’ genes. For 16 of them, exact functional assignments could be found in one or more public databases. Additionally, we were able to suggest general functional characterization for 27 more genes (comprising ∼80% total). Findings from this analysis include the identification of a pyruvate-formate lyase-like operon, likely to be expressed not only in H.influenzae but also in several other bacteria. Further, we also observed three genes that are likely to participate in the transport and/or metabolism of sialic acid, an important component of the H.influenzae lipo-oligosaccharide. Accurate functional annotation of uncharacterized genes calls for an integrative approach, combining expression studies with extensive computational analysis and curation, followed by eventual experimental verification of the computational predictions. PMID:15121896

  5. New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome.

    Science.gov (United States)

    Garazha, Andrew; Ivanova, Alena; Suntsova, Maria; Malakhova, Galina; Roumiantsev, Sergey; Zhavoronkov, Alex; Buzdin, Anton

    2015-01-01

    Endogenous retroviruses (ERVs) and LTR retrotransposons (LRs) occupy ∼8% of human genome. Deep sequencing technologies provide clues to understanding of functional relevance of individual ERVs/LRs by enabling direct identification of transcription factor binding sites (TFBS) and other landmarks of functional genomic elements. Here, we performed the genome-wide identification of human ERVs/LRs containing TFBS according to the ENCODE project. We created the first interactive ERV/LRs database that groups the individual inserts according to their familial nomenclature, number of mapped TFBS and divergence from their consensus sequence. Information on any particular element can be easily extracted by the user. We also created a genome browser tool, which enables quick mapping of any ERV/LR insert according to genomic coordinates, known human genes and TFBS. These tools can be used to easily explore functionally relevant individual ERV/LRs, and for studying their impact on the regulation of human genes. Overall, we identified ∼110,000 ERV/LR genomic elements having TFBS. We propose a hypothesis of "domestication" of ERV/LR TFBS by the genome milieu including subsequent stages of initial epigenetic repression, partial functional release, and further mutation-driven reshaping of TFBS in tight coevolution with the enclosing genomic loci.

  6. Smell identification function as a severity and progression marker in Alzheimer's disease.

    Science.gov (United States)

    Velayudhan, Latha; Pritchard, Megan; Powell, John F; Proitsi, Petroula; Lovestone, Simon

    2013-07-01

    Olfactory dysfunction, impaired smell identification in particular, is known as a diagnostic and a marker of conversion in Alzheimer's disease (AD). We aimed to evaluate the associations of olfactory identification impairments with cognition, illness severity, and progression in AD patients. Fifty-seven outpatients with late onset mild to moderate AD and 24 elderly non-demented controls (NDC) were assessed, at baseline and after three months, for Mini-Mental State Examination (MMSE), University of Pennsylvania Smell Identification Test (UPSIT), and Bristol Activities of Daily Living and Neuropsychiatry Inventory. AD participants were classified as Rapid Cognitive Decliners (RCD) defined on a priori with a loss of ≥2 points in MMSE within the previous six months. AD participants had lower olfactory scores than NDC. RCD had lower olfaction scores compared with Non-Rapid Cognitive Decliners (NRCD). Although the baseline UPSIT scores were associated with baseline MMSE scores, it did not interact significantly with change in MMSE over the follow-up period. Using a median split for olfactory scores, the AD participants were classified as Rapid Olfactory Progressors (ROP) (UPSIT ≤ 15) and Slow Olfactory Progressors correlating significantly with RCD/NRCD groups. The ROP group with higher olfactory impairment indicated more symptomatic illness or severity, i.e. lower cognition, higher functional dependence, and presence of behavioral symptoms. Our study supports association of smell identification function with cognition and its utility as an adjunct clinical measure to assess severity in AD. Further work, including larger longitudinal studies, is needed to explore its value in predicting AD progression.

  7. Beneficial mycorrhizal symbionts affecting the production of health-promoting phytochemicals.

    Science.gov (United States)

    Sbrana, Cristiana; Avio, Luciano; Giovannetti, Manuela

    2014-06-01

    Fresh fruits and vegetables are largely investigated for their content in vitamins, mineral nutrients, dietary fibers, and plant secondary metabolites, collectively called phytochemicals, which play a beneficial role in human health. Quantity and quality of phytochemicals may be detected by using different analytical techniques, providing accurate quantification and identification of single molecules, along with their molecular structures, and allowing metabolome analyses of plant-based foods. Phytochemicals concentration and profiles are affected by biotic and abiotic factors linked to plant genotype, crop management, harvest season, soil quality, available nutrients, light, and water. Soil health and biological fertility play a key role in the production of safe plant foods, as a result of the action of beneficial soil microorganisms, in particular of the root symbionts arbuscular mycorrhizal fungi. They improve plant nutrition and health and induce changes in secondary metabolism leading to enhanced biosynthesis of health-promoting phytochemicals, such as polyphenols, carotenoids, flavonoids, phytoestrogens, and to a higher activity of antioxidant enzymes. In this review we discuss reports on health-promoting phytochemicals and analytical methods used for their identification and quantification in plants, and on arbuscular mycorrhizal fungi impact on fruits and vegetables nutritional and nutraceutical value. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Hepatoprotective effects of kombucha tea: identification of functional strains and quantification of functional components.

    Science.gov (United States)

    Wang, Yong; Ji, Baoping; Wu, Wei; Wang, Ruojun; Yang, Zhiwei; Zhang, Di; Tian, Wenli

    2014-01-30

    Kombucha tea (KT), a traditional health beverage containing potential hepatoprotective agents, is fermented from sugared tea by a symbiotic culture of yeast and bacteria for 8 days. However, the functional strains that produce components for the hepatoprotective property of KT remain unclear. Multiple strains are involved in traditional KT production. Therefore, KT has not been standardized or produced commercially. This study aimed to identify the functional strains and quantify the functional components with hepatoprotective effects in kombucha tea. Gluconacetobacter sp. A4 was one of the microorganisms in KT in which the D-saccharic acid-1,4-lactone (DSL) produced by G. sp. A4 was significantly higher than that produced by original tea fungus at 8 days of fermentation. Traditional KT (TKT, tea broth fermented by mixed tea fungus), modified KT (MKT, fermented by single G. sp. A4), and DSL significantly inhibited the acetaminophen-induced increase of alanine aminotransferase, alkaline phosphatase, triglyceride and malondialdehyde, as well as facilitating the reduction of total antioxidant capacity in mice. Furthermore, MKT and TKT are both similar to DSL in terms of protection against acetaminophen-induced liver injury in mice. These results suggested a positive relationship between DSL content and the hepatoprotective effect of TKT, MKT and DSL groups. G. sp. A4 was concluded to be a potential functional strain and DSL might be the key functional component for the hepatoprotective property in KT. The stronger capability of G. sp. A4 in producing DSL makes it a better choice for the commercial production of KT. © 2013 Society of Chemical Industry.

  9. Identification of functional corridors with movement characteristics of brown bears on the Kenai Peninsula, Alaska

    Science.gov (United States)

    Graves, T.A.; Farley, S.; Goldstein, M.I.; Servheen, C.

    2007-01-01

    We identified primary habitat and functional corridors across a landscape using Global Positioning System (GPS) collar locations of brown bears (Ursus arctos). After deriving density, speed, and angular deviation of movement, we classified landscape function for a group of animals with a cluster analysis. We described areas with high amounts of sinuous movement as primary habitat patches and areas with high amounts of very directional, fast movement as highly functional bear corridors. The time between bear locations and scale of analysis influenced the number and size of corridors identified. Bear locations should be collected at intervals ???6 h to correctly identify travel corridors. Our corridor identification technique will help managers move beyond the theoretical discussion of corridors and linkage zones to active management of landscape features that will preserve connectivity. ?? 2007 Springer Science+Business Media, Inc.

  10. Resting-state functional connectivity and pitch identification ability in non-musicians

    Directory of Open Access Journals (Sweden)

    Jiancheng eHou

    2015-02-01

    Full Text Available Previous studies have used task-related fMRI to investigate the neural basis of pitch identification (PI, but no study has examined the associations between resting-state functional connectivity (RSFC and PI ability. Using a large sample of Chinese non-musicians (N = 320, with 56 having prior musical training, the current study examined the associations among musical training, PI ability, and RSFC. Results showed that musical training was associated with increased RSFC within the networks for multiple cognitive functions (such as vision, phonology, semantics, auditory encoding, and executive functions. PI ability was associated with RSFC with regions for perceptual and auditory encoding for participants with musical training, and with RSFC with regions for short-term memory, semantics, and phonology for participants without musical training.

  11. Identification of fractional-order systems with time delays using block pulse functions

    Science.gov (United States)

    Tang, Yinggan; Li, Ning; Liu, Minmin; Lu, Yao; Wang, Weiwei

    2017-07-01

    In this paper, a novel method based on block pulse functions is proposed to identify continuous-time fractional-order systems with time delays. First, the operational matrices of block pulse functions for fractional integral operator and time delay operator are derived. Then, these operational matrices are applied to convert the continuous-time fractional-order systems with time delays to an algebraic equation. Finally, the system's parameters along with the differentiation orders and the time delays are all simultaneously estimated through minimizing a quadric error function. The proposed method reduces the computation complexity of the identification process, and also it does not require the system's differentiation orders to be commensurate. The effectiveness of the proposed method are demonstrated by several numerical examples.

  12. Symbiont-derived beta-1,3-glucanases in a social insect: mutualism beyond nutrition

    Directory of Open Access Journals (Sweden)

    Rebeca B Rosengaus

    2014-11-01

    Full Text Available Termites have had a long co-evolutionary history with prokaryotic and eukaryotic gut microbes. Historically, the role of these anaerobic obligate symbionts has been attributed to the nutritional welfare of the host. We provide evidence that protozoa (and/or their associated bacteria colonizing the hindgut of the dampwood termite Zootermopsis angusticollis, synthesize multiple functional beta-1,3-glucanases, enzymes known for breaking down beta-1,3-glucans, the main component of fungal cell walls. These enzymes, we propose, may help in both digestion of ingested fungal hyphae and protection against invasion by fungal pathogens. This research points to an additional novel role for the mutualistic hindgut microbial consortia of termites, an association that may extend beyond ligno-cellulolytic activity and nitrogen fixation to include a reduction in the risks of mycosis at both the individual- and colony-levels while nesting in and feeding on microbial-rich decayed wood.

  13. Diversity and genomes of uncultured microbial symbionts in the termite gut.

    Science.gov (United States)

    Hongoh, Yuichi

    2010-01-01

    Termites play a key role in the global carbon cycle as decomposers. Their ability to thrive solely on dead plant matter is chiefly attributable to the activities of gut microbes, which comprise protists, bacteria, and archaea. Although the majority of the gut microbes are as yet unculturable, molecular analyses have gradually been revealing their diversity and symbiotic mechanisms. Culture-independent studies indicate that a single termite species harbors several hundred species of gut microbes unique to termites, and that the microbiota is consistent within a host termite species. To elucidate the functions of these unculturable symbionts, environmental genomics has recently been applied. Particularly, single-species-targeting metagenomics has provided a breakthrough in the understanding of symbiotic roles, such as the nitrogen fixation, of uncultured, individual microbial species. A combination of single-species-targeting metagenomics, conventional metagenomics, and metatranscriptomics should be a powerful tool to dissect this complex, multi-layered symbiotic system.

  14. Identification and Characterisation CRN Effectors in Phytophthora capsici Shows Modularity and Functional Diversity.

    Directory of Open Access Journals (Sweden)

    Remco Stam

    Full Text Available Phytophthora species secrete a large array of effectors during infection of their host plants. The Crinkler (CRN gene family encodes a ubiquitous but understudied class of effectors with possible but as of yet unknown roles in infection. To appreciate CRN effector function in Phytophthora, we devised a simple Crn gene identification and annotation pipeline to improve effector prediction rates. We predicted 84 full-length CRN coding genes and assessed CRN effector domain diversity in sequenced Oomycete genomes. These analyses revealed evidence of CRN domain innovation in Phytophthora and expansion in the Peronosporales. We performed gene expression analyses to validate and define two classes of CRN effectors, each possibly contributing to infection at different stages. CRN localisation studies revealed that P. capsici CRN effector domains target the nucleus and accumulate in specific sub-nuclear compartments. Phenotypic analyses showed that few CRN domains induce necrosis when expressed in planta and that one cell death inducing effector, enhances P. capsici virulence on Nicotiana benthamiana. These results suggest that the CRN protein family form an important class of intracellular effectors that target the host nucleus during infection. These results combined with domain expansion in hemi-biotrophic and necrotrophic pathogens, suggests specific contributions to pathogen lifestyles. This work will bolster CRN identification efforts in other sequenced oomycete species and set the stage for future functional studies towards understanding CRN effector functions.

  15. The Physiology of Microbial Symbionts in Fungus-Farming Termites

    DEFF Research Database (Denmark)

    Rodrigues da Costa, Rafael

    with their symbionts are main decomposer of organic matter in Africa, and this is reflect of a metabolic complementarity to decompose plant biomass in the genome of the three organisms involved in this symbiosis. Many of the physiological aspects of this symbiosis remain obscure, and here I focus on physiology...... termites where this is either absent or minimal, and this indicates evolutionary adaptations to dietary intakes displayed by different termite species. In addition to these two physiological aspects of this tripartite symbiosis, we questioned the physiological mechanisms displayed by Termitomyces...

  16. Dynamic energy budgets in syntrophic symbiotic relationships between heterotrophic hosts and photoautotrophic symbionts.

    NARCIS (Netherlands)

    Muller, E.B.; Kooijman, S.A.L.M.; Edmunds, P.J.; Doyle, F.J.; Nisbet, R.M.

    2009-01-01

    In this paper we develop and investigate a dynamic energy budget (DEB) model describing the syntrophic symbiotic relationship between a heterotrophic host and an internal photoautotrophic symbiont. The model specifies the flows of matter and energy among host, symbiont and environment with minimal

  17. High Symbiont Relatedness Stabilizes Mutualistic Cooperation in Fungus-Growing Termites

    DEFF Research Database (Denmark)

    Aanen, Duur K; de Fine Licht, Henrik H; Debets, Alfons J M

    2009-01-01

    of spore production in proportion to strain frequency. This positive reinforcement results in an exclusive lifetime association of each host colony with a single fungal symbiont and hinders the evolution of cheating. Our findings explain why vertical symbiont transmission in fungus-growing termites is rare...

  18. Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts.

    Science.gov (United States)

    Sanders, J G; Beinart, R A; Stewart, F J; Delong, E F; Girguis, P R

    2013-08-01

    Despite the ubiquity of chemoautotrophic symbioses at hydrothermal vents, our understanding of the influence of environmental chemistry on symbiont metabolism is limited. Transcriptomic analyses are useful for linking physiological poise to environmental conditions, but recovering samples from the deep sea is challenging, as the long recovery times can change expression profiles before preservation. Here, we present a novel, in situ RNA sampling and preservation device, which we used to compare the symbiont metatranscriptomes associated with Alviniconcha, a genus of vent snail, in which specific host-symbiont combinations are predictably distributed across a regional geochemical gradient. Metatranscriptomes of these symbionts reveal key differences in energy and nitrogen metabolism relating to both environmental chemistry (that is, the relative expression of genes) and symbiont phylogeny (that is, the specific pathways employed). Unexpectedly, dramatic differences in expression of transposases and flagellar genes suggest that different symbiont types may also have distinct life histories. These data further our understanding of these symbionts' metabolic capabilities and their expression in situ, and suggest an important role for symbionts in mediating their hosts' interaction with regional-scale differences in geochemistry.

  19. A specific mix of generalists: bacterial symbionts in Mediterranean Ircinia spp.

    Science.gov (United States)

    Erwin, Patrick M; López-Legentil, Susanna; González-Pech, Raúl; Turon, Xavier

    2012-03-01

    Microbial symbionts form abundant and diverse components of marine sponge holobionts, yet the ecological and evolutionary factors that dictate their community structure are unresolved. Here, we characterized the bacterial symbiont communities of three sympatric host species in the genus Ircinia from the NW Mediterranean Sea, using electron microscopy and replicated 16S rRNA gene sequence clone libraries. All Ircinia host species harbored abundant and phylogenetically diverse symbiont consortia, comprised primarily of sequences related to other sponge-derived microorganisms. Community-level analyses of bacterial symbionts revealed host species-specific genetic differentiation and structuring of Ircinia-associated microbiota. Phylogenetic analyses of host sponges showed a close evolutionary relationship between Ircinia fasciculata and Ircinia variabilis, the two host species exhibiting more similar symbiont communities. In addition, several bacterial operational taxonomic units were shared between I. variabilis and Ircinia oros, the two host species inhabiting semi-sciophilous communities in more cryptic benthic habitats, and absent in I. fasciculata, which occurs in exposed, high-irradiance habitats. The generalist nature of individual symbionts and host-specific structure of entire communities suggest that: (1) a 'specific mix of generalists' framework applies to bacterial symbionts in Ircinia hosts and (2) factors specific to each host species contribute to the distinct symbiont mix observed in Ircinia hosts. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  20. Presumptive horizontal symbiont transmission in the fungus-growing termite Macrotermes natalensis

    NARCIS (Netherlands)

    Fine Licht, de H.H.; Boomsma, J.J.; Aanen, D.K.

    2006-01-01

    All colonies of the fungus-growing termite Macrotermes natalensis studied so far are associated with a single genetically variable lineage of Termitomyces symbionts. Such limited genetic variation of symbionts and the absence of sexual fruiting bodies (mushrooms) on M. natalensis mounds would be

  1. Heat Stress Affects Facultative Symbiont-Mediated Protection from a Parasitoid Wasp.

    Science.gov (United States)

    Heyworth, Eleanor R; Ferrari, Julia

    2016-01-01

    Many insects carry facultative bacterial symbionts, which provide benefits including resistance to natural enemies and abiotic stresses. Little is known about how these beneficial phenotypes are affected when biotic or abiotic threats occur simultaneously. The pea aphid (Acyrthosiphon pisum) can host several well-characterized symbiont species. The symbiont known as X-type can protect against both parasitoid wasps and heat stress. Here, we used three pea aphid genotypes that were naturally infected with X-type and the symbiont Spiroplasma sp. We compared aphids coinfected with these two symbionts with those cured from X-type and infected with only Spiroplasma to investigate the ability of X-type to confer benefits to the host when two threats are experienced simultaneously. Our aim is to explore how robust symbiont protection may be outside a benign laboratory environment. Aphids were subjected to heat shock either before or after attack by parasitoid wasps. Under a benign temperature regime, the aphids carrying X-type tended to be better protected from the parasitoid than those cured. When the aphids experienced a heat shock before being parasitized aphids carrying X-type were more susceptible than those cured. Regardless of infection with the symbiont, the aphids benefitted from being heat shocked after parasitization. The results demonstrate how resistance to parasitoid wasps can be strongly environment-dependent and that a beneficial phenotype conferred by a symbiont under controlled conditions in the laboratory does not necessarily equate to a consistently useful effect in natural populations.

  2. Inherited microbial symbionts increase herbivore abundances and alter arthropod diversity on a native grass.

    Science.gov (United States)

    Faeth, Stanley H; Shochat, Eyal

    2010-05-01

    Some microbial symbionts of plants are maternally inherited and thus functionally increase genetic and phenotypic variation within plant populations. This variation, coupled with that of the host plant and environment, may alter abundances, diversity, and trophic structure of associated plant and animal communities. Fungal endophytes in the genus Neotyphodium are vertically transmitted, asexual microbial symbionts of grasses that remain asymptomatic and rely upon their hosts for resources and transmission via seeds, often providing benefits to their hosts, including protection against herbivores. Endophyte infections may influence associated arthropod communities in agronomic grasses, but the long-term effects of endophytes and variation in host genotype and resource availability on arthropod communities in native grass populations are unknown. We conducted a long-term field experiment with four maternal genotypes of an infected (E+) native grass (Festuca arizonica) from whence the endophyte was experimentally removed (E-) and water availability was controlled, to test the effects of infection, plant genotype, and resources on abundances, biomass, diversity (richness and evenness), and trophic structure of the arthropod community. Generally, E+ grasses harbored more arthropods, including more herbivores, predators, and detritivores, suggesting that the effects of endophytes cascaded upward through trophic levels in terms of abundances, at least in early ontogeny of the host. That E+ plants harbored more herbivorous insects than E- plants suggests that infection does not increase but instead decreases resistance to herbivores, contrary to prevailing concepts of endophytes as defensive mutualists. Infection did not alter overall species richness of the arthropod community or richness of herbivores but reduced natural enemy richness, especially that of parasites, and increased richness of detritivores. Reduced richness and shifts in evenness of natural enemies on E

  3. Prediction of detailed enzyme functions and identification of specificity determining residues by random forests.

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    Chioko Nagao

    Full Text Available Determining enzyme functions is essential for a thorough understanding of cellular processes. Although many prediction methods have been developed, it remains a significant challenge to predict enzyme functions at the fourth-digit level of the Enzyme Commission numbers. Functional specificity of enzymes often changes drastically by mutations of a small number of residues and therefore, information about these critical residues can potentially help discriminate detailed functions. However, because these residues must be identified by mutagenesis experiments, the available information is limited, and the lack of experimentally verified specificity determining residues (SDRs has hindered the development of detailed function prediction methods and computational identification of SDRs. Here we present a novel method for predicting enzyme functions by random forests, EFPrf, along with a set of putative SDRs, the random forests derived SDRs (rf-SDRs. EFPrf consists of a set of binary predictors for enzymes in each CATH superfamily and the rf-SDRs are the residue positions corresponding to the most highly contributing attributes obtained from each predictor. EFPrf showed a precision of 0.98 and a recall of 0.89 in a cross-validated benchmark assessment. The rf-SDRs included many residues, whose importance for specificity had been validated experimentally. The analysis of the rf-SDRs revealed both a general tendency that functionally diverged superfamilies tend to include more active site residues in their rf-SDRs than in less diverged superfamilies, and superfamily-specific conservation patterns of each functional residue. EFPrf and the rf-SDRs will be an effective tool for annotating enzyme functions and for understanding how enzyme functions have diverged within each superfamily.

  4. Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests

    Science.gov (United States)

    Nagao, Chioko; Nagano, Nozomi; Mizuguchi, Kenji

    2014-01-01

    Determining enzyme functions is essential for a thorough understanding of cellular processes. Although many prediction methods have been developed, it remains a significant challenge to predict enzyme functions at the fourth-digit level of the Enzyme Commission numbers. Functional specificity of enzymes often changes drastically by mutations of a small number of residues and therefore, information about these critical residues can potentially help discriminate detailed functions. However, because these residues must be identified by mutagenesis experiments, the available information is limited, and the lack of experimentally verified specificity determining residues (SDRs) has hindered the development of detailed function prediction methods and computational identification of SDRs. Here we present a novel method for predicting enzyme functions by random forests, EFPrf, along with a set of putative SDRs, the random forests derived SDRs (rf-SDRs). EFPrf consists of a set of binary predictors for enzymes in each CATH superfamily and the rf-SDRs are the residue positions corresponding to the most highly contributing attributes obtained from each predictor. EFPrf showed a precision of 0.98 and a recall of 0.89 in a cross-validated benchmark assessment. The rf-SDRs included many residues, whose importance for specificity had been validated experimentally. The analysis of the rf-SDRs revealed both a general tendency that functionally diverged superfamilies tend to include more active site residues in their rf-SDRs than in less diverged superfamilies, and superfamily-specific conservation patterns of each functional residue. EFPrf and the rf-SDRs will be an effective tool for annotating enzyme functions and for understanding how enzyme functions have diverged within each superfamily. PMID:24416252

  5. A Novel, Extremely Elongated, and Endocellular Bacterial Symbiont Supports Cuticle Formation of a Grain Pest Beetle

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    Bin Hirota

    2017-09-01

    Full Text Available The saw-toothed grain beetle, Oryzaephilus surinamensis (Silvanidae, is a cosmopolitan stored-product pest. Early studies on O. surinamensis in the 1930s described the presence of peculiar bacteriomes harboring endosymbiotic bacteria in the abdomen. Since then, however, the microbiological nature of the symbiont has been elusive. Here we investigated the endosymbiotic system of O. surinamensis in detail. In the abdomen of adults, pupae, and larvae, four oval bacteriomes were consistently identified, whose cytoplasm was full of extremely elongated tubular bacterial cells several micrometers wide and several hundred micrometers long. Molecular phylogenetic analysis identified the symbiont as a member of the Bacteroidetes, in which the symbiont was the most closely related to the endosymbiont of a grain pest beetle, Rhyzopertha dominica (Bostrichidae. The symbiont was detected in developing embryos, corroborating vertical symbiont transmission through host generations. The symbiont gene showed AT-biased nucleotide composition and accelerated molecular evolution, plausibly reflecting degenerative evolution of the symbiont genome. When the symbiont infection was experimentally removed, the aposymbiotic insects grew and reproduced normally, but exhibited a slightly but significantly more reddish cuticle and lighter body mass. These results indicate that the symbiont of O. surinamensis is not essential for the host’s growth and reproduction but contributes to the host’s cuticle formation. Symbiont genome sequencing and detailed comparison of fitness parameters between symbiotic and aposymbiotic insects under various environmental conditions will provide further insights into the symbiont’s biological roles for the stored-product pest.

  6. Worldwide populations of the aphid Aphis craccivora are infected with diverse facultative bacterial symbionts.

    Science.gov (United States)

    Brady, Cristina M; Asplen, Mark K; Desneux, Nicolas; Heimpel, George E; Hopper, Keith R; Linnen, Catherine R; Oliver, Kerry M; Wulff, Jason A; White, Jennifer A

    2014-01-01

    Facultative bacterial endosymbionts can play an important role in the evolutionary trajectory of their hosts. Aphids (Hemiptera: Aphididae) are infected with a wide variety of facultative endosymbionts that can confer ecologically relevant traits, which in turn may drive microevolutionary processes in a dynamic selective environment. However, relatively little is known about how symbiont diversity is structured in most aphid species. Here, we investigate facultative symbiont species richness and prevalence among world-wide populations of the cowpea aphid, Aphis craccivora Koch. We surveyed 44 populations of A. craccivora, and detected 11 strains of facultative symbiotic bacteria, representing six genera. There were two significant associations between facultative symbiont and aphid food plant: the symbiont Arsenophonus was found at high prevalence in A. craccivora populations collected from Robinia sp. (locust), whereas the symbiont Hamiltonella was almost exclusively found in A. craccivora populations from Medicago sativa (alfalfa). Aphids collected from these two food plants also had divergent mitochondrial haplotypes, potentially indicating the formation of specialized aphid lineages associated with food plant (host-associated differentiation). The role of facultative symbionts in this process remains to be determined. Overall, observed facultative symbiont prevalence in A. craccivora was lower than that of some other well-studied aphids (e.g., Aphis fabae and Acyrthosiphon pisum), possibly as a consequence of A. craccivora's almost purely parthenogenetic life history. Finally, most (70 %) of the surveyed populations were polymorphic for facultative symbiont infection, indicating that even when symbiont prevalence is relatively low, symbiont-associated phenotypic variation may allow population-level evolutionary responses to local selection.

  7. Peptidomic approaches to the identification and characterization of functional peptides in Hydra.

    Science.gov (United States)

    Takahashi, Toshio; Fujisawa, Toshitaka

    2010-01-01

    Little is known about peptides that control developmental processes such as cell differentiation and pattern formation in metazoans. The cnidarian Hydra is one of the most basal metazoans and is a key model system for studying the peptides involved in these processes. We developed a novel peptidomic approach to the isolation and identification of functional signalling peptides from Hydra (the Hydra peptide project). First, peptides extracted from the tissue of Hydra magnipapillata are purified to homogeneity using high-performance liquid chromatography (HPLC). The isolated peptides are then tested for their ability to alter gene expression in Hydra using differential display-PCR (DD-PCR). If gene expression is altered, the peptide is considered as a putative signalling peptide and is subjected to amino acid sequencing. Following the sequencing, synthetic peptides are produced and compared to their native counterparts by HPLC and/or mass spectrometry (MS). The synthetic peptides, which are available in larger quantities than their native analogues, are then tested in a variety of biological assays in Hydra to determine their functions. Here we present our strategies and a systematic approach to the identification and characterization of novel signalling peptides in Hydra. We also describe our high-throughput reverse-phase nano-flow liquid chromatography matrix-assisted laser desorption ionization time-of-flight mass spectrometry (LC-MALDI-TOF-MS/MS) approach, which was proved to be a powerful tool in the discovery of novel signalling peptides.

  8. Distance-Ranked Fault Identification of Reconfigurable Hardware Bitstreams via Functional Input

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    Naveed Imran

    2014-01-01

    Full Text Available Distance-Ranked Fault Identification (DRFI is a dynamic reconfiguration technique which employs runtime inputs to conduct online functional testing of fielded FPGA logic and interconnect resources without test vectors. At design time, a diverse set of functionally identical bitstream configurations are created which utilize alternate hardware resources in the FPGA fabric. An ordering is imposed on the configuration pool as updated by the PageRank indexing precedence. The configurations which utilize permanently damaged resources and hence manifest discrepant outputs, receive lower rank are thus less preferred for instantiation on the FPGA. Results indicate accurate identification of fault-free configurations in a pool of pregenerated bitstreams with a low number of reconfigurations and input evaluations. For MCNC benchmark circuits, the observed reduction in input evaluations is up to 75% when comparing the DRFI technique to unguided evaluation. The DRFI diagnosis method is seen to isolate all 14 healthy configurations from a pool of 100 pregenerated configurations, and thereby offering a 100% isolation accuracy provided the fault-free configurations exist in the design pool. When a complete recovery is not feasible, graceful degradation may be realized which is demonstrated by the PSNR improvement of images processed in a video encoder case study.

  9. Identification and functional characterization of a novel bipartite nuclear localization sequence in ARID1A

    Energy Technology Data Exchange (ETDEWEB)

    Bateman, Nicholas W. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD (United States); Shoji, Yutaka [Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids 49503, MI (United States); Conrads, Kelly A.; Stroop, Kevin D. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); Hamilton, Chad A. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD (United States); Gynecologic Oncology Service, Department of Obstetrics and Gynecology, Walter Reed National Military Medical Center, 8901 Wisconsin Ave, MD, Bethesda, 20889 (United States); Department of Obstetrics and Gynecology, Uniformed Services University of the Health Sciences, Bethesda 20814, MD (United States); Darcy, Kathleen M. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD (United States); Maxwell, George L. [Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Falls Church, VA 22042 (United States); Risinger, John I. [Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids 49503, MI (United States); and others

    2016-01-01

    AT-rich interactive domain-containing protein 1A (ARID1A) is a recently identified nuclear tumor suppressor frequently altered in solid tumor malignancies. We have identified a bipartite-like nuclear localization sequence (NLS) that contributes to nuclear import of ARID1A not previously described. We functionally confirm activity using GFP constructs fused with wild-type or mutant NLS sequences. We further show that cyto-nuclear localized, bipartite NLS mutant ARID1A exhibits greater stability than nuclear-localized, wild-type ARID1A. Identification of this undescribed functional NLS within ARID1A contributes vital insights to rationalize the impact of ARID1A missense mutations observed in patient tumors. - Highlights: • We have identified a bipartite nuclear localization sequence (NLS) in ARID1A. • Confirmation of the NLS was performed using GFP constructs. • NLS mutant ARID1A exhibits greater stability than wild-type ARID1A.

  10. Poststroke aphasia recovery assessed with functional magnetic resonance imaging and a picture identification task.

    Science.gov (United States)

    Szaflarski, Jerzy P; Eaton, Kenneth; Ball, Angel L; Banks, Christi; Vannest, Jennifer; Allendorfer, Jane B; Page, Stephen; Holland, Scott K

    2011-01-01

    Stroke patients often display deficits in language function, such as correctly naming objects. Our aim was to evaluate the reliability and the patterns of poststroke language recovery using a picture identification task during functional magnetic resonance imaging (fMRI) at 4 T. Four healthy subjects and 4 subjects with left middle cerebral artery stroke with chronic (>1 year) aphasia were enrolled in the study. In each subject, 10 fMRI scans were performed over a 10-week period using a picture-identification task. The active condition involved presenting subject with a panel of 4 figures (eg, drawings of 4 animals) every 6 seconds and asking the subject to indicate which figure matched the written name in the center. The control condition was a same/different judgment task with pairs of geometric figures (squares, octagons, or combination) presented every 6 seconds. Thirty-second active/control blocks were repeated 5 times each, and responses were recorded. The stoke subjects and controls had similar demographic characteristics, including age (46 vs 53 years), personal handedness (Edinburg Handedness Inventory, 89 vs 95), familial handedness (93 vs 95), and years of education (14.3 vs 14.8). For the active condition, the controls performed better than the stroke subjects (97.7% vs 89.1%; P R positive blood oxygenation level-dependent (BOLD) activations in frontal and temporal language areas and symmetric retrosplenial and posterior cingulate areas and symmetric negative BOLD activations in bilateral frontotemporal language networks. In contrast, the stroke subjects exhibited positive BOLD activations predominantly in peristroke areas and negative BOLD activations in the unaffected (right) hemisphere. Both groups displayed high activation reliability (as measured by the intraclass correlation coefficient [ICC]) in the left frontal and temporal language areas, although in the stroke subjects the ICC in the frontal regions was spread over a much larger peristroke

  11. Dynamic Acquisition and Loss of Dual-Obligate Symbionts in the Plant-Sap-Feeding Adelgidae (Hemiptera: Sternorrhyncha: Aphidoidea

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    Carol D. von Dohlen

    2017-06-01

    Full Text Available Sap-sucking insects typically engage in obligate relationships with symbiotic bacteria that play nutritional roles in synthesizing nutrients unavailable or in scarce supply from the plant-sap diets of their hosts. Adelgids are sap-sucking insects with complex life cycles that involve alternation between conifer tree species. While all adelgid species feed on spruce during the sexual phase of their life cycle, each adelgid species belongs to a major lineage that feeds on a distinct genus of conifers as their alternate host. Previous work on adelgid symbionts had discovered pairs of symbionts within each host species, and unusual diversity across the insect family, but left several open questions regarding the status of bacterial associates. Here, we explored the consistency of symbionts within and across adelgid lineages, and sought evidence for facultative vs. obligate symbiont status. Representative species were surveyed for symbionts using 16S ribosomal DNA gene sequencing, confirming that different symbiont pairs were consistently present within each major adelgid lineage. Several approaches were used to establish whether symbionts exhibited characteristics of long-term, obligate mutualists. Patterns of symbiont presence across adelgid species and diversification with host insects suggested obligate relationships. Fluorescent in situ hybridization and electron microscopy localized symbionts to bacteriocyte cells within the bacteriome of each species (with one previously known exception, and detection of symbionts in eggs indicated their vertical transmission. Common characteristics of long-term obligate symbionts, such as nucleotide compositional bias and pleomorphic symbiont cell shape were also observed. Superimposing microbial symbionts on the adelgid phylogeny revealed a dynamic pattern of symbiont gains and losses over a relatively short period of time compared to other symbionts associated with sap-sucking insects, with each adelgid

  12. Host-symbiont co-speciation and reductive genome evolution in gut symbiotic bacteria of acanthosomatid stinkbugs

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    Kikuchi, Yoshitomo; Hosokawa, Takahiro; Nikoh, Naruo; Meng, Xian-Ying; Kamagata, Yoichi; Fukatsu, Takema

    2009-01-01

    Background Host-symbiont co-speciation and reductive genome evolution have been commonly observed among obligate endocellular insect symbionts, while such examples have rarely been identified among extracellular ones, the only case reported being from gut symbiotic bacteria of stinkbugs of the family Plataspidae. Considering that gut symbiotic communities are vulnerable to invasion of foreign microbes, gut symbiotic associations have been thought to be evolutionarily not stable. Stinkbugs of the family Acanthosomatidae harbor a bacterial symbiont in the midgut crypts, the lumen of which is completely sealed off from the midgut main tract, thereby retaining the symbiont in the isolated cryptic cavities. We investigated histological, ecological, phylogenetic, and genomic aspects of the unique gut symbiosis of the acanthosomatid stinkbugs. Results Phylogenetic analyses showed that the acanthosomatid symbionts constitute a distinct clade in the γ-Proteobacteria, whose sister groups are the obligate endocellular symbionts of aphids Buchnera and the obligate gut symbionts of plataspid stinkbugs Ishikawaella. In addition to the midgut crypts, the symbionts were located in a pair of peculiar lubricating organs associated with the female ovipositor, by which the symbionts are vertically transmitted via egg surface contamination. The symbionts were detected not from ovaries but from deposited eggs, and surface sterilization of eggs resulted in symbiont-free hatchlings. The symbiont-free insects suffered retarded growth, high mortality, and abnormal morphology, suggesting important biological roles of the symbiont for the host insects. The symbiont phylogeny was generally concordant with the host phylogeny, indicating host-symbiont co-speciation over evolutionary time despite the extracellular association. Meanwhile, some local host-symbiont phylogenetic discrepancies were found, suggesting occasional horizontal symbiont transfers across the host lineages. The symbionts

  13. Early identification: Language skills and social functioning in deaf and hard of hearing preschool children.

    Science.gov (United States)

    Netten, Anouk P; Rieffe, Carolien; Theunissen, Stephanie C P M; Soede, Wim; Dirks, Evelien; Korver, Anna M H; Konings, Saskia; Oudesluys-Murphy, Anne Marie; Dekker, Friedo W; Frijns, Johan H M

    2015-12-01

    Permanent childhood hearing impairment often results in speech and language problems that are already apparent in early childhood. Past studies show a clear link between language skills and the child's social-emotional functioning. The aim of this study was to examine the level of language and communication skills after the introduction of early identification services and their relation with social functioning and behavioral problems in deaf and hard of hearing children. Nationwide cross-sectional observation of a cohort of 85 early identified deaf and hard of hearing preschool children (aged 30-66 months). Parents reported on their child's communicative abilities (MacArthur-Bates Communicative Development Inventory III), social functioning and appearance of behavioral problems (Strengths and Difficulties Questionnaire). Receptive and expressive language skills were measured using the Reynell Developmental Language Scale and the Schlichting Expressive Language Test, derived from the child's medical records. Language and communicative abilities of early identified deaf and hard of hearing children are not on a par with hearing peers. Compared to normative scores from hearing children, parents of deaf and hard of hearing children reported lower social functioning and more behavioral problems. Higher communicative abilities were related to better social functioning and less behavioral problems. No relation was found between the degree of hearing loss, age at amplification, uni- or bilateral amplification, mode of communication and social functioning and behavioral problems. These results suggest that improving the communicative abilities of deaf and hard of hearing children could improve their social-emotional functioning. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  14. Identification, functional characterization and developmental regulation of sesquiterpene synthases from sunflower capitate glandular trichomes

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    Ro Dae-Kyun

    2009-07-01

    Full Text Available Abstract Background Sesquiterpene lactones are characteristic metabolites of Asteraceae (or Compositae which often display potent bioactivities and are sequestered in specialized organs such as laticifers, resin ducts, and trichomes. For characterization of sunflower sesquiterpene synthases we employed a simple method to isolate pure trichomes from anther appendages which facilitated the identification of these genes and investigation of their enzymatic functions and expression patterns during trichome development. Results Glandular trichomes of sunflower (Helianthus annuus L. were isolated, and their RNA was extracted to investigate the initial steps of sesquiterpene lactone biosynthesis. Reverse transcription-PCR experiments led to the identification of three sesquiterpene synthases. By combination of in vitro and in vivo characterization of sesquiterpene synthase gene products in Escherichia coli and Saccharomyces cerevisiae, respectively, two enzymes were identified as germacrene A synthases, the key enzymes of sesquiterpene lactone biosynthesis. Due to the very low in vitro activity, the third enzyme was expressed in vivo in yeast as a thioredoxin-fusion protein for functional characterization. In in vivo assays, it was identified as a multiproduct enzyme with the volatile sesquiterpene hydrocarbon δ-cadinene as one of the two main products with α-muuorlene, β-caryophyllene, α-humulene and α-copaene as minor products. The second main compound remained unidentified. For expression studies, glandular trichomes from the anther appendages of sunflower florets were isolated in particular developmental stages from the pre- to the post-secretory phase. All three sesquiterpene synthases were solely upregulated during the biosynthetically active stages of the trichomes. Expression in different aerial plant parts coincided with occurrence and maturity of trichomes. Young roots with root hairs showed expression of the sesquiterpene synthase genes

  15. Interspecific competition between entomopathogenic nematodes (Steinernema is modified by their bacterial symbionts (Xenorhabdus

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    Pages Sylvie

    2006-09-01

    Full Text Available Abstract Background Symbioses between invertebrates and prokaryotes are biological systems of particular interest in order to study the evolution of mutualism. The symbioses between the entomopathogenic nematodes Steinernema and their bacterial symbiont Xenorhabdus are very tractable model systems. Previous studies demonstrated (i a highly specialized relationship between each strain of nematodes and its naturally associated bacterial strain and (ii that mutualism plays a role in several important life history traits of each partner such as access to insect host resources, dispersal and protection against various biotic and abiotic factors. The goal of the present study was to address the question of the impact of Xenorhabdus symbionts on the progression and outcome of interspecific competition between individuals belonging to different Steinernema species. For this, we monitored experimental interspecific competition between (i two nematode species: S. carpocapsae and S. scapterisci and (ii their respective symbionts: X. nematophila and X. innexi within an experimental insect-host (Galleria mellonella. Three conditions of competition between nematodes were tested: (i infection of insects with aposymbiotic IJs (i.e. without symbiont of both species (ii infection of insects with aposymbiotic IJs of both species in presence of variable proportion of their two Xenorhabdus symbionts and (iii infection of insects with symbiotic IJs (i.e. naturally associated with their symbionts of both species. Results We found that both the progression and the outcome of interspecific competition between entomopathogenic nematodes were influenced by their bacterial symbionts. Thus, the results obtained with aposymbiotic nematodes were totally opposite to those obtained with symbiotic nematodes. Moreover, the experimental introduction of different ratios of Xenorhabdus symbionts in the insect-host during competition between Steinernema modified the proportion of

  16. Superparasitism Drives Heritable Symbiont Epidemiology and Host Sex Ratio in a Wasp.

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    Steven R Parratt

    2016-06-01

    Full Text Available Heritable microbial symbionts have profound impacts upon the biology of their arthropod hosts. Whilst our current understanding of the dynamics of these symbionts is typically cast within a framework of vertical transmission only, horizontal transmission has been observed in a number of cases. For instance, several symbionts can transmit horizontally when their parasitoid hosts share oviposition patches with uninfected conspecifics, a phenomenon called superparasitism. Despite this, horizontal transmission, and the host contact structures that facilitates it, have not been considered in heritable symbiont epidemiology. Here, we tested for the importance of host contact, and resulting horizontal transmission, for the epidemiology of a male-killing heritable symbiont (Arsenophonus nasoniae in parasitoid wasp hosts. We observed that host contact through superparasitism is necessary for this symbiont's spread in populations of its primary host Nasonia vitripennis, such that when superparasitism rates are high, A. nasoniae almost reaches fixation, causes highly female biased population sex ratios and consequently causes local host extinction. We further tested if natural interspecific variation in superparasitism behaviours predicted symbiont dynamics among parasitoid species. We found that A. nasoniae was maintained in laboratory populations of a closely related set of Nasonia species, but declined in other, more distantly related pteromalid hosts. The natural proclivity of a species to superparasitise was the primary factor determining symbiont persistence. Our results thus indicate that host contact behaviour is a key factor for heritable microbe dynamics when horizontal transmission is possible, and that 'reproductive parasite' phenotypes, such as male-killing, may be of secondary importance in the dynamics of such symbiont infections.

  17. Patterns of interaction specificity of fungus-growing termites and Termitomyces symbionts in South Africa

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    de Beer Z Wilhelm

    2007-07-01

    Full Text Available Abstract Background Termites of the subfamily Macrotermitinae live in a mutualistic symbiosis with basidiomycete fungi of the genus Termitomyces. Here, we explored interaction specificity in fungus-growing termites using samples from 101 colonies in South-Africa and Senegal, belonging to eight species divided over three genera. Knowledge of interaction specificity is important to test the hypothesis that inhabitants (symbionts are taxonomically less diverse than 'exhabitants' (hosts and to test the hypothesis that transmission mode is an important determinant for interaction specificity. Results Analysis of Molecular Variance among symbiont ITS sequences across termite hosts at three hierarchical levels showed that 47 % of the variation occurred between genera, 18 % between species, and the remaining 35 % between colonies within species. Different patterns of specificity were evident. High mutual specificity was found for the single Macrotermes species studied, as M. natalensis was associated with a single unique fungal haplotype. The three species of the genus Odontotermes showed low symbiont specificity: they were all associated with a genetically diverse set of fungal symbionts, but their fungal symbionts showed some host specificity, as none of the fungal haplotypes were shared between the studied Odontotermes species. Finally, bilaterally low specificity was found for the four tentatively recognized species of the genus Microtermes, which shared and apparently freely exchanged a common pool of divergent fungal symbionts. Conclusion Interaction specificity was high at the genus level and generally much lower at the species level. A comparison of the observed diversity among fungal symbionts with the diversity among termite hosts, indicated that the fungal symbiont does not follow the general pattern of an endosymbiont, as we found either similar diversity at both sides or higher diversity in the symbiont. Our results further challenge the

  18. Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice.

    Science.gov (United States)

    Boyd, Bret M; Allen, Julie M; Nguyen, Nam-Phuong; Vachaspati, Pranjal; Quicksall, Zachary S; Warnow, Tandy; Mugisha, Lawrence; Johnson, Kevin P; Reed, David L

    2017-07-01

    Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here, we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement. Examination of the highly reduced symbiont genomes (0.53-0.57 Mb) reveals much of the genomes are dedicated to vitamin synthesis. This is unchanged in the smallest symbiont genome and one that appears to have been reorganized. Specifically, symbionts from human lice, chimpanzee lice, and gorilla lice carry a small plasmid that encodes synthesis of vitamin B5, a vitamin critical to the bacteria-louse symbiosis. This plasmid is absent in an old world monkey louse symbiont, where this pathway is on its primary chromosome. This suggests the unique genomic configuration brought about by the plasmid is not essential for symbiosis, but once obtained, it has persisted for up to 25 My. We also find evidence that human, chimpanzee, and gorilla louse endosymbionts have lost a pathway for synthesis of vitamin B1, whereas the monkey louse symbiont has retained this pathway. It is unclear whether these changes are adaptive, but they may point to evolutionary responses of louse symbionts to shifts in primate biology. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  19. Studying channelopathies at the functional level using a system identification approach

    Science.gov (United States)

    Faisal, A. Aldo

    2007-09-01

    The electrical activity of our brain's neurons is controlled by voltage-gated ion channels. Mutations in these ion channels have been recently associated with clinical conditions, so called channelopathies. The involved ion channels have been well characterised at a molecular and biophysical level. However, the impact of these mutations on neuron function have been only rudimentary studied. It remains unclear how operation and performance (in terms of input-output characteristics and reliability) are affected. Here, I show how system identification techniques provide neuronal performance measures which allow to quantitatively asses the impact of channelopathies by comparing whole cell input-output relationships. I illustrate the feasibility of this approach by comparing the effects on neuronal signalling of two human sodium channel mutations (NaV 1.1 W1204R, R1648H), linked to generalized epilepsy with febrile seizures, to the wild-type NaV 1.1 channel.

  20. Thiolsulfonate functionalized polystyrene resin: preparation and application in the isolation and identification of electrophilic mutagens.

    Science.gov (United States)

    Wu, E; Carlson, Robert M

    2007-01-01

    A new approach for isolation and identification of elecrtophilic mutagens from complex matrix was developed. Thiosulfonic anion was immobilized onto polystyrene beads and used as separation media. Potassium polystyryl-thiosulfonate, prepared from polystyrylsulfonyl chloride and KHS, was observed to selectively react with model electrophilic mutagens such as alkyl halides, a-chloroketones and alpha-chloroesters to produce polystyryl-thiosulfonic esters. After separation from other nonreactive organic compounds, the beads then reacted with ethanethiol to produce unsymmetrical ethyl disulfides which are easily detected by GC/MS. For one mutagenic compound, only one unsymmetrical disulfide was found to contain its structure part. Thus, the structure of the parent mutagens could be deduced from that of the unsymmetrical disulfides. The degree of functionalization of the potassium polystyryl-thiosulfonate resin was 1.11 mmol/g. Its reactivity was discussed and its recycling method was reported here.

  1. A nonlinear identification method to study effective connectivity in functional MRI.

    Science.gov (United States)

    Li, Xingfeng; Marrelec, Guillaume; Hess, Robert F; Benali, Habib

    2010-02-01

    In this paper we propose a novel approach for characterizing effective connectivity in functional magnetic resonance imaging (fMRI) data. Unlike most other methods, our approach is nonlinear and does not rely on a priori specification of a model that contains structural information of neuronal populations. Instead, it relies on a nonlinear autoregressive exogenous model and nonlinear system identification theory; the model's nonlinear connectivities are determined using a least squares method. A statistical test was developed to quantify the significance of the influence that regions exert on one another. We compared this approach with a linear method and applied it to the human visual cortex network. Results show that this method can be used to model nonlinear interaction between different regions for fMRI data.

  2. [The application of genome editing in identification of plant gene function and crop breeding].

    Science.gov (United States)

    Zhou, Xiang-chun; Xing, Yong-zhong

    2016-03-01

    Plant genome can be modified via current biotechnology with high specificity and excellent efficiency. Zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system are the key engineered nucleases used in the genome editing. Genome editing techniques enable gene targeted mutagenesis, gene knock-out, gene insertion or replacement at the target sites during the endogenous DNA repair process, including non-homologous end joining (NHEJ) and homologous recombination (HR), triggered by the induction of DNA double-strand break (DSB). Genome editing has been successfully applied in the genome modification of diverse plant species, such as Arabidopsis thaliana, Oryza sativa, and Nicotiana tabacum. In this review, we summarize the application of genome editing in identification of plant gene function and crop breeding. Moreover, we also discuss the improving points of genome editing in crop precision genetic improvement for further study.

  3. A novel bacterial symbiont association in the hispid beetle, Octodonta nipae (Coleoptera: Chrysomelidae), their dynamics and phylogeny.

    Science.gov (United States)

    Ali, Habib; Muhammad, Abrar; Islam, Saif Ul; Islam, Waqar; Hou, Youming

    2018-03-27

    The hispid leaf beetle, Octodonta nipae (Maulik), (Coleoptera: Chrysomelidae), is a devastating pest of palm cultivation worldwide. Endosymbiotic bacteria in the genus Wolbachia are arguably one of the most abundant bacterial group associated with arthropods. Owing to its critical effects on host reproduction, Wolbachia has garnered much attention as a prospective future tool for insect pest management. However, their association, infection dynamics, and functionality remain unknown in this insect pest. Here, we diagnosis for the first time, the infection prevalence, and occurrence of Wolbachia in O. nipae. Experimental evidence by the exploration of wsp gene vindicate that O. nipae is naturally infected with bacterial symbiont of genus Wolbachia, showing a complete maternal inheritance with shared a common Wolbachia strain (wNip). Moreover, MLST (gatB, fbpA, coxA, ftsZ, and hcpA) analysis enabled the detections of new sequence type (ST-484), suggesting a particular genotypic association of O. nipae and Wolbachia. Subsequently, quantitative real-time PCR (qPCR) assay demonstrated variable infection density across different life stages (eggs, larvae, pupae and adult male and female), body parts (head, thorax, abdomen), and tissues (ovaries, testes, and guts). Infection density was higher in egg and female adult stage, as well as abdomen and reproductive tissues as compared to other samples. Interestingly, Wolbachia harbored dominantly in a female than the male adult, while, no significant differences were observed between male and female body parts and tissues. Phylogeny of Wolbachia infection associated with O. nipae rectified from all tested life stages were unique and fall within the same monophyletic supergroup-A of Wolbachia clades. The infection density of symbiont is among the valuable tool to understand their biological influence on hosts, and this latest discovery would facilitate the future investigations to understand the host-symbiont complications and

  4. Caste-specific symbiont policing by workers of Acromyrmex fungus-growing ants

    DEFF Research Database (Denmark)

    Ivens, Aniek B.F.; Nash, David R.; Poulsen, Michael

    2009-01-01

    The interaction between leaf-cutting ants and their fungus garden mutualists is ideal for studying the evolutionary stability of interspecific cooperation. Although the mutualism has a long history of diffuse coevolution, there is ample potential for conflicts between the partners over the mixing...... and transmission of symbionts. Symbiont transmission is vertical by default, and both the ants and resident fungus actively protect the fungal monoculture growing in their nest against secondary introductions of genetically dissimilar symbionts from other colonies. An earlier study showed that mixtures of major...

  5. Presumptive horizontal symbiont transmission in the fungus-growing termite Macrotermes natalensis

    DEFF Research Database (Denmark)

    de Fine Licht, Henrik Hjarvard; Boomsma, Jacobus Jan; Aanen, Duur Kornelis

    2006-01-01

    All colonies of the fungus-growing termite Macrotermes natalensis studied so far are associated with a single genetically variable lineage of Termitomyces symbionts. Such limited genetic variation of symbionts and the absence of sexual fruiting bodies (mushrooms) on M. natalensis mounds would...... transmission mode among Macrotermes species implies that vertical symbiont transmission can evolve rapidly. The unexpected finding of horizontal transmission makes the apparent absence of Termitomyces mushrooms on M. natalensis mounds puzzling. To our knowledge, this is the first detailed study of the genetic...

  6. Grandeur Alliances: Symbiont Metabolic Integration and Obligate Arthropod Hematophagy.

    Science.gov (United States)

    Rio, Rita V M; Attardo, Geoffrey M; Weiss, Brian L

    2016-09-01

    Several arthropod taxa live exclusively on vertebrate blood. This food source lacks essential metabolites required for the maintenance of metabolic homeostasis, and as such, these arthropods have formed symbioses with nutrient-supplementing microbes that facilitate their host's 'hematophagous' feeding ecology. Herein we highlight metabolic contributions of bacterial symbionts that reside within tsetse flies, bed bugs, lice, reduviid bugs, and ticks, with specific emphasis on B vitamin and cofactor biosynthesis. Importantly, these arthropods can transmit pathogens of medical and veterinary relevance and/or cause infestations that induce psychological and dermatological distress. Microbial metabolites, and the biochemical pathways that generate them, can serve as specific targets of novel control mechanisms aimed at disrupting the metabolism of hematophagous arthropods, thus combatting pest invasion and vector-borne pathogen transmission. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. How rhizobial symbionts invade plants: the Sinorhizobium–Medicago model

    Science.gov (United States)

    Jones, Kathryn M.; Kobayashi, Hajime; Davies, Bryan W.; Taga, Michiko E.; Walker, Graham C.

    2009-01-01

    Nitrogen-fixing rhizobial bacteria and leguminous plants have evolved complex signal exchange mechanisms that allow a specific bacterial species to induce its host plant to form invasion structures through which the bacteria can enter the plant root. Once the bacteria have been endocytosed within a host-membrane-bound compartment by root cells, the bacteria differentiate into a new form that can convert atmospheric nitrogen into ammonia. Bacterial differentiation and nitrogen fixation are dependent on the microaerobic environment and other support factors provided by the plant. In return, the plant receives nitrogen from the bacteria, which allows it to grow in the absence of an external nitrogen source. Here, we review recent discoveries about the mutual recognition process that allows the model rhizobial symbiont Sinorhizobium meliloti to invade and differentiate inside its host plant alfalfa (Medicago sativa) and the model host plant barrel medic (Medicago truncatula). PMID:17632573

  8. Species Diversity and Identification of Plant Functional Types of Woodland in Shimbar Protected Area, Khuzestan Provience

    Directory of Open Access Journals (Sweden)

    M. Dinarvand

    2016-05-01

    Full Text Available Measuring the diversity of plant functional types, identifying their characteristics, and their classification will help to identification of woodland germination capacity and implementing appropriate range management programs. The study was designed to measure the species diversity and to identify plant functional types in three adjacent ecological sites in Shimbar or Shirin Bahar region. During winter, spring and summer since 2013 to 2014, the data regarding the percentage of species coverage were taken from 106 plots using stratified random sampling method in the south facing slopes, north facing slopes and the wetland. Species diversity (Alpha diversity and habitat diversity (Beta diversity were measured using PAST and SDR softwares. According to the Shannon-Wiener and Simpson indices the greatest species diversity were found in the wetland, south slopes and north slopes respectively. Species richness was higher in northern slope than northern slopes and the lowest in wetland. For classifying and determining response of vegetation to environmental factors and identifying plant functional types, about 66 resistance to disturbance characters were measured and subjected to clustering by Ward method in R software. The annual and perennial species were classified into 21 and trees and shrubs to 8 classes.

  9. Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments.

    Science.gov (United States)

    Dos Santos, Débora Farage Knupp; Istvan, Paula; Quirino, Betania Ferraz; Kruger, Ricardo Henrique

    2017-02-01

    Antibiotic resistance has become a major concern for human and animal health, as therapeutic alternatives to treat multidrug-resistant microorganisms are rapidly dwindling. The problem is compounded by low investment in antibiotic research and lack of new effective antimicrobial drugs on the market. Exploring environmental antibiotic resistance genes (ARGs) will help us to better understand bacterial resistance mechanisms, which may be the key to identifying new drug targets. Because most environment-associated microorganisms are not yet cultivable, culture-independent techniques are essential to determine which organisms are present in a given environmental sample and allow the assessment and utilization of the genetic wealth they represent. Metagenomics represents a powerful tool to achieve these goals using sequence-based and functional-based approaches. Functional metagenomic approaches are particularly well suited to the identification new ARGs from natural environments because, unlike sequence-based approaches, they do not require previous knowledge of these genes. This review discusses functional metagenomics-based ARG research and describes new possibilities for surveying the resistome in environmental samples.

  10. Identification and functional analysis of an alternative promoter of human intersectin 1 gene

    Directory of Open Access Journals (Sweden)

    Rynditch A. V.

    2010-04-01

    Full Text Available Aim. Intersectin 1 (ITSN1 gene encodes an evolutionarily conserved adaptor protein that functions in clathrin-mediated endocytosis, cell signalling, apoptosis and cytoskeleton rearrangements. Its expression is characterized by multiple alternative splicing. Alternative promoter usage is an additional way to create diversity and flexibility in the regulation of gene expression. The aim of this study was to identify possible alternative promoters of ITSN1 gene. Methods. In silico prediction, 5' RACE, RT-PCR and reporter gene expression assay were used for identification and functional characterization of alternative promoter region. Results. We detected an alternative promoter of human ITSN1 gene which is located in intron 5 and generates 5' truncated transcripts containing in-frame ATG codon with strong Kozak sequence and could encode an N-terminally truncated isoforms lacking first EH domain. The region located 246–190 bp upstream of exon 6 is required for alternative promoter activity. ITSN1 transcripts generated from an alternative promoter were detected in human kidney, liver, lung and brain tissues. However, the level of their expression was significantly lower than that of major ITSN1 isoforms. Conclusion. The results obtained suggest that alternative promoter region located in intron 5 of ITSN1 gene functions as a weak promoter. Further experiments are required to clarify the role of 5' truncated ITSN1 transcripts.

  11. Identification and functional analysis of novel phosphorylation sites in the RNA surveillance protein Upf1.

    Science.gov (United States)

    Lasalde, Clarivel; Rivera, Andrea V; León, Alfredo J; González-Feliciano, José A; Estrella, Luis A; Rodríguez-Cruz, Eva N; Correa, María E; Cajigas, Iván J; Bracho, Dina P; Vega, Irving E; Wilkinson, Miles F; González, Carlos I

    2014-02-01

    One third of inherited genetic diseases are caused by mRNAs harboring premature termination codons as a result of nonsense mutations. These aberrant mRNAs are degraded by the Nonsense-Mediated mRNA Decay (NMD) pathway. A central component of the NMD pathway is Upf1, an RNA-dependent ATPase and helicase. Upf1 is a known phosphorylated protein, but only portions of this large protein have been examined for phosphorylation sites and the functional relevance of its phosphorylation has not been elucidated in Saccharomyces cerevisiae. Using tandem mass spectrometry analyses, we report the identification of 11 putative phosphorylated sites in S. cerevisiae Upf1. Five of these phosphorylated residues are located within the ATPase and helicase domains and are conserved in higher eukaryotes, suggesting a biological significance for their phosphorylation. Indeed, functional analysis demonstrated that a small carboxy-terminal motif harboring at least three phosphorylated amino acids is important for three Upf1 functions: ATPase activity, NMD activity and the ability to promote translation termination efficiency. We provide evidence that two tyrosines within this phospho-motif (Y-738 and Y-742) act redundantly to promote ATP hydrolysis, NMD efficiency and translation termination fidelity.

  12. A Soft Parameter Function Penalized Normalized Maximum Correntropy Criterion Algorithm for Sparse System Identification

    Directory of Open Access Journals (Sweden)

    Yingsong Li

    2017-01-01

    Full Text Available A soft parameter function penalized normalized maximum correntropy criterion (SPF-NMCC algorithm is proposed for sparse system identification. The proposed SPF-NMCC algorithm is derived on the basis of the normalized adaptive filter theory, the maximum correntropy criterion (MCC algorithm and zero-attracting techniques. A soft parameter function is incorporated into the cost function of the traditional normalized MCC (NMCC algorithm to exploit the sparsity properties of the sparse signals. The proposed SPF-NMCC algorithm is mathematically derived in detail. As a result, the proposed SPF-NMCC algorithm can provide an efficient zero attractor term to effectively attract the zero taps and near-zero coefficients to zero, and, hence, it can speed up the convergence. Furthermore, the estimation behaviors are obtained by estimating a sparse system and a sparse acoustic echo channel. Computer simulation results indicate that the proposed SPF-NMCC algorithm can achieve a better performance in comparison with the MCC, NMCC, LMS (least mean square algorithms and their zero attraction forms in terms of both convergence speed and steady-state performance.

  13. Efficient α, β-motif finder for identification of phenotype-related functional modules

    Directory of Open Access Journals (Sweden)

    Schmidt Matthew C

    2011-11-01

    Full Text Available Abstract Background Microbial communities in their natural environments exhibit phenotypes that can directly cause particular diseases, convert biomass or wastewater to energy, or degrade various environmental contaminants. Understanding how these communities realize specific phenotypic traits (e.g., carbon fixation, hydrogen production is critical for addressing health, bioremediation, or bioenergy problems. Results In this paper, we describe a graph-theoretical method for in silico prediction of the cellular subsystems that are related to the expression of a target phenotype. The proposed (α, β-motif finder approach allows for identification of these phenotype-related subsystems that, in addition to metabolic subsystems, could include their regulators, sensors, transporters, and even uncharacterized proteins. By comparing dozens of genome-scale networks of functionally associated proteins, our method efficiently identifies those statistically significant functional modules that are in at least α networks of phenotype-expressing organisms but appear in no more than β networks of organisms that do not exhibit the target phenotype. It has been shown via various experiments that the enumerated modules are indeed related to phenotype-expression when tested with different target phenotypes like hydrogen production, motility, aerobic respiration, and acid-tolerance. Conclusion Thus, we have proposed a methodology that can identify potential statistically significant phenotype-related functional modules. The functional module is modeled as an (α, β-clique, where α and β are two criteria introduced in this work. We also propose a novel network model, called the two-typed, divided network. The new network model and the criteria make the problem tractable even while very large networks are being compared. The code can be downloaded from http://www.freescience.org/cs/ABClique/

  14. Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation

    NARCIS (Netherlands)

    Petersen, J.M.; Kemper, A.; Gruber-Vodicka, H.R.; Cardini, U.; van der Geest, M.; Kleiner, M.; Bulgheresi, S.; Mußmann, M; Herbold, C.W.; Seah, B.K.B.; Antony, C.P.; Liu, D.; Belitz, A.; Weber, M.

    2016-01-01

    Chemosynthetic symbioses are partnerships between invertebrate animals and chemosynthetic bacteria. The latter are theprimary producers, providing most of the organic carbon needed for the animal host’s nutrition. We sequenced genomesof the chemosynthetic symbionts from the lucinid bivalve Loripes

  15. Co-Speciation of Earthworms and their nephridial symbionts, Acidovorax Spp

    DEFF Research Database (Denmark)

    Lund, Marie Braad; Fritz, Michael; Holmstrup, Martin

    2006-01-01

    Earthworms (Annelida; Lumbricidae) harbour species-specific symbiotic bacteria in their nephridia (excretory organs) where the symbionts densely colonize a specific part of the nephridia called the ampulla [1]. The symbiosis is universal among earthworms, the symbionts form a monophyletic cluster...... within the genus Acidovorax [2], and they are transmitted vertically [3]. For these reasons, we suggest that the earthworm-Acidovorax association has evolved by co-speciation. This hypothesis was tested by a comparative study of earthworm and symbiont phylogeny. Different earthworm species were collected...... in Denmark and DNA was extracted from their nephridia. Earthworm phylogeny was resolved on the basis of mitochondrial cytochrome c oxidase subunit I (COI) by direct PCR amplification and sequencing from the nephridial DNA extract. Symbiont 16S rRNA gene sequences were retrieved by cloning and sequencing...

  16. Simultaneous identification of transfer functions and combustion noise of a turbulent flame

    Science.gov (United States)

    Merk, M.; Jaensch, S.; Silva, C.; Polifke, W.

    2018-05-01

    The Large Eddy Simulation/System Identification (LES/SI) approach allows to deduce a flame transfer function (FTF) from LES of turbulent reacting flow: Time series of fluctuations of reference velocity and global heat release rate resulting from broad-band excitation of a simulated turbulent flame are post-processed via SI techniques to derive a low order model of the flame dynamics, from which the FTF is readily deduced. The current work investigates an extension of the established LES/SI approach: In addition to estimation of the FTF, a low order model for the combustion noise source is deduced from the same time series data. By incorporating such a noise model into a linear thermoacoustic model, it is possible to predict the overall level as well as the spectral distribution of sound pressure in confined combustion systems that do not exhibit self-excited thermoacoustic instability. A variety of model structures for estimation of a noise model are tested in the present study. The suitability and quality of these model structures are compared against each other, their sensitivity regarding certain time series properties is studied. The influence of time series length, signal-to-noise ratio as well as acoustic reflection coefficient of the boundary conditions on the identification are examined. It is shown that the Box-Jenkins model structure is superior to simpler approaches for the simultaneous identification of models that describe the FTF as well as the combustion noise source. Subsequent to the question of the most adequate model structure, the choice of optimal model order is addressed, as in particular the optimal parametrization of the noise model is not obvious. Akaike's Information Criterion and a model residual analysis are applied to draw qualitative and quantitative conclusions on the most suitable model order. All investigations are based on a surrogate data model, which allows a Monte Carlo study across a large parameter space with modest

  17. Androgen-Forming Stem Leydig cells: Identification, Function and Therapeutic Potential

    Directory of Open Access Journals (Sweden)

    Yunhui Zhang

    2008-01-01

    Full Text Available Leydig cells are the primary source of testosterone in the male, and differentiation of Leydig cells in the testes is one of the primary events in the development of the male body and fertility. Stem Leydig cells (SLCs exist in the testis throughout postnatal life, but a lack of cell surface markers previously hindered attempts to obtain purified SLC fractions. Once isolated, the properties of SLCs provide interesting clues for the ontogeny of these cells within the embryo. Moreover, the clinical potential of SLCs might be used to reverse age-related declines in testosterone levels in aging men, and stimulate reproductive function in hypogonadal males. This review focuses on the source, identification and outlook for therapeutic applications of SLCs. Separate pools of SLCs may give rise to fetal and adult generations of Leydig cell, which may account for their observed functional differences. These differences should in turn be taken into account when assessing the consequences of environmental pollutants such as the phthalate ester, diethylhexylphthalate (DEHP.

  18. Hydrological functional unit identification - linking observables and concepts towards a minimal adequate catchment representation

    Science.gov (United States)

    Jackisch, C.

    2012-04-01

    Understanding catchment structures and properties as most probable result of past work during their evolution under the continuous depletion of gradients opens a connection of landscape properties to dominating processes. While a qualitative description from the expert's perspective can comprehend most of these; a distinct objective delineation into functional units, their topology and their connectivity appears far more problematic as a) spatio-temporal scale, b) degrees of freedom and c) aspects of self-organisation have to be brought in accordance. Our study highlights several conceptual approaches aiming to link hydrological landscape understanding, observation and modelling. Moreover, a GIS-based case study for the Attert basin is presented, which shows that from a multitude of possible class combinations, already very few cover the vast majority of the catchment. Consequently, dominating processes, prevailing topologies, most insightful data demands and possible non ad hoc model representations are outlined. The result is a step towards a minimal adequate catchment representation. To base this on physical descriptions with truly observable parameters, we further revise most insightful data for functional unit identification and observation and if and how it can be derived in the landscape and from products available.

  19. Improved Radio Frequency Identification Indoor Localization Method via Radial Basis Function Neural Network

    Directory of Open Access Journals (Sweden)

    Dongliang Guo

    2014-01-01

    Full Text Available Indoor localization technique has received much attention in recent years. Many techniques have been developed to solve the problem. Among the recent proposed methods, radio frequency identification (RFID indoor localization technology has the advantages of low-cost, noncontact, non-line-of-sight, and high precision. This paper proposed two radial basis function (RBF neural network based indoor localization methods. The RBF neural networks are trained to learn the mapping relationship between received signal strength indication values and position of objects. Traditional method used the received signal strength directly as the input of neural network; we added another input channel by taking the difference of the received signal strength, thus improving the reliability and precision of positioning. Fuzzy clustering is used to determine the center of radial basis function. In order to reduce the impact of signal fading due to non-line-of-sight and multipath transmission in indoor environment, we improved the Gaussian filter to process received signal strength values. The experimental results show that the proposed method outperforms the existing methods as well as improves the reliability and precision of the RFID indoor positioning system.

  20. Functional Identification of a Pulvinar Path from Superior Colliculus to MT

    Science.gov (United States)

    Berman, Rebecca A.; Wurtz, Robert H.

    2010-01-01

    The idea of a second visual pathway, in which visual signals travel from brainstem to cortex via the pulvinar thalamus, has had considerable influence as an alternative to the primary geniculo-striate pathway. Existence of this second pathway in primates, however, is not well established. A major question centers on whether the pulvinar acts as a relay, particularly in the path from the superior colliculus (SC) to the motion area in middle temporal (MT) cortex. We used physiological microstimulation to identify pulvinar neurons belonging to the path from SC to MT in the macaque. We made three salient observations. First, we identified many neurons in the visual pulvinar that received input from SC or projected to MT, as well as a largely separate set of neurons that received input from MT. Second, and more importantly, we identified a subset of neurons as relay neurons that both received SC input and projected to MT. The identification of these relay neurons demonstrates a continuous functional path from SC to MT through the pulvinar in primates. Third, we histologically localized a subset of SC-MT relay neurons to the subdivision of inferior pulvinar known to project densely to MT, but also localized SC-MT relay neurons to an adjacent subdivision. This pattern indicates that the pulvinar pathway is not limited to a single anatomically-defined region. These findings bring new perspective to the functional organization of the pulvinar and its role in conveying signals to the cerebral cortex. PMID:20445060

  1. Integrating network, sequence and functional features using machine learning approaches towards identification of novel Alzheimer genes.

    Science.gov (United States)

    Jamal, Salma; Goyal, Sukriti; Shanker, Asheesh; Grover, Abhinav

    2016-10-18

    Alzheimer's disease (AD) is a complex progressive neurodegenerative disorder commonly characterized by short term memory loss. Presently no effective therapeutic treatments exist that can completely cure this disease. The cause of Alzheimer's is still unclear, however one of the other major factors involved in AD pathogenesis are the genetic factors and around 70 % risk of the disease is assumed to be due to the large number of genes involved. Although genetic association studies have revealed a number of potential AD susceptibility genes, there still exists a need for identification of unidentified AD-associated genes and therapeutic targets to have better understanding of the disease-causing mechanisms of Alzheimer's towards development of effective AD therapeutics. In the present study, we have used machine learning approach to identify candidate AD associated genes by integrating topological properties of the genes from the protein-protein interaction networks, sequence features and functional annotations. We also used molecular docking approach and screened already known anti-Alzheimer drugs against the novel predicted probable targets of AD and observed that an investigational drug, AL-108, had high affinity for majority of the possible therapeutic targets. Furthermore, we performed molecular dynamics simulations and MM/GBSA calculations on the docked complexes to validate our preliminary findings. To the best of our knowledge, this is the first comprehensive study of its kind for identification of putative Alzheimer-associated genes using machine learning approaches and we propose that such computational studies can improve our understanding on the core etiology of AD which could lead to the development of effective anti-Alzheimer drugs.

  2. The role of symbiont genetic distance and potential adaptability in host preference towards Pseudonocardia symbionts in Acromyrmex leaf-cutting ants

    DEFF Research Database (Denmark)

    Thomas-Poulsen, Michael; Maynard, Janielle; Roland, Damien L.

    2011-01-01

    Fungus-growing ants display symbiont preference in behavioral assays, both towards the fungus they cultivate for food and Actinobacteria they maintain on their cuticle for antibiotic production against parasites. These Actinobacteria, genus Pseudonocardia Henssen (Pseudonocardiacea: Actinomycetales......), help defend the ants’ fungal mutualist from specialized parasites. In Acromyrmex Mayr (Hymenoptera: Formicidae) leaf-cutting ants, individual colonies maintain either a single or a few strains of Pseudonocardia, and the symbiont is primarily vertically transmitted between generations by colony...... with two non-native strains, elucidating the role of genetic distance on preference between strains and Pseudonocardia origin. Our findings suggest that ants tend to prefer bacteria more closely related to their native bacterium and that genetic similarity is probably more important than whether symbionts...

  3. The herbaceous landlord: integrating the effects of symbiont consortia within a single host

    Directory of Open Access Journals (Sweden)

    Roo Vandegrift

    2015-11-01

    Full Text Available Plants are typically infected by a consortium of internal fungal associates, including endophytes in their leaves, as well as arbuscular mycorrhizal fungi (AMF and dark septate endophytes (DSE in their roots. It is logical that these organisms will interact with each other and the abiotic environment in addition to their host, but there has been little work to date examining the interactions of multiple symbionts within single plant hosts, or how the relationships among symbionts and their host change across environmental conditions. We examined the grass Agrostis capillaris in the context of a climate manipulation experiment in prairies in the Pacific Northwest, USA. Each plant was tested for presence of foliar endophytes in the genus Epichloë, and we measured percent root length colonized (PRLC by AMF and DSE. We hypothesized that the symbionts in our system would be in competition for host resources, that the outcome of that competition could be driven by the benefit to the host, and that the host plants would be able to allocate carbon to the symbionts in such a way as to maximize fitness benefit within a particular environmental context. We found a correlation between DSE and AMF PRLC across climatic conditions; we also found a fitness cost to increasing DSE colonization, which was negated by presence of Epichloë endophytes. These results suggest that selective pressure on the host is likely to favor host/symbiont relationships that structure the community of symbionts in the most beneficial way possible for the host, not necessarily favoring the individual symbiont that is most beneficial to the host in isolation. These results highlight the need for a more integrative, systems approach to the study of host/symbiont consortia.

  4. Identification of the optimal donor quality scoring system and measure of early renal function in kidney transplantation.

    LENUS (Irish Health Repository)

    Moore, Jason

    2009-02-27

    The early identification of kidney allografts at risk of later dysfunction has implications for clinical practice. Donor quality scoring systems (preoperative) and measures of early allograft function (first week postoperative) have previously shown practical utility. This study aimed to determine the optimal parameter(s) (preoperative and postoperative) with greatest predictive power for the development of subsequent allograft dysfunction.

  5. Identification and Functional Characterization of the Caenorhabditis elegans Riboflavin Transporters rft-1 and rft-2

    Science.gov (United States)

    Biswas, Arundhati; Elmatari, Daniel; Rothman, Jason; LaMunyon, Craig W.; Said, Hamid M.

    2013-01-01

    Two potential orthologs of the human riboflavin transporter 3 (hRFVT3) were identified in the C. elegans genome, Y47D7A.16 and Y47D7A.14, which share 33.7 and 30.5% identity, respectively, with hRFVT3. The genes are tandemly arranged, and we assign them the names rft-1 (for Y47D7A.16) and rft-2 (for Y47D7A.14). Functional characterization of the coding sequences in a heterologous expression system demonstrated that both were specific riboflavin transporters, although the rft-1 encoded protein had greater transport activity. A more detailed examination of rft-1 showed its transport of riboflavin to have an acidic pH dependence, saturability (apparent Km = 1.4±0.5 µM), inhibition by riboflavin analogues, and Na+ independence. The expression of rft-1 mRNA was relatively higher in young larvae than in adults, and mRNA expression dropped in response to RF supplementation. Knocking down the two transporters individually via RNA interference resulted in a severe loss of fertility that was compounded in a double knockdown. Transcriptional fusions constructed with two fluorophores (rft-1::GFP, and rft-2::mCherry) indicated that rft-1 is expressed in the intestine and a small subset of neuronal support cells along the entire length of the animal. Expression of rft-2 is localized mainly to the intestine and pharynx. We also observed a drop in the expression of the two reporters in animals that were maintained in high riboflavin levels. These results report for the first time the identification of two riboflavin transporters in C. elegans and demonstrate their expression and importance to metabolic function in worms. Absence of transporter function renders worms sterile, making them useful in understanding human disease associated with mutations in hRFVT3. PMID:23483992

  6. SciMiner: web-based literature mining tool for target identification and functional enrichment analysis.

    Science.gov (United States)

    Hur, Junguk; Schuyler, Adam D; States, David J; Feldman, Eva L

    2009-03-15

    SciMiner is a web-based literature mining and functional analysis tool that identifies genes and proteins using a context specific analysis of MEDLINE abstracts and full texts. SciMiner accepts a free text query (PubMed Entrez search) or a list of PubMed identifiers as input. SciMiner uses both regular expression patterns and dictionaries of gene symbols and names compiled from multiple sources. Ambiguous acronyms are resolved by a scoring scheme based on the co-occurrence of acronyms and corresponding description terms, which incorporates optional user-defined filters. Functional enrichment analyses are used to identify highly relevant targets (genes and proteins), GO (Gene Ontology) terms, MeSH (Medical Subject Headings) terms, pathways and protein-protein interaction networks by comparing identified targets from one search result with those from other searches or to the full HGNC [HUGO (Human Genome Organization) Gene Nomenclature Committee] gene set. The performance of gene/protein name identification was evaluated using the BioCreAtIvE (Critical Assessment of Information Extraction systems in Biology) version 2 (Year 2006) Gene Normalization Task as a gold standard. SciMiner achieved 87.1% recall, 71.3% precision and 75.8% F-measure. SciMiner's literature mining performance coupled with functional enrichment analyses provides an efficient platform for retrieval and summary of rich biological information from corpora of users' interests. http://jdrf.neurology.med.umich.edu/SciMiner/. A server version of the SciMiner is also available for download and enables users to utilize their institution's journal subscriptions. Supplementary data are available at Bioinformatics online.

  7. Identification of the functional domains of the telomere protein Rap1 in Schizosaccharomyces pombe.

    Directory of Open Access Journals (Sweden)

    Ikumi Fujita

    Full Text Available The telomere at the end of a linear chromosome plays crucial roles in genome stability. In the fission yeast Schizosaccharomyces pombe, the Rap1 protein, one of the central players at the telomeres, associates with multiple proteins to regulate various telomere functions, such as the maintenance of telomere DNA length, telomere end protection, maintenance of telomere heterochromatin, and telomere clustering in meiosis. The molecular bases of the interactions between Rap1 and its partners, however, remain largely unknown. Here, we describe the identification of the interaction domains of Rap1 with its partners. The Bqt1/Bqt2 complex, which is required for normal meiotic progression, Poz1, which is required for telomere length control, and Taz1, which is required for the recruitment of Rap1 to telomeres, bind to distinct domains in the C-terminal half of Rap1. Intriguingly, analyses of a series of deletion mutants for rap1(+ have revealed that the long N-terminal region (1-456 a.a. [amino acids] of Rap1 (full length: 693 a.a. is not required for telomere DNA length control, telomere end protection, and telomere gene silencing, whereas the C-terminal region (457-693 a.a. containing Poz1- and Taz1-binding domains plays important roles in those functions. Furthermore, the Bqt1/Bqt2- and Taz1-binding domains are essential for normal spore formation after meiosis. Our results suggest that the C-terminal half of Rap1 is critical for the primary telomere functions, whereas the N-terminal region containing the BRCT (BRCA1 C-terminus and Myb domains, which are evolutionally conserved among the Rap1 family proteins, does not play a major role at the telomeres.

  8. Evidence of indirect symbiont conferred protection against the predatory lady beetle Harmonia axyridis in the pea aphid.

    Science.gov (United States)

    Kovacs, Jennifer L; Wolf, Candice; Voisin, Dené; Wolf, Seth

    2017-07-11

    Defensive symbionts can provide significant fitness advantages to their hosts. Facultative symbionts can protect several species of aphid from fungal pathogens, heat shock, and parasitism by parasitoid wasps. Previous work found that two of these facultative symbionts can also indirectly protect pea aphids from predation by the lady beetle Hippocampus convergens. When aphids reproduce asexually, there is extremely high relatedness among aphid clone-mates and often very limited dispersal. Under these conditions, symbionts may indirectly protect aphid clone-mates from predation by negatively affecting the survival of a predator after the consumption of aphids harboring the same vertically transmitted facultative symbionts. In this study, we wanted to determine whether this indirect protection extended to another lady beetle species, Harmonia axyridis. We fed Ha. axyridis larvae aphids from one of four aphid sub-clonal symbiont lines which all originated from the same naturally symbiont free clonal aphid lineage. Three of the sub-clonal lines harbor different facultative symbionts that were introduced to the lines via microinjection. Therefore these sub-clonal lineages vary primarily in their symbiont composition, not their genetic background. We found that aphid facultative symbionts affected larval survival as well as pupal survival in their predator Ha. axyridis. Additionally, Ha. axyridis larvae fed aphids with the Regiella symbiont had significantly longer larval developmental times than beetle larvae fed other aphids, and females fed aphids with the Regiella symbiont as larvae weighed less as adults. These fitness effects were different from those previously found in another aphid predator Hi. convergens suggesting that the fitness effects may not be the same in different aphid predators. Overall, our findings suggest that some aphid symbionts may indirectly benefit their clonal aphid hosts by negatively impacting the development and survival of a lady beetle

  9. The different potential of sponge bacterial symbionts in N₂ release indicated by the phylogenetic diversity and abundance analyses of denitrification genes, nirK and nosZ.

    Science.gov (United States)

    Zhang, Xia; He, Liming; Zhang, Fengli; Sun, Wei; Li, Zhiyong

    2013-01-01

    Nitrogen cycle is a critical biogeochemical process of the oceans. The nitrogen fixation by sponge cyanobacteria was early observed. Until recently, sponges were found to be able to release nitrogen gas. However the gene-level evidence for the role of bacterial symbionts from different species sponges in nitrogen gas release is limited. And meanwhile, the quanitative analysis of nitrogen cycle-related genes of sponge microbial symbionts is relatively lacking. The nirK gene encoding nitrite reductase which catalyzes soluble nitrite into gas NO and nosZ gene encoding nitrous oxide reductase which catalyzes N₂O into N₂ are two key functional genes in the complete denitrification pathway. In this study, using nirK and nosZ genes as markers, the potential of bacterial symbionts in six species of sponges in the release of N2 was investigated by phylogenetic analysis and real-time qPCR. As a result, totally, 2 OTUs of nirK and 5 OTUs of nosZ genes were detected by gene library-based saturated sequencing. Difference phylogenetic diversity of nirK and nosZ genes were observed at OTU level in sponges. Meanwhile, real-time qPCR analysis showed that Xestospongia testudinaria had the highest abundance of nosZ gene, while Cinachyrella sp. had the greatest abundance of nirK gene. Phylogenetic analysis showed that the nirK and nosZ genes were probably of Alpha-, Beta-, and Gammaproteobacteria origin. The results from this study suggest that the denitrification potential of bacteria varies among sponges because of the different phylogenetic diversity and relative abundance of nosZ and nirK genes in sponges. Totally, both the qualitative and quantitative analyses of nirK and nosZ genes indicated the different potential of sponge bacterial symbionts in the release of nitrogen gas.

  10. The different potential of sponge bacterial symbionts in N₂ release indicated by the phylogenetic diversity and abundance analyses of denitrification genes, nirK and nosZ.

    Directory of Open Access Journals (Sweden)

    Xia Zhang

    Full Text Available Nitrogen cycle is a critical biogeochemical process of the oceans. The nitrogen fixation by sponge cyanobacteria was early observed. Until recently, sponges were found to be able to release nitrogen gas. However the gene-level evidence for the role of bacterial symbionts from different species sponges in nitrogen gas release is limited. And meanwhile, the quanitative analysis of nitrogen cycle-related genes of sponge microbial symbionts is relatively lacking. The nirK gene encoding nitrite reductase which catalyzes soluble nitrite into gas NO and nosZ gene encoding nitrous oxide reductase which catalyzes N₂O into N₂ are two key functional genes in the complete denitrification pathway. In this study, using nirK and nosZ genes as markers, the potential of bacterial symbionts in six species of sponges in the release of N2 was investigated by phylogenetic analysis and real-time qPCR. As a result, totally, 2 OTUs of nirK and 5 OTUs of nosZ genes were detected by gene library-based saturated sequencing. Difference phylogenetic diversity of nirK and nosZ genes were observed at OTU level in sponges. Meanwhile, real-time qPCR analysis showed that Xestospongia testudinaria had the highest abundance of nosZ gene, while Cinachyrella sp. had the greatest abundance of nirK gene. Phylogenetic analysis showed that the nirK and nosZ genes were probably of Alpha-, Beta-, and Gammaproteobacteria origin. The results from this study suggest that the denitrification potential of bacteria varies among sponges because of the different phylogenetic diversity and relative abundance of nosZ and nirK genes in sponges. Totally, both the qualitative and quantitative analyses of nirK and nosZ genes indicated the different potential of sponge bacterial symbionts in the release of nitrogen gas.

  11. Production and Metabolism of Indole Acetic Acid in Root Nodules and Symbiont (Rhizobium undicola Isolated from Root Nodule of Aquatic Medicinal Legume Neptunia oleracea Lour.

    Directory of Open Access Journals (Sweden)

    Pallab Kumar Ghosh

    2015-01-01

    Full Text Available Indole acetic acid is a phytohormone which plays a vital role in plant growth and development. The purpose of this study was to shed some light on the production of IAA in roots, nodules, and symbionts of an aquatic legume Neptunia oleracea and its possible role in nodular symbiosis. The symbiont (N37 was isolated from nodules of this plant and identified as Rhizobium undicola based on biochemical characteristics, 16S rDNA sequence homology, and DNA-DNA hybridization results. The root nodules were found to contain more IAA and tryptophan than root; however, no detectable amount of IAA was found in root. The IAA metabolizing enzymes IAA oxidase, IAA peroxidase (E.C.1.11.1.7, and polyphenol oxidase (E.C.1.14.18.1 were higher in root than nodule but total phenol and IAA content were reversed. The strain N37 was found to produce copious amount of IAA in YEM broth medium with tryptophan and reached its stationary phase at 20 h. An enrichment of the medium with mannitol, ammonium sulphate, B12, and 4-hydroxybenzaldehyde was found to promote the IAA production. The presence of IAA metabolizing enzymes and IAA production with PGPR traits including ACC deaminase activity of the symbionts was essential for plant microbe interaction and nodule function.

  12. Development and In silico Evaluation of Large-Scale Metabolite Identification Methods using Functional Group Detection for Metabolomics

    Directory of Open Access Journals (Sweden)

    Joshua M Mitchell

    2014-07-01

    Full Text Available Large-scale identification of metabolites is key to elucidating and modeling metabolism at the systems level. Advances in metabolomics technologies, particularly ultra-high resolution mass spectrometry enable comprehensive and rapid analysis of metabolites. However, a significant barrier to meaningful data interpretation is the identification of a wide range of metabolites including unknowns and the determination of their role(s in various metabolic networks. Chemoselective (CS probes to tag metabolite functional groups combined with high mass accuracy provide additional structural constraints for metabolite identification and quantification. We have developed a novel algorithm, Chemically Aware Substructure Search (CASS that efficiently detects functional groups within existing metabolite databases, allowing for combined molecular formula and functional group (from CS tagging queries to aid in metabolite identification without a priori knowledge. Analysis of the isomeric compounds in both Human Metabolome Database (HMDB and KEGG Ligand demonstrated a high percentage of isomeric molecular formulae (43% and 28% respectively, indicating the necessity for techniques such as CS-tagging. Furthermore, these two databases have only moderate overlap in molecular formulae. Thus, it is prudent to use multiple databases in metabolite assignment, since each major metabolite database represents different portions of metabolism within the biosphere. In silico analysis of various CS-tagging strategies under different conditions for adduct formation demonstrate that combined FT-MS derived molecular formulae and CS-tagging can uniquely identify up to 71% of KEGG and 37% of the combined KEGG/HMDB database versus 41% and 17% respectively without adduct formation. This difference between database isomer disambiguation highlights the strength of CS-tagging for non-lipid metabolite identification. However, unique identification of complex lipids still needs

  13. Application of Peptide LC Retention Time Information in a Discriminant Function for Peptide Identification by Tandem Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Strittmatter, Eric F.; Kangas, Lars J.; Petritis, Konstantinos; Mottaz, Heather M.; Anderson, Gordon A.; Shen, Yufeng; Jacobs, Jon M.; Camp, David G.; Smith, Richard D.

    2004-07-09

    We describe the application of a peptide retention time reversed phase liquid chromatography (RPLC) prediction model previously reported (Petritis et al. Anal. Chem. 99, 2002, 11049) for improved peptide identification. The model uses peptide sequence information to generate a theoretical (predicted) elution time that can be compared with the observed elution time. Using data from a set of known proteins, the retention time parameter was incorporated into a discriminant function for use with tandem mass spectrometry (MS/MS) data analyzed with the peptide/protein identification program SEQUEST. For singly charged ions, the number of identifications increased by 12% when the elution time metric is included compared to when mass spectral data is the sole source of information in the context of a Drosophila melanogaster database. A 3-4% improvement was obtained for doubly and triply charged ions for the same biological system. Application to the larger Rattus norvegicus (rat) and human proteome databases resulted in an 8-9% overall increase in the number of identifications, when both the discriminant function and elution time are used. The effect of adding “runner-up” hits (peptide matches that are not the highest scoring for a spectra) from SEQUEST is also explored, and we find that the number of confident identifications is further increased when these hits are also considered. Finally, application of the discriminant functions derived in this work with ~2.2 million spectra from 330 LC-MS/MS analyses of peptides from human plasma protein resulted in a 19% increase in confident peptide identifications (9551 vs 8049) using elution time information. Further improvements from the use of elution time information can be expected as both the experimental control of elution time reproducibility and the predictive capability are improved.

  14. Linking eye design with host symbiont relationships in pontoniine shrimps (Crustacea, Decapoda, Palaemonidae.

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    Nicola C Dobson

    Full Text Available Symbiosis is prevalent in the marine environment with many studies examining the effects of such interactions between host and symbiont. Pontoniine shrimps are a group whose ecology is characterised by symbiotic interactions. This investigation examines the gross morphology of Pontoniinae compound eyes and superficial optical parameters with reference to their symbiotic relationship or lifestyle category; free-living, ectosymbiont, endosymbiont (bivalves or endosymbiont (non-bivalves. The eye morphologies of free-living and ectosymbiotic species are very similar, yet differ from both forms of endosymbiotic species. Endosymbionts have significantly smaller and simpler eyes with larger facets and bigger interommatidial angles and eye parameters for increased sensitivity levels. However bivalve endosymbionts form an intermediary group between non-bivalve endosymbionts and ectosymbionts as a result of their more active lifestyle. The accessory eye or "nebenauge", although of uncertain function, commonly occurs in free-living Pontoniinae species but rarely in endosymbionts apart from in more primitive species. The variation in morphology reflects tensions between functional requirements and ecological pressures that have strongly influenced eye design in Pontoniinae.

  15. Identification and functional demonstration of miRNAs in the fungus Cryptococcus neoformans.

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    Nan Jiang

    Full Text Available microRNAs (miRNAs, endogenous posttranscriptional repressors by base-pairing of their cognate mRNAs in plants and animals, have mostly been thought lost in the kingdom of fungi. Here, we report the identification of miRNAs from the fungus Cryptococcus neoformans. With bioinformatics and Northern blotting approaches, we found that these miRNAs and their hairpin precursors were present in this fungus. The size of miR1 and miR2 is 22 nt and 18 nt, respectively. The precursors are about ∼70 nt in length that is close to mammalian pre-miRNAs. Characteristic features of miRNAs are also found in miR1/2. We demonstrated that the identified miRNAs, miR1 and miR2, caused transgene silencing via the canonical RNAi pathway. Bioinformantics analysis helps to reveal a number of identical sequences of the miR1/2 in transposable elements (TEs and pseudogenes, prompting us to think that fungal miRNAs might be involved in the regulation of the activity of transposons and the expression of pseudogenes. This study identified functional miRNAs in C. neoformans, and sheds light on the diversity and evolutionary origin of eukaryotic miRNAs.

  16. Identification by functional MRI of human cerebral region activated by taste stimulation

    International Nuclear Information System (INIS)

    Kakimoto, Naoya

    2000-01-01

    The purpose of this study was the examination of possible imaging of the primary taste region of human cerebral cortex by functional MRI (fMRI). Subjects were 19-36 years old, healthy adult male and female volunteers given information concerning the purpose, significance and method of the study. MRI equipment was 1.5 T Signa Horizon (GE) with Head Coil. Images were processed by the software FuncTool on the Advantage Windows Workstation (GE). Taste stimulation was done by swab bearing the solution of 4% quinine hydrochloride, 20% sodium chloride or distilled water (control) or by dripping from the syringe of the solutions, 8% tartaric acid or 80% sugar. Preliminary examinations with the swab suggested the possibility of the identification. Further, with use of dripping apparatus, the taste active region was shown to be identified by fMRI and of which area tended to be larger in male than in female: a significant difference was seen for the quinine hydrochloride. As above, the method was suggested to be a diagnostic mean for the taste perception. (K.H.)

  17. Enhanced identification and functional protective role of carbon nanoparticles on parathyroid in thyroid cancer surgery

    Science.gov (United States)

    Shi, Chenlei; Tian, Bo; Li, Shengze; Shi, Tiefeng; Qin, Huadong; Liu, Shaoyan

    2016-01-01

    Abstract The aim of this study was to determine the effects of nanocarbon particles in combination with meticulous capsular dissection on enhancing the identification and protecting the function of parathyroid glands in thyroid cancer surgery. The data of 97 patients with papillary thyroid tumors diagnosed and treated at the Second Affiliated Hospital, Harbin Medical University between January 2014 and February 2015 were reviewed. Data regarding the sex, age, calcium and parathyroid hormone (PTH) levels, tumor size, multifocality, T stage, and extrathyroid invasion were collected. The incidence of surgeries in which the parathyroid glands were cut mistakenly, the concentration of serum calcium and parathyroid hormone before surgery (baseline) and after surgery on days 1, 3, and 7, and 1 and 6 months in the patients of the two groups (the nanocarbon and control groups) were analyzed. Fifty-two patients underwent meticulous capsular dissection combined with nanocarbon treatment (nanocarbon group), and 45 underwent meticulous capsular dissection alone (control group). The nanocarbon group showed a significantly higher total and average number of revealed parathyroid glands (average number is the mean for different individuals have different number) and a lower incidence of the parathyroid glands being mistakenly cut, in addition to a lower level of hypoparathyroidism than control group following surgery (P parathyroid in thyroid cancer surgery, reduce the risk of mistakenly cutting the parathyroid, and reduce the incidence of postoperative hypoparathyroidism. PMID:27861338

  18. Acquisition of a Novel Sulfur-Oxidizing Symbiont in the Gutless Marine Worm Inanidrilus exumae

    Science.gov (United States)

    2018-01-01

    ABSTRACT Gutless phallodrilines are marine annelid worms without a mouth or gut, which live in an obligate association with multiple bacterial endosymbionts that supply them with nutrition. In this study, we discovered an unusual symbiont community in the gutless phallodriline Inanidrilus exumae that differs markedly from the microbiomes of all 22 of the other host species examined. Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization revealed that I. exumae harbors cooccurring gamma-, alpha-, and deltaproteobacterial symbionts, while all other known host species harbor gamma- and either alpha- or deltaproteobacterial symbionts. Surprisingly, the primary chemoautotrophic sulfur oxidizer “Candidatus Thiosymbion” that occurs in all other gutless phallodriline hosts does not appear to be present in I. exumae. Instead, I. exumae harbors a bacterial endosymbiont that resembles “Ca. Thiosymbion” morphologically and metabolically but originates from a novel lineage within the class Gammaproteobacteria. This endosymbiont, named Gamma 4 symbiont here, had a 16S rRNA gene sequence that differed by at least 7% from those of other free-living and symbiotic bacteria and by 10% from that of “Ca. Thiosymbion.” Sulfur globules in the Gamma 4 symbiont cells, as well as the presence of genes characteristic for autotrophy (cbbL) and sulfur oxidation (aprA), indicate that this symbiont is a chemoautotrophic sulfur oxidizer. Our results suggest that a novel lineage of free-living bacteria was able to establish a stable and specific association with I. exumae and appears to have displaced the “Ca. Thiosymbion” symbionts originally associated with these hosts. IMPORTANCE All 22 gutless marine phallodriline species examined to date live in a highly specific association with endosymbiotic, chemoautotrophic sulfur oxidizers called “Ca. Thiosymbion.” These symbionts evolved from a single common ancestor and represent the ancestral trait for

  19. Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation

    Directory of Open Access Journals (Sweden)

    Lee Sanghyuk

    2008-09-01

    Full Text Available Abstract Background Sox10, a member of the Sry-related HMG-Box gene family, is a critical transcription factor for several important cell lineages, most notably the neural crest stem cells and the derivative peripheral glial cells and melanocytes. Thus far, only a handful of direct target genes are known for this transcription factor limiting our understanding of the biological network it governs. Results We describe identification of multiple direct regulatory target genes of Sox10 through a procedure based on function and conservation. By combining RNA interference technique and DNA microarray technology, we have identified a set of genes that show significant down-regulation upon introduction of Sox10 specific siRNA into Schwannoma cells. Subsequent comparative genomics analyses led to potential binding sites for Sox10 protein conserved across several mammalian species within the genomic region proximal to these genes. Multiple sites belonging to 4 different genes (proteolipid protein, Sox10, extracellular superoxide dismutase, and pleiotrophin were shown to directly interact with Sox10 by chromatin immunoprecipitation assay. We further confirmed the direct regulation through the identified cis-element for one of the genes, extracellular superoxide dismutase, using electrophoretic mobility shift assay and reporter assay. Conclusion In sum, the process of combining differential expression profiling and comparative genomics successfully led to further defining the role of Sox10, a critical transcription factor for the development of peripheral glia. Our strategy utilizing relatively accessible techniques and tools should be applicable to studying the function of other transcription factors.

  20. Towards a semen proteome of the dengue vector mosquito: protein identification and potential functions.

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    Laura K Sirot

    2011-03-01

    Full Text Available No commercially licensed vaccine or treatment is available for dengue fever, a potentially lethal infection that impacts millions of lives annually. New tools that target mosquito control may reduce vector populations and break the cycle of dengue transmission. Male mosquito seminal fluid proteins (Sfps are one such target since these proteins, in aggregate, modulate the reproduction and feeding patterns of the dengue vector, Aedes aegypti. As an initial step in identifying new targets for dengue vector control, we sought to identify the suite of proteins that comprise the Ae. aegypti ejaculate and determine which are transferred to females during mating.Using a stable-isotope labeling method coupled with proteomics to distinguish male- and female-derived proteins, we identified Sfps and sperm proteins transferred from males to females. Sfps were distinguished from sperm proteins by comparing the transferred proteins to sperm-enriched samples derived from testes and seminal vesicles. We identified 93 male-derived Sfps and 52 predicted sperm proteins that are transferred to females during mating. The Sfp protein classes we detected suggest roles in protein activation/inactivation, sperm utilization, and ecdysteroidogenesis. We also discovered that several predicted membrane-bound and intracellular proteins are transferred to females in the seminal fluids, supporting the hypothesis that Ae. aegypti Sfps are released from the accessory gland cells through apocrine secretion, as occurs in mammals. Many of the Ae. aegypti predicted sperm proteins were homologous to Drosophila melanogaster sperm proteins, suggesting conservation of their sperm-related function across Diptera.This is the first study to directly identify Sfps transferred from male Ae. aegypti to females. Our data lay the groundwork for future functional analyses to identify individual seminal proteins that may trigger female post-mating changes (e.g., in feeding patterns and egg

  1. Evidence of indirect symbiont conferred protection against the predatory lady beetle Harmonia axyridis in the pea aphid

    OpenAIRE

    Kovacs, Jennifer L.; Wolf, Candice; Voisin, Den?; Wolf, Seth

    2017-01-01

    Background Defensive symbionts can provide significant fitness advantages to their hosts. Facultative symbionts can protect several species of aphid from fungal pathogens, heat shock, and parasitism by parasitoid wasps. Previous work found that two of these facultative symbionts can also indirectly protect pea aphids from predation by the lady beetle Hippocampus convergens. When aphids reproduce asexually, there is extremely high relatedness among aphid clone-mates and often very limited disp...

  2. Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts

    Science.gov (United States)

    Schreiber, Lars; Kjeldsen, Kasper U.; Funch, Peter; Jensen, Jeppe; Obst, Matthias; López-Legentil, Susanna; Schramm, Andreas

    2016-01-01

    Ascidians are marine filter feeders and harbor diverse microbiota that can exhibit a high degree of host-specificity. Pharyngeal samples of Scandinavian and Mediterranean ascidians were screened for consistently associated bacteria by culture-dependent and -independent approaches. Representatives of the Endozoicomonas (Gammaproteobacteria, Hahellaceae) clade were detected in the ascidian species Ascidiella aspersa, Ascidiella scabra, Botryllus schlosseri, Ciona intestinalis, Styela clava, and multiple Ascidia/Ascidiella spp. In total, Endozoicomonas was detected in more than half of all specimens screened, and in 25–100% of the specimens for each species. The retrieved Endozoicomonas 16S rRNA gene sequences formed an ascidian-specific subclade, whose members were detected by fluorescence in situ hybridization (FISH) as extracellular microcolonies in the pharynx. Two strains of the ascidian-specific Endozoicomonas subclade were isolated in pure culture and characterized. Both strains are chemoorganoheterotrophs and grow on mucin (a mucus glycoprotein). The strains tested negative for cytotoxic or antibacterial activity. Based on these observations, we propose ascidian-associated Endozoicomonas to be commensals, living off the mucus continuously secreted into the pharynx. Members of the ascidian-specific Endozoicomonas subclade were also detected in seawater from the Scandinavian sampling site, which suggests acquisition of the symbionts by horizontal transmission. The combined results indicate a host-specific, yet facultative symbiosis between ascidians and Endozoicomonas. PMID:27462299

  3. Endozoicomonas are specific, facultative symbionts of sea squirts

    Directory of Open Access Journals (Sweden)

    Lars Schreiber

    2016-07-01

    Full Text Available Ascidians are marine filter feeders and harbor diverse microbiota that can exhibit a high degree of host-specificity. Pharyngeal samples of Scandinavian and Mediterranean ascidians were screened for consistently associated bacteria by culture-dependent and -independent approaches. Representatives of the Endozoicomonas (Gammaproteobacteria, Hahellaceae clade were detected in the ascidian species Ascidiella aspersa, A. scabra, Botryllus schlosseri, Ciona intestinalis, Styela clava, and multiple Ascidia/Ascidiella spp. In total, Endozoicomonas was detected in more than half of all specimens screened, and in 25% to 100% of the specimens for each species. The retrieved Endozoicomonas 16S rRNA gene sequences formed an ascidian-specific subclade, whose members were detected by fluorescence in situ hybridization (FISH as extracellular microcolonies in the pharynx. Two strains of the ascidian-specific Endozoicomonas subclade were isolated in pure culture and characterized. Both strains are chemoorganoheterotrophs and grow on mucin (a mucus glycoprotein. The strains tested negative for cytotoxic or antibacterial activity. Based on these observations, we propose ascidian-associated Endozoicomonas to be commensals, living off the mucus continuously secreted into the pharynx. Members of the ascidian-specific Endozoicomonas subclade were also detected in seawater from the Scandinavian sampling site, which suggests acquisition of the symbionts by horizontal transmission. The combined results indicate a host-specific, yet facultative symbiosis between ascidians and Endozoicomonas.

  4. Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont

    Science.gov (United States)

    Lindsey, Amelia R. I.; Werren, John H.; Richards, Stephen; Stouthamer, Richard

    2016-01-01

    Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum. The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain. PMID:27194801

  5. Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont.

    Science.gov (United States)

    Lindsey, Amelia R I; Werren, John H; Richards, Stephen; Stouthamer, Richard

    2016-07-07

    Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain. Copyright © 2016 Lindsey et al.

  6. Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont

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    Amelia R. I. Lindsey

    2016-07-01

    Full Text Available Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre infecting the minute parasitoid wasp Trichogramma pretiosum. The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain.

  7. Distribution and ecology of Frankliniella occidentalis (Thysanoptera: Thripidae) bacterial symbionts.

    Science.gov (United States)

    Chanbusarakum, Lisa J; Ullman, Diane E

    2009-08-01

    Bacterial populations in Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) collected in diverse California environments consisted of two bacterial symbionts: BFo-1 and BFo-2 (B = bacteria, Fo = Frankliniella occidentalis, numbers reflect different types). Dual infections of BFo-1 and BFo-2 were found in 50% of the thrips, 18% had neither bacterium, and 24 and 8% were infected solely with BFo-1 and BFo-2, respectively. No other bacteria consistently infected F. occidentalis. Dual infections occurred more often in male thrips and in thrips of both sexes from southern mountain and valley sites. As average collection year or month minimum temperature decreased, infections of BFo-1, alone or in dual infections, increased significantly. As yearly precipitation increased, infection with BFo-1 alone also increased. F. occidentalis color morphology did not affect bacterial infection. BFo-1 created weak biofilms at 25 and 32 degrees C; BFo-2 made strong biofilms at 25 degrees C and no biofilms at 32 degrees C. When the bacteria were grown in culture together, weak biofilms formed at both temperatures studied, although there was no way to determine what each bacterium contributed to the biofilm. BFo-1 and BFo-2 grew at similar rates at 25 and 30 degrees C. Our data show BFo-1 and BFo-2 occur in natural populations of F. occidentalis and support the hypothesis BFo have a symbiotic relationship with F. occidentalis. Regional differences in bacterial prevalence suggest bacterial infection is associated with environmental conditions, and altitude, temperature, and precipitation may be important factors.

  8. Coral bleaching under thermal stress: putative involvement of host/symbiont recognition mechanisms

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    Tambutte Sylvie

    2009-08-01

    Full Text Available Abstract Background Coral bleaching can be defined as the loss of symbiotic zooxanthellae and/or their photosynthetic pigments from their cnidarian host. This major disturbance of reef ecosystems is principally induced by increases in water temperature. Since the beginning of the 1980s and the onset of global climate change, this phenomenon has been occurring at increasing rates and scales, and with increasing severity. Several studies have been undertaken in the last few years to better understand the cellular and molecular mechanisms of coral bleaching but the jigsaw puzzle is far from being complete, especially concerning the early events leading to symbiosis breakdown. The aim of the present study was to find molecular actors involved early in the mechanism leading to symbiosis collapse. Results In our experimental procedure, one set of Pocillopora damicornis nubbins was subjected to a gradual increase of water temperature from 28°C to 32°C over 15 days. A second control set kept at constant temperature (28°C. The differentially expressed mRNA between the stressed states (sampled just before the onset of bleaching and the non stressed states (control were isolated by Suppression Subtractive Hybridization. Transcription rates of the most interesting genes (considering their putative function were quantified by Q-RT-PCR, which revealed a significant decrease in transcription of two candidates six days before bleaching. RACE-PCR experiments showed that one of them (PdC-Lectin contained a C-Type-Lectin domain specific for mannose. Immunolocalisation demonstrated that this host gene mediates molecular interactions between the host and the symbionts suggesting a putative role in zooxanthellae acquisition and/or sequestration. The second gene corresponds to a gene putatively involved in calcification processes (Pdcyst-rich. Its down-regulation could reflect a trade-off mechanism leading to the arrest of the mineralization process under stress

  9. The geographical patterns of symbiont diversity in the invasive legume Mimosa pudica can be explained by the competitiveness of its symbionts and by the host genotype.

    Science.gov (United States)

    Melkonian, Rémy; Moulin, Lionel; Béna, Gilles; Tisseyre, Pierre; Chaintreuil, Clémence; Heulin, Karine; Rezkallah, Naïma; Klonowska, Agnieszka; Gonzalez, Sophie; Simon, Marcelo; Chen, Wen-Ming; James, Euan K; Laguerre, Gisèle

    2014-07-01

    Variations in the patterns of diversity of symbionts have been described worldwide on Mimosa pudica, a pan-tropical invasive species that interacts with both α and β-rhizobia. In this study, we investigated if symbiont competitiveness can explain these variations and the apparent prevalence of β- over α-rhizobia. We developed an indirect method to measure the proportion of nodulation against a GFP reference strain and tested its reproducibility and efficiency. We estimated the competitiveness of 54 strains belonging to four species of β-rhizobia and four of α-rhizobia, and the influence of the host genotype on their competitiveness. Our results were compared with biogeographical patterns of symbionts and host varieties. We found: (i) a strong strain effect on competitiveness largely explained by the rhizobial species, with Burkholderia phymatum being the most competitive species, followed by B. tuberum, whereas all other species shared similar and reduced levels of competitiveness; (ii) plant genotype can increase the competitiveness of Cupriavidus taiwanensis. The latter data support the likelihood of the strong adaptation of C. taiwanensis with the M. pudica var. unijuga and help explain its prevalence as a symbiont of this variety over Burkholderia species in some environments, most notably in Taiwan. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  10. A novel extracellular gut symbiont in the marine worm Priapulus caudatus (Priapulida) reveals an alphaproteobacterial symbiont clade of the Ecdysozoa

    DEFF Research Database (Denmark)

    Kroer, Paul; Kjeldsen, Kasper Urup; Nyengaard, Jens Randel

    2016-01-01

    Tenuibacter priapulorum’. Within Rickettsiales, they form a phylogenetically well-defined, family-level clade with uncultured symbionts of marine, terrestrial, and freshwater arthropods. Cand. Tenuibacter priapulorum expands the host range of this candidate family from Arthropoda to the entire Ecdysozoa...

  11. Niche acclimatization in Red Sea corals is dependent on flexibility of host-symbiont association

    KAUST Repository

    Ziegler, Maren

    2015-08-06

    Knowledge of host-symbiont specificity and acclimatization capacity of corals is crucial for understanding implications of environmental change. Whilst some corals have been shown to associate with a number of symbionts that may comprise different physiologies, most corals associate with only one dominant Symbiodinium species at a time. Coral communities in the Red Sea thrive under large fluctuations of environmental conditions, but the degree and mechanisms of coral acclimatization are largely unexplored. Here we investigated the potential for niche acclimatization in 2 dominant corals from the central Red Sea, Pocillopora verrucosa and Porites lutea, in relation to the fidelity of the underlying coral-symbiont association. Repeated sampling over 2 seasons along a cross-shelf and depth gradient revealed a stable symbiont association in P. verrucosa and flexible association in P. lutea. A statistical biological-environmental matching routine revealed that the high plasticity of photophysiology and photopigments in the stable Symbiodinium microadriaticum (type A1) community in P. verrucosa were correlated with environmental influences along spatio-temporal dimensions. In contrast, photophysiology and pigments were less variable within each symbiont type from P. lutea indicating that niche acclimatization was rather regulated by a flexible association with a variable Symbiodinium community. Based on these data, we advocate an extended concept of phenotypic plasticity of the coral holobiont, in which the scleractinian host either associates with a specific Symbiodinium type with a broad physiological tolerance, or the host-symbiont pairing is more flexible to accommodate for different symbiont associations, each adapted to specific environmental settings.

  12. Candidatus Sodalis melophagi sp. nov.: phylogenetically independent comparative model to the tsetse fly symbiont Sodalis glossinidius.

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    Tomáš Chrudimský

    Full Text Available Bacteria of the genus Sodalis live in symbiosis with various groups of insects. The best known member of this group, a secondary symbiont of tsetse flies Sodalis glossinidius, has become one of the most important models in investigating establishment and evolution of insect-bacteria symbiosis. It represents a bacterium in the early/intermediate state of the transition towards symbiosis, which allows for exploring such interesting topics as: usage of secretory systems for entering the host cell, tempo of the genome modification, and metabolic interaction with a coexisting primary symbiont. In this study, we describe a new Sodalis species which could provide a useful comparative model to the tsetse symbiont. It lives in association with Melophagus ovinus, an insect related to tsetse flies, and resembles S. glossinidius in several important traits. Similar to S. glossinidius, it cohabits the host with another symbiotic bacterium, the bacteriome-harbored primary symbiont of the genus Arsenophonus. As a typical secondary symbiont, Candidatus Sodalis melophagi infects various host tissues, including bacteriome. We provide basic morphological and molecular characteristics of the symbiont and show that these traits also correspond to the early/intermediate state of the evolution towards symbiosis. Particularly, we demonstrate the ability of the bacterium to live in insect cell culture as well as in cell-free medium. We also provide basic characteristics of type three secretion system and using three reference sequences (16 S rDNA, groEL and spaPQR region we show that the bacterium branched within the genus Sodalis, but originated independently of the two previously described symbionts of hippoboscoids. We propose the name Candidatus Sodalis melophagi for this new bacterium.

  13. Candidatus Sodalis melophagi sp. nov.: phylogenetically independent comparative model to the tsetse fly symbiont Sodalis glossinidius.

    Science.gov (United States)

    Chrudimský, Tomáš; Husník, Filip; Nováková, Eva; Hypša, Václav

    2012-01-01

    Bacteria of the genus Sodalis live in symbiosis with various groups of insects. The best known member of this group, a secondary symbiont of tsetse flies Sodalis glossinidius, has become one of the most important models in investigating establishment and evolution of insect-bacteria symbiosis. It represents a bacterium in the early/intermediate state of the transition towards symbiosis, which allows for exploring such interesting topics as: usage of secretory systems for entering the host cell, tempo of the genome modification, and metabolic interaction with a coexisting primary symbiont. In this study, we describe a new Sodalis species which could provide a useful comparative model to the tsetse symbiont. It lives in association with Melophagus ovinus, an insect related to tsetse flies, and resembles S. glossinidius in several important traits. Similar to S. glossinidius, it cohabits the host with another symbiotic bacterium, the bacteriome-harbored primary symbiont of the genus Arsenophonus. As a typical secondary symbiont, Candidatus Sodalis melophagi infects various host tissues, including bacteriome. We provide basic morphological and molecular characteristics of the symbiont and show that these traits also correspond to the early/intermediate state of the evolution towards symbiosis. Particularly, we demonstrate the ability of the bacterium to live in insect cell culture as well as in cell-free medium. We also provide basic characteristics of type three secretion system and using three reference sequences (16 S rDNA, groEL and spaPQR region) we show that the bacterium branched within the genus Sodalis, but originated independently of the two previously described symbionts of hippoboscoids. We propose the name Candidatus Sodalis melophagi for this new bacterium.

  14. Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts

    Science.gov (United States)

    Macintyre, Lynsey; Zhang, Tong; Viegelmann, Christina; Juarez Martinez, Ignacio; Cheng, Cheng; Dowdells, Catherine; Abdelmohsen, Usama Ramadan; Gernert, Christine; Hentschel, Ute; Edrada-Ebel, RuAngelie

    2014-01-01

    Marine invertebrate-associated symbiotic bacteria produce a plethora of novel secondary metabolites which may be structurally unique with interesting pharmacological properties. Selection of strains usually relies on literature searching, genetic screening and bioactivity results, often without considering the chemical novelty and abundance of secondary metabolites being produced by the microorganism until the time-consuming bioassay-guided isolation stages. To fast track the selection process, metabolomic tools were used to aid strain selection by investigating differences in the chemical profiles of 77 bacterial extracts isolated from cold water marine invertebrates from Orkney, Scotland using liquid chromatography-high resolution mass spectrometry (LC-HRMS) and nuclear magnetic resonance (NMR) spectroscopy. Following mass spectrometric analysis and dereplication using an Excel macro developed in-house, principal component analysis (PCA) was employed to differentiate the bacterial strains based on their chemical profiles. NMR 1H and correlation spectroscopy (COSY) were also employed to obtain a chemical fingerprint of each bacterial strain and to confirm the presence of functional groups and spin systems. These results were then combined with taxonomic identification and bioassay screening data to identify three bacterial strains, namely Bacillus sp. 4117, Rhodococcus sp. ZS402 and Vibrio splendidus strain LGP32, to prioritize for scale-up based on their chemically interesting secondary metabolomes, established through dereplication and interesting bioactivities, determined from bioassay screening. PMID:24905482

  15. Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes

    DEFF Research Database (Denmark)

    Verma, Manoj Kumar; Ahmed, Vasim; Gupta, Shashank

    2018-01-01

    gut microbiome to identify candidate genes responsible for the salt stress tolerance. A plasmid borne metagenomic library of Bacteroidetes enriched human fecal metagenomic DNA led to identification of unique salt osmotolerance clones SR6 and SR7. Subsequent gene analysis combined with functional...... groups in a North Indian population. This study unravels an alternative method for imparting ionic stress tolerance, which may be prevalent in the human gut microbiome....... is an important aspect of gut microbes for their survival and colonization. Identification of these survival mechanisms is a pivotal step towards understanding genomic suitability of a symbiont for successful human gut colonization. Here we highlight our recent work applying functional metagenomics to study human...

  16. Co-niche construction between hosts and symbionts: ideas and evidence.

    Science.gov (United States)

    Borges, Renee M

    2017-07-01

    Symbiosis is a process that can generate evolutionary novelties and can extend the phenotypic niche space of organisms. Symbionts can act together with their hosts to co-construct host organs, within which symbionts are housed. Once established within hosts, symbionts can also influence various aspects of host phenotype, such as resource acquisition, protection from predation by acquisition of toxicity, as well as behaviour. Once symbiosis is established, its fidelity between generations must be ensured. Hosts evolve various mechanisms to screen unwanted symbionts and to facilitate faithful transmission of mutualistic partners between generations. Microbes are the most important symbionts that have influenced plant and animal phenotypes; multicellular organisms engage in developmental symbioses with microbes at many stages in ontogeny. The co-construction of niches may result in composite organisms that are physically nested within each other. While it has been advocated that these composite organisms need new evolutionary theories and perspectives to describe their properties and evolutionary trajectories, it appears that standard evolutionary theories are adequate to explore selection pressures on their composite or individual traits. Recent advances in our understanding of composite organisms open up many important questions regarding the stability and transmission of these units.

  17. Orally Delivered Scorpion Antimicrobial Peptides Exhibit Activity against Pea Aphid (Acyrthosiphon pisum and Its Bacterial Symbionts

    Directory of Open Access Journals (Sweden)

    Karen Luna-Ramirez

    2017-08-01

    Full Text Available Aphids are severe agricultural pests that damage crops by feeding on phloem sap and vectoring plant pathogens. Chemical insecticides provide an important aphid control strategy, but alternative and sustainable control measures are required to avoid rapidly emerging resistance, environmental contamination, and the risk to humans and beneficial organisms. Aphids are dependent on bacterial symbionts, which enable them to survive on phloem sap lacking essential nutrients, as well as conferring environmental stress tolerance and resistance to parasites. The evolution of aphids has been accompanied by the loss of many immunity-related genes, such as those encoding antibacterial peptides, which are prevalent in other insects, probably because any harm to the bacterial symbionts would inevitably affect the aphids themselves. This suggests that antimicrobial peptides (AMPs could replace or at least complement conventional insecticides for aphid control. We fed the pea aphids (Acyrthosiphon pisum with AMPs from the venom glands of scorpions. The AMPs reduced aphid survival, delayed their reproduction, displayed in vitro activity against aphid bacterial symbionts, and reduced the number of symbionts in vivo. Remarkably, we found that some of the scorpion AMPs compromised the aphid bacteriome, a specialized organ that harbours bacterial symbionts. Our data suggest that scorpion AMPs holds the potential to be developed as bio-insecticides, and are promising candidates for the engineering of aphid-resistant crops.

  18. Earthworms and their Nephridial Symbionts: Co-diversification and Maintenance of the Symbiosis

    DEFF Research Database (Denmark)

    Lund, Marie Braad; Holmstrup, Martin; Davidson, Seana K.

    Earthworms harbor in their nephridia (excretory organs) symbiotic bacteria which densely colonize a specific part of the nephridia, called the ampulla [1]. The symbiosis is species-specific and the symbionts form their own monophyletic genus Verminephrobacter (β-proteobacteria) [2] and are vertic......Earthworms harbor in their nephridia (excretory organs) symbiotic bacteria which densely colonize a specific part of the nephridia, called the ampulla [1]. The symbiosis is species-specific and the symbionts form their own monophyletic genus Verminephrobacter (β-proteobacteria) [2......] and are vertically transmitted [3]. For these reasons we hypothesized that the earthworm-Verminephrobacter association evolved by co-diversification. This hypothesis was investigated by a comparison of earthworm and symbiont phylogenies. The earthworm phylogeny was based on Cytochrome c oxidase subunit I (COI...... suggests that the symbiosis has been stably maintained over evolutionary time dating back to the last common lumbricid earthworm ancestor. How this evolutionarily stable association is maintained is unknown; symbiont-free worms can be reared in lab culture and therefore the symbionts are not essential...

  19. Cyanobacterial diversity and a new acaryochloris-like symbiont from Bahamian sea-squirts.

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    Susanna López-Legentil

    Full Text Available Symbiotic interactions between ascidians (sea-squirts and microbes are poorly understood. Here we characterized the cyanobacteria in the tissues of 8 distinct didemnid taxa from shallow-water marine habitats in the Bahamas Islands by sequencing a fragment of the cyanobacterial 16S rRNA gene and the entire 16S-23S rRNA internal transcribed spacer region (ITS and by examining symbiont morphology with transmission electron (TEM and confocal microscopy (CM. As described previously for other species, Trididemnum spp. mostly contained symbionts associated with the Prochloron-Synechocystis group. However, sequence analysis of the symbionts in Lissoclinum revealed two unique clades. The first contained a novel cyanobacterial clade, while the second clade was closely associated with Acaryochloris marina. CM revealed the presence of chlorophyll d (chl d and phycobiliproteins (PBPs within these symbiont cells, as is characteristic of Acaryochloris species. The presence of symbionts was also observed by TEM inside the tunic of both the adult and larvae of L. fragile, indicating vertical transmission to progeny. Based on molecular phylogenetic and microscopic analyses, Candidatus Acaryochloris bahamiensis nov. sp. is proposed for this symbiotic cyanobacterium. Our results support the hypothesis that photosymbiont communities in ascidians are structured by host phylogeny, but in some cases, also by sampling location.

  20. Preclinical in vivo imaging for fat tissue identification, quantification and functional characterization

    Directory of Open Access Journals (Sweden)

    Pasquina Marzola

    2016-09-01

    with increasing interest, will be also briefly described. For each technique the physical principles of signal detection will be overviewed and some relevant studies will be summarized. Far from being exhaustive, this review has the purpose to highlight some strategies useful for the in vivo identification, quantification and functional characterization of adipose tissues mainly from the point of view of biophysics and physiology.

  1. Logic minimization and rule extraction for identification of functional sites in molecular sequences

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    Cruz-Cano Raul

    2012-08-01

    Full Text Available Abstract Background Logic minimization is the application of algebraic axioms to a binary dataset with the purpose of reducing the number of digital variables and/or rules needed to express it. Although logic minimization techniques have been applied to bioinformatics datasets before, they have not been used in classification and rule discovery problems. In this paper, we propose a method based on logic minimization to extract predictive rules for two bioinformatics problems involving the identification of functional sites in molecular sequences: transcription factor binding sites (TFBS in DNA and O-glycosylation sites in proteins. TFBS are important in various developmental processes and glycosylation is a posttranslational modification critical to protein functions. Methods In the present study, we first transformed the original biological dataset into a suitable binary form. Logic minimization was then applied to generate sets of simple rules to describe the transformed dataset. These rules were used to predict TFBS and O-glycosylation sites. The TFBS dataset is obtained from the TRANSFAC database, while the glycosylation dataset was compiled using information from OGLYCBASE and the Swiss-Prot Database. We performed the same predictions using two standard classification techniques, Artificial Neural Networks (ANN and Support Vector Machines (SVM, and used their sensitivities and positive predictive values as benchmarks for the performance of our proposed algorithm. SVM were also used to reduce the number of variables included in the logic minimization approach. Results For both TFBS and O-glycosylation sites, the prediction performance of the proposed logic minimization method was generally comparable and, in some cases, superior to the standard ANN and SVM classification methods with the advantage of providing intelligible rules to describe the datasets. In TFBS prediction, logic minimization produced a very small set of simple rules. In

  2. Accessing carboxylesterase diversity from termite hindgut symbionts through metagenomics.

    Science.gov (United States)

    Rashamuse, Konanani; Mabizela-Mokoena, Nobalanda; Sanyika, Tendai Walter; Mabvakure, Batsirai; Brady, Dean

    2012-01-01

    A shotgun metagenomic library was constructed from termite hindgut symbionts and subsequently screened for esterase activities. A total of 68 recombinant clones conferring esterolytic phenotypes were identified, of which the 14 most active were subcloned and sequenced. The nucleotide lengths of the esterase-encoding open reading frames (ORFs) ranged from 783 to 2,592 bp and encoded proteins with predicted molecular masses of between 28.8 and 97.5 kDa. The highest identity scores in the GenBank database, from a global amino acid alignment ranged from 39 to 83%. The identified ORFs revealed the presence of the G-X-S-X-D, G-D-S-X, and S-X-X-K sequence motifs that have been reported to harbour a catalytic serine residue in other previously reported esterase primary structures. Five of the ORFs (EstT5, EstT7, EstT9, EstT10, and EstT12) could not be classified into any of the original eight esterase families. One of the ORFs (EstT9) showed a unique primary structure consisting of an amidohydrolase-esterase fusion. Six of the 14 esterase-encoding genes were recombinantly expressed in Escherichia coli and the purified enzymes exhibited temperature optima of between 40-50°C. Substrate-profiling studies revealed that the characterised enzymes were 'true' carboxylesterases based on their preferences for short to medium chain length p-nitrophenyl ester substrates. This study has demonstrated a successful application of a metagenomic approach in accessing novel esterase-encoding genes from the gut of termites that could otherwise have been missed by classical culture enrichment approaches. Copyright © 2012 S. Karger AG, Basel.

  3. The Florence Nightingale effect: Organizational identification explains the peculiar link between others’ suffering and workplace functioning in the homelessness sector

    Directory of Open Access Journals (Sweden)

    Laura J Ferris

    2016-01-01

    Full Text Available Frontline employees in the helping professions often perform their duties against a difficult backdrop, including a complex client base and ongoing themes of crisis, suffering, and distress. These factors combine to create an environment in which workers are vulnerable to workplace stress and burnout. The present study tested two models to understand how frontline workers in the homelessness sector deal with the suffering of their clients. First, we examined whether relationships between suffering and workplace functioning (job satisfaction and burnout would be mediated by organizational identification. Second, we examined whether emotional distance from clients (i.e. infrahumanization, measured as reduced attribution of secondary emotions would predict improved workplace functioning (less burnout and greater job satisfaction, particularly when client contact is high. The study involved a mixed-methods design comprising interview (N = 26 and cross-sectional survey data (N = 60 with a sample of frontline staff working in the homelessness sector. Participants were asked to rate the level of client suffering and attribute emotions in a hypothetical client task, and to complete questionnaire measures of burnout, job satisfaction, and organizational identification. We found no relationships between secondary emotion attribution and burnout or satisfaction. Instead, we found that perceiving higher client suffering was linked with higher job satisfaction and lower burnout. Mediation analyses revealed a mediating role for identification, such that recognizing suffering predicted greater identification with the organization, which fully mediated the relationship between suffering and job satisfaction, and also between suffering and burnout. Qualitative analysis of interview data also resonated with this conceptualization. We introduce this novel finding as the ‘Florence Nightingale effect’. With this sample drawn from the homelessness sector, we

  4. The Florence Nightingale Effect: Organizational Identification Explains the Peculiar Link Between Others’ Suffering and Workplace Functioning in the Homelessness Sector

    Science.gov (United States)

    Ferris, Laura J.; Jetten, Jolanda; Johnstone, Melissa; Girdham, Elise; Parsell, Cameron; Walter, Zoe C.

    2016-01-01

    Frontline employees in the helping professions often perform their duties against a difficult backdrop, including a complex client base and ongoing themes of crisis, suffering, and distress. These factors combine to create an environment in which workers are vulnerable to workplace stress and burnout. The present study tested two models to understand how frontline workers in the homelessness sector deal with the suffering of their clients. First, we examined whether relationships between suffering and workplace functioning (job satisfaction and burnout) would be mediated by organizational identification. Second, we examined whether emotional distance from clients (i.e., infrahumanization, measured as reduced attribution of secondary emotions) would predict improved workplace functioning (less burnout and greater job satisfaction), particularly when client contact is high. The study involved a mixed-methods design comprising interview (N = 26) and cross-sectional survey data (N = 60) with a sample of frontline staff working in the homelessness sector. Participants were asked to rate the level of client suffering and attribute emotions in a hypothetical client task, and to complete questionnaire measures of burnout, job satisfaction, and organizational identification. We found no relationships between secondary emotion attribution and burnout or satisfaction. Instead, we found that perceiving higher client suffering was linked with higher job satisfaction and lower burnout. Mediation analyses revealed a mediating role for identification, such that recognizing suffering predicted greater identification with the organization, which fully mediated the relationship between suffering and job satisfaction, and also between suffering and burnout. Qualitative analysis of interview data also resonated with this conceptualization. We introduce this novel finding as the ‘Florence Nightingale effect’. With this sample drawn from the homelessness sector, we provide

  5. Plant-mediated interspecific horizontal transmission of an intracellular symbiont in insects

    KAUST Repository

    Gonella, Elena

    2015-11-13

    Intracellular reproductive manipulators, such as Candidatus Cardinium and Wolbachia are vertically transmitted to progeny but rarely show co-speciation with the host. In sap-feeding insects, plant tissues have been proposed as alternative horizontal routes of interspecific transmission, but experimental evidence is limited. Here we report results from experiments that show that Cardinium is horizontally transmitted between different phloem sap-feeding insect species through plants. Quantitative PCR and in situ hybridization experiments indicated that the leafhopper Scaphoideus titanus releases Cardinium from its salivary glands during feeding on both artificial media and grapevine leaves. Successional time-course feeding experiments with S. titanus initially fed sugar solutions or small areas of grapevine leaves followed by feeding by the phytoplasma vector Macrosteles quadripunctulatus or the grapevine feeder Empoasca vitis revealed that the symbionts were transmitted to both species. Explaining interspecific horizontal transmission through plants improves our understanding of how symbionts spread, their lifestyle and the symbiont-host intermixed evolutionary pattern.

  6. Intracellular Oceanospirillales inhabit the gills of the hydrothermal vent snail Alviniconcha with chemosynthetic, γ-Proteobacterial symbionts.

    Science.gov (United States)

    Beinart, R A; Nyholm, S V; Dubilier, N; Girguis, P R

    2014-12-01

    Associations between bacteria from the γ-Proteobacterial order Oceanospirillales and marine invertebrates are quite common. Members of the Oceanospirillales exhibit a diversity of interactions with their various hosts, ranging from the catabolism of complex compounds that benefit host growth to attacking and bursting host nuclei. Here, we describe the association between a novel Oceanospirillales phylotype and the hydrothermal vent snail Alviniconcha. Alviniconcha typically harbour chemoautotrophic γ- or ε-Proteobacterial symbionts inside their gill cells. Via fluorescence in situ hybridization and transmission electron microscopy, we observed an Oceanospirillales phylotype (named AOP for ‘Alviniconcha Oceanospirillales phylotype’) in membrane-bound vacuoles that were separate from the known γ- or ε-Proteobacterial symbionts. Using quantitative polymerase chain reaction, we surveyed 181 Alviniconcha hosting γ-Proteobacterial symbionts and 102 hosting ε-Proteobacterial symbionts, and found that the population size of AOP was always minor relative to the canonical symbionts (median 0.53% of the total quantified 16S rRNA genes). Additionally, we detected AOP more frequently in Alviniconcha hosting γ-Proteobacterial symbionts than in those hosting ε-Proteobacterial symbionts (96% and 5% of individuals respectively). The high incidence of AOP in γ-Proteobacteria hosting Alviniconcha implies that it could play a significant ecological role either as a host parasite or as an additional symbiont with unknown physiological capacities.

  7. Aphid thermal tolerance is governed by a point mutation in bacterial symbionts.

    Directory of Open Access Journals (Sweden)

    Helen E Dunbar

    2007-05-01

    Full Text Available Symbiosis is a ubiquitous phenomenon generating biological complexity, affecting adaptation, and expanding ecological capabilities. However, symbionts, which can be subject to genetic limitations such as clonality and genomic degradation, also impose constraints on hosts. A model of obligate symbiosis is that between aphids and the bacterium Buchnera aphidicola, which supplies essential nutrients. We report a mutation in Buchnera of the aphid Acyrthosiphon pisum that recurs in laboratory lines and occurs in field populations. This single nucleotide deletion affects a homopolymeric run within the heat-shock transcriptional promoter for ibpA, encoding a small heat-shock protein. This Buchnera mutation virtually eliminates the transcriptional response of ibpA to heat stress and lowers its expression even at cool or moderate temperatures. Furthermore, this symbiont mutation dramatically affects host fitness in a manner dependent on thermal environment. Following a short heat exposure as juveniles, aphids bearing short-allele symbionts produced few or no progeny and contained almost no Buchnera, in contrast to aphids bearing symbionts without the deletion. Conversely, under constant cool conditions, aphids containing symbionts with the short allele reproduced earlier and maintained higher reproductive rates. The short allele has appreciable frequencies in field populations (up to 20%, further supporting the view that lowering of ibpA expression improves host fitness under some conditions. This recurring Buchnera mutation governs thermal tolerance of aphid hosts. Other cases in which symbiont microevolution has a major effect on host ecological tolerance are likely to be widespread because of the high mutation rates of symbiotic bacteria and their crucial roles in host metabolism and development.

  8. Tsetse immune system maturation requires the presence of obligate symbionts in larvae.

    Directory of Open Access Journals (Sweden)

    Brian L Weiss

    2011-05-01

    Full Text Available Beneficial microbial symbionts serve important functions within their hosts, including dietary supplementation and maintenance of immune system homeostasis. Little is known about the mechanisms that enable these bacteria to induce specific host phenotypes during development and into adulthood. Here we used the tsetse fly, Glossina morsitans, and its obligate mutualist, Wigglesworthia glossinidia, to investigate the co-evolutionary adaptations that influence the development of host physiological processes. Wigglesworthia is maternally transmitted to tsetse's intrauterine larvae through milk gland secretions. We can produce flies that lack Wigglesworthia (Gmm(Wgm- yet retain their other symbiotic microbes. Such offspring give rise to adults that exhibit a largely normal phenotype, with the exception being that they are reproductively sterile. Our results indicate that when reared under normal environmental conditions Gmm(Wgm- adults are also immuno-compromised and highly susceptible to hemocoelic E. coli infections while age-matched wild-type individuals are refractory. Adults that lack Wigglesworthia during larval development exhibit exceptionally compromised cellular and humoral immune responses following microbial challenge, including reduced expression of genes that encode antimicrobial peptides (cecropin and attacin, hemocyte-mediated processes (thioester-containing proteins 2 and 4 and prophenoloxidase, and signal-mediating molecules (inducible nitric oxide synthase. Furthermore, Gmm(Wgm- adults harbor a reduced population of sessile and circulating hemocytes, a phenomenon that likely results from a significant decrease in larval expression of serpent and lozenge, both of which are associated with the process of early hemocyte differentiation. Our results demonstrate that Wigglesworthia must be present during the development of immature progeny in order for the immune system to function properly in adult tsetse. This phenomenon provides

  9. Global diversity of marine isopods (except Asellota and crustacean symbionts).

    Science.gov (United States)

    Poore, Gary C B; Bruce, Niel L

    2012-01-01

    The crustacean order Isopoda (excluding Asellota, crustacean symbionts and freshwater taxa) comprise 3154 described marine species in 379 genera in 37 families according to the WoRMS catalogue. The history of taxonomic discovery over the last two centuries is reviewed. Although a well defined order with the Peracarida, their relationship to other orders is not yet resolved but systematics of the major subordinal taxa is relatively well understood. Isopods range in size from less than 1 mm to Bathynomus giganteus at 365 mm long. They inhabit all marine habitats down to 7280 m depth but with few doubtful exceptions species have restricted biogeographic and bathymetric ranges. Four feeding categories are recognised as much on the basis of anecdotal evidence as hard data: detritus feeders and browsers, carnivores, parasites, and filter feeders. Notable among these are the Cymothooidea that range from predators and scavengers to external blood-sucking micropredators and parasites. Isopods brood 10-1600 eggs depending on individual species. Strong sexual dimorphism is characteristic of several families, notably in Gnathiidae where sessile males live with a harem of females while juvenile praniza stages are ectoparasites of fish. Protandry is known in Cymothoidae and protogyny in Anthuroidea. Some Paranthuridae are neotenous. About half of all coastal, shelf and upper bathyal species have been recorded in the MEOW temperate realms, 40% in tropical regions and the remainder in polar seas. The greatest concentration of temperate species is in Australasia; more have been recorded from temperate North Pacific than the North Atlantic. Of tropical regions, the Central Indo-Pacific is home to more species any other region. Isopods are decidedly asymmetrical latitudinally with 1.35 times as many species in temperate Southern Hemisphere than the temperate North Atlantic and northern Pacific, and almost four times as many Antarctic as Arctic species. More species are known from the

  10. Global diversity of marine isopods (except Asellota and crustacean symbionts.

    Directory of Open Access Journals (Sweden)

    Gary C B Poore

    Full Text Available The crustacean order Isopoda (excluding Asellota, crustacean symbionts and freshwater taxa comprise 3154 described marine species in 379 genera in 37 families according to the WoRMS catalogue. The history of taxonomic discovery over the last two centuries is reviewed. Although a well defined order with the Peracarida, their relationship to other orders is not yet resolved but systematics of the major subordinal taxa is relatively well understood. Isopods range in size from less than 1 mm to Bathynomus giganteus at 365 mm long. They inhabit all marine habitats down to 7280 m depth but with few doubtful exceptions species have restricted biogeographic and bathymetric ranges. Four feeding categories are recognised as much on the basis of anecdotal evidence as hard data: detritus feeders and browsers, carnivores, parasites, and filter feeders. Notable among these are the Cymothooidea that range from predators and scavengers to external blood-sucking micropredators and parasites. Isopods brood 10-1600 eggs depending on individual species. Strong sexual dimorphism is characteristic of several families, notably in Gnathiidae where sessile males live with a harem of females while juvenile praniza stages are ectoparasites of fish. Protandry is known in Cymothoidae and protogyny in Anthuroidea. Some Paranthuridae are neotenous. About half of all coastal, shelf and upper bathyal species have been recorded in the MEOW temperate realms, 40% in tropical regions and the remainder in polar seas. The greatest concentration of temperate species is in Australasia; more have been recorded from temperate North Pacific than the North Atlantic. Of tropical regions, the Central Indo-Pacific is home to more species any other region. Isopods are decidedly asymmetrical latitudinally with 1.35 times as many species in temperate Southern Hemisphere than the temperate North Atlantic and northern Pacific, and almost four times as many Antarctic as Arctic species. More species

  11. Cytogenetic and symbiont analysis of five members of the B. dorsalis complex (Diptera, Tephritidae): no evidence of chromosomal or symbiont-based speciation events.

    Science.gov (United States)

    Augustinos, Antonios A; Drosopoulou, Elena; Gariou-Papalexiou, Aggeliki; Asimakis, Elias D; Cáceres, Carlos; Tsiamis, George; Bourtzis, Kostas; Penelope Mavragani-Tsipidou; Zacharopoulou, Antigone

    2015-01-01

    The Bactrocera dorsalis species complex, currently comprising about 90 entities has received much attention. During the last decades, considerable effort has been devoted to delimiting the species of the complex. This information is of great importance for agriculture and world trade, since the complex harbours several pest species of major economic importance and other species that could evolve into global threats. Speciation in Diptera is usually accompanied by chromosomal rearrangements, particularly inversions that are assumed to reduce/eliminate gene flow. Other candidates currently receiving much attention regarding their possible involvement in speciation are reproductive symbionts, such as Wolbachia, Spiroplasma, Arsenophonus, Rickettsia and Cardinium. Such symbionts tend to spread quickly through natural populations and can cause a variety of phenotypes that promote pre-mating and/or post-mating isolation and, in addition, can affect the biology, physiology, ecology and evolution of their insect hosts in various ways. Considering all these aspects, we present: (a) a summary of the recently gained knowledge on the cytogenetics of five members of the Bactrocera dorsalis complex, namely Bactrocera dorsalis s.s., Bactrocera invadens, Bactrocera philippinensis, Bactrocera papayae and Bactrocera carambolae, supplemented by additional data from a Bactrocera dorsalis s.s. colony from China, as well as by a cytogenetic comparison between the dorsalis complex and the genetically close species, Bactrocera tryoni, and, (b) a reproductive symbiont screening of 18 different colonized populations of these five taxa. Our analysis did not reveal any chromosomal rearrangements that could differentiate among them. Moreover, screening for reproductive symbionts was negative for all colonies derived from different geographic origins and/or hosts. There are many different factors that can lead to speciation, and our data do not support chromosomal and/or symbiotic

  12. Polyketide genes in the marine sponge Plakortis simplex: a new group of mono-modular type I polyketide synthases from sponge symbionts.

    Science.gov (United States)

    Della Sala, Gerardo; Hochmuth, Thomas; Costantino, Valeria; Teta, Roberta; Gerwick, William; Gerwick, Lena; Piel, Jörn; Mangoni, Alfonso

    2013-12-01

    Sponge symbionts are a largely unexplored source of new and unusual metabolic pathways. Insights into the distribution and function of metabolic genes of sponge symbionts are crucial to dissect and exploit their biotechnological potential. Screening of the metagenome of the marine sponge Plakortis simplex led to the discovery of the swf family, a new group of mono-modular type I polyketide synthase/fatty acid synthase (PKS/FAS) specifically associated with sponge symbionts. Two different examples of the swf cluster were present in the metagenome of P. simplex. A third example of the cluster is present in the previously sequenced genome of a poribacterium from the sponge Aplysina aerophoba but was formerly considered orthologous to the wcb/rkp cluster. The swf cluster was also found in six additional species of sponges. Therefore, the swf cluster represents the second group of mono-modular PKS, after the supA family, to be widespread in marine sponges. The putative swf operon consists of swfA (type I PKS/FAS), swfB (reductase and sulphotransferase domains) and swfC (radical S-adenosylmethionine, or radical SAM). Activation of the acyl carrier protein (ACP) domain of the SwfA protein to its holo-form by co-expression with Svp is the first functional proof of swf type genes in marine sponges. However, the precise biosynthetic role of the swf clusters remains unknown. © 2013 The Authors. Environmental Microbiology Reports published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  13. From dysplastic nevus to melanoma: functional proteomic approach for the identification of bio markers

    International Nuclear Information System (INIS)

    De Pol, A.

    2009-01-01

    The project ultimately aims to identify bio markers from serum or other biological fluids helpful for early diagnosis of melanoma. Parametric analysis combined with advanced skin imaging technology, such as con focal microscopy, is directed to the identification of different types of benign melanocyte lesions, as well as to the characterization of different melanomas and dysplastic nevi, in order to understand different tumour progression behaviours and to identify possible melanoma precursors

  14. Identification of Candidate Functional Elements in the Genome from ChIP-seq Data.

    Science.gov (United States)

    Marinov, Georgi K

    2017-01-01

    ChIP-seq datasets provide a wealth of information for the identification of candidate regulatory elements in the genome. For this potential to be fully realized, methods for evaluating data quality and for distinguishing reproducible signal from technical and biological noise are necessary. Here, the computational methods for addressing these challenges developed by the ENCODE Consortium are described and the key considerations for analyzing and interpreting ChIP-seq data are discussed.

  15. Olfactory identification and its relationship to executive functions, memory, and disability one year after severe traumatic brain injury.

    Science.gov (United States)

    Sigurdardottir, Solrun; Andelic, Nada; Skandsen, Toril; Anke, Audny; Roe, Cecilie; Holthe, Oyvor Oistensen; Wehling, Eike

    2016-01-01

    To explore the frequency of posttraumatic olfactory (dys)function 1 year after severe traumatic brain injury (TBI) and determine whether there is a relationship between olfactory identification and neuropsychological test performance, injury severity and TBI-related disability. A population-based multicenter study including 129 individuals with severe TBI (99 males; 16 to 85 years of age) that could accomplish neuropsychological examinations. Olfactory (dys)function (anosmia, hyposmia, normosmia) was assessed by the University of Pennsylvania Smell Identification Test (UPSIT) or the Brief Smell Identification Test (B-SIT). Three tests of the Delis-Kaplan Executive Function System (D-KEFS) were used to assess processing speed, verbal fluency, inhibition and set-shifting, and the California Verbal Learning Test-II was used to examine verbal memory. The Glasgow Outcome Scale-Extended (GOSE) was used to measure disability level. Employing 2 different smell tests in 2 equal-sized subsamples, the UPSIT sample (n = 65) classified 34% with anosmia and 52% with hyposmia, while the B-SIT sample (n = 64) classified 20% with anosmia and 9% with hyposmia. Individuals classified with anosmia by the B-SIT showed significantly lower scores for set-shifting, category switching fluency and delayed verbal memory compared to hyposmia and normosmia groups. Only the B-SIT scores were significantly correlated with neuropsychological performance and GOSE scores. Brain injury severity (Rotterdam CT score) and subarachnoid hemorrhage were related to anosmia. Individuals classified with anosmia demonstrated similar disability as those with hyposmia/normosmia. Different measures of olfaction may yield different estimates of anosmia. Nevertheless, around 1 third of individuals with severe TBI suffered from anosmia, which may also indicate poorer cognitive outcome. (c) 2015 APA, all rights reserved).

  16. Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata.

    Science.gov (United States)

    Sharp, Koty H; Pratte, Zoe A; Kerwin, Allison H; Rotjan, Randi D; Stewart, Frank J

    2017-09-15

    Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state (Symbiodinium density in the coral) on microbiome community composition. Change in season had a strong effect on A. poculata microbiome composition. The seasonal shift was greatest upon the winter to spring transition, during which time A. poculata microbiome composition became more similar among host individuals. Within each of the four seasons, microbiome composition differed significantly from that of surrounding seawater but was surprisingly uniform between symbiotic and aposymbiotic corals, even in summer, when differences in Symbiodinium density between brown and white colonies are the highest, indicating that the observed seasonal shifts are not likely due to fluctuations in Symbiodinium density. Our results suggest that symbiotic state may not be a primary driver of coral microbial community organization in A. poculata, which is a surprise given the long-held assumption that excess photosynthate is of importance to coral-associated microbes. Rather, other environmental or host factors, in this case, seasonal changes in host physiology associated with winter quiescence, may drive microbiome diversity. Additional studies of A. poculata and other facultatively symbiotic corals will provide important comparisons to studies of reef-building tropical corals and therefore

  17. Host immunostimulation and substrate utilization of the gut symbiont Akkermansia muciniphila

    NARCIS (Netherlands)

    Ottman, N.A.

    2015-01-01

    Host immunostimulation and substrate utilization of the gut symbiont Akkermansia muciniphila

    Noora A. Ottman

    The human gastrointestinal tract is colonized by a complex community of micro-organisms, the gut microbiota. The majority of these

  18. Characterization of a newly discovered symbiont of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae).

    Science.gov (United States)

    Bing, Xiao-Li; Yang, Jiao; Zchori-Fein, Einat; Wang, Xiao-Wei; Liu, Shu-Sheng

    2013-01-01

    Bemisia tabaci (Hemiptera: Aleyrodidae) is a species complex containing >28 cryptic species, some of which are important crop pests worldwide. Like many other sap-sucking insects, whiteflies harbor an obligatory symbiont, "Candidatus Portiera aleyrodidarum," and a number of secondary symbionts. So far, six genera of secondary symbionts have been identified in B. tabaci. In this study, we report and describe the finding of an additional bacterium in the indigenous B. tabaci cryptic species China 1 (formerly known as B. tabaci biotype ZHJ3). Phylogenetic analysis based on the 16S rRNA and gltA genes showed that the bacterium belongs to the Alphaproteobacteria subdivision of the Proteobacteria and has a close relationship with human pathogens of the genus Orientia. Consequently, we temporarily named it Orientia-like organism (OLO). OLO was found in six of eight wild populations of B. tabaci China 1, with the infection rate ranging from 46.2% to 76.8%. Fluorescence in situ hybridization (FISH) of B. tabaci China 1 in nymphs and adults revealed that OLOs are confined to the bacteriome and co-occur with "Ca. Portiera aleyrodidarum." The vertical transmission of OLO was demonstrated by detection of OLO at the anterior pole end of the oocytes through FISH. Quantitative PCR analysis of population dynamics suggested a complex interaction between "Ca. Portiera aleyrodidarum" and OLO. Based on these results, we propose "Candidatus Hemipteriphilus asiaticus" for the classification of this symbiont from B. tabaci.

  19. Horizontal transmission of the insect symbiont Rickettsia is plant-mediated

    Science.gov (United States)

    Caspi-Fluger, Ayelet; Inbar, Moshe; Mozes-Daube, Netta; Katzir, Nurit; Portnoy, Vitaly; Belausov, Eduard; Hunter, Martha S.; Zchori-Fein, Einat

    2012-01-01

    Bacteria in the genus Rickettsia, best known as vertebrate pathogens vectored by blood-feeding arthropods, can also be found in phytophagous insects. The presence of closely related bacterial symbionts in evolutionarily distant arthropod hosts presupposes a means of horizontal transmission, but no mechanism for this transmission has been described. Using a combination of experiments with live insects, molecular analyses and microscopy, we found that Rickettsia were transferred from an insect host (the whitefly Bemisia tabaci) to a plant, moved inside the phloem, and could be acquired by other whiteflies. In one experiment, Rickettsia was transferred from the whitefly host to leaves of cotton, basil and black nightshade, where the bacteria were restricted to the phloem cells of the plant. In another experiment, Rickettsia-free adult whiteflies, physically segregated but sharing a cotton leaf with Rickettsia-plus individuals, acquired the Rickettsia at a high rate. Plants can serve as a reservoir for horizontal transmission of Rickettsia, a mechanism which may explain the occurrence of phylogenetically similar symbionts among unrelated phytophagous insect species. This plant-mediated transmission route may also exist in other insect–symbiont systems and, since symbionts may play a critical role in the ecology and evolution of their hosts, serve as an immediate and powerful tool for accelerated evolution. PMID:22113034

  20. Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

    Directory of Open Access Journals (Sweden)

    Xiaorui Chen

    2017-10-01

    Full Text Available Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle.

  1. Isolation of symbionts and GC-MS analysis of lichens collected from ...

    African Journals Online (AJOL)

    In Nigeria, a good number of lichen species have been recorded and so far not much work has been done to isolate or identify the symbionts. The utility of lichen comes from a range of secondary compounds produced by them. In view of this, two lichen samples, foliose (Parmalia reticulata Taylor) and fruticose Usnea ...

  2. Symbiont shift towards Rhizobium nodulation in a group of phylogenetically related Phaseolus species.

    Science.gov (United States)

    Servín-Garcidueñas, Luis E; Zayas-Del Moral, Alejandra; Ormeño-Orrillo, Ernesto; Rogel, Marco A; Delgado-Salinas, Alfonso; Sánchez, Federico; Martínez-Romero, Esperanza

    2014-10-01

    Bean plants from the Phaseolus genus are widely consumed and represent a nitrogen source for human nutrition. They provide biological fertilization by establishing root nodule symbiosis with nitrogen-fixing bacteria. To establish a successful interaction, bean plants and their symbiotic bacteria need to synchronize a proper molecular crosstalk. Within the Phaseolus genus, P. vulgaris has been the prominent species to study nodulation with Rhizobium symbionts. However the Phaseolus genus comprises diverse species whose symbionts have not been analyzed. Here we identified and studied nodule bacteria from representative Phaseolus species not previously analyzed and from all the described wild species related to P. vulgaris. We found Bradyrhizobium in nodules from most species representing all Phaseolus clades except in five phylogenetically related species from the P. vulgaris clade. Therefore we propose that Bradyrhizobium nodulation is common in Phaseolus and that there was a symbiont preference shift to Rhizobium nodulation in few related species. This work sets the basis to further study the genetic basis of this symbiont substitution. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Cardinium symbionts induce haploid thelytoky in most clones of three closely related Brevipalpus species

    NARCIS (Netherlands)

    Groot, T.V.M.; Breeuwer, J.A.J.

    2006-01-01

    Bacterial symbionts that manipulate the reproduction of their host to increase their own transmission are widespread. Most of these bacteria are Wolbachia, but recently a new bacterium, named Cardinium, was discovered that is capable of the same manipulations. In the host species Brevipalpus

  4. Parasitoid gene expression changes after adaptation to symbiont-protected hosts.

    Science.gov (United States)

    Dennis, Alice B; Patel, Vilas; Oliver, Kerry M; Vorburger, Christoph

    2017-11-01

    Reciprocal selection between aphids, their protective endosymbionts, and the parasitoid wasps that prey upon them offers an opportunity to study the basis of their coevolution. We investigated adaptation to symbiont-conferred defense by rearing the parasitoid wasp Lysiphlebus fabarum on aphids (Aphis fabae) possessing different defensive symbiont strains (Hamiltonella defensa). After ten generations of experimental evolution, wasps showed increased abilities to parasitize aphids possessing the H. defensa strain they evolved with, but not aphids possessing the other strain. We show that the two symbiont strains encode different toxins, potentially creating different targets for counter-adaptation. Phenotypic and behavioral comparisons suggest that neither life-history traits nor oviposition behavior differed among evolved parasitoid lineages. In contrast, comparative transcriptomics of adult female wasps identified a suite of differentially expressed genes among lineages, even when reared in a common, symbiont-free, aphid host. In concurrence with the specificity of each parasitoid lineages' infectivity, most differentially expressed parasitoid transcripts were also lineage-specific. These transcripts are enriched with putative venom toxins and contain highly expressed, potentially defensive viral particles. Together, these results suggest that wild populations of L. fabarum employ a complicated offensive arsenal with sufficient genetic variation for wasps to adapt rapidly and specifically to their hosts' microbial defenses. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  5. Complementary symbiont contributions to plant decomposition in a fungus-farming termite

    NARCIS (Netherlands)

    Poulsen, Michael; Hu, Haofu; Li, Cai; Chen, Zhensheng; Xu, Luohao; Otani, Saria; Nygaard, Sanne; Nobre, Tania; Klaubauf, S.; Schindler, Philipp M; Hauser, Frank; Pan, Hailin; Yang, Zhikai; Sonnenberg, Anton S M; de Beer, Z Wilhelm; Zhang, Yong; Wingfield, Michael J; Grimmelikhuijzen, Cornelis J P; de Vries, Ronald P; Korb, Judith; Aanen, Duur K; Wang, Jun; Boomsma, Jacobus J; Zhang, Guojie; van den Brink, J.

    2014-01-01

    Termites normally rely on gut symbionts to decompose organic matter but the Macrotermitinae domesticated Termitomyces fungi to produce their own food. This transition was accompanied by a shift in the composition of the gut microbiota, but the complementary roles of these bacteria in the symbiosis

  6. Complementary symbiont contributions to plant decomposition in a fungus-farming termite

    DEFF Research Database (Denmark)

    Thomas-Poulsen, Michael; Hu, Haofu; Li, Cai

    2014-01-01

    Termites normally rely on gut symbionts to decompose organic matter but the Macrotermitinae domesticated Termitomyces fungi to produce their own food. This transition was accompanied by a shift in the composition of the gut microbiota, but the complementary roles of these bacteria in the symbiosi...

  7. Marine Maladies? Worms, Germs, and Other Symbionts from the Northern Gulf of Mexico.

    Science.gov (United States)

    Overstreet, Robin M.

    Parasites and related symbionts of marine and estuarine hosts of the northern Gulf of Mexico are described in this guidebook. It is meant primarily to serve as a teaching aid for the novice student, but it also contains more technical aspects for the experienced parasitologist. Forms and examples of symbiosis are explained in an introductory…

  8. Gastrointestinal symbionts of chimpanzees in Cantanhez National Park, Guinea-Bissau with respect to habitat fragmentation

    Czech Academy of Sciences Publication Activity Database

    Sá, R. M.; Petrášová, J.; Pomajbíková, K.; Profousová, I.; Petrželková, Klára Judita; Sousa, C.; Cable, J.; Bruford, M. W.; Modrý, David

    2013-01-01

    Roč. 75, č. 10 (2013), s. 1032-1041 ISSN 0275-2565 Institutional support: RVO:68081766 ; RVO:60077344 Keywords : Cantanhez National Park * fragmentation * Pan troglodytes verus * parasites * symbionts * Trichuris sp Subject RIV: EG - Zoology Impact factor: 2.136, year: 2013

  9. Global identification of stochastic dynamical systems under different pseudo-static operating conditions: The functionally pooled ARMAX case

    Science.gov (United States)

    Sakellariou, J. S.; Fassois, S. D.

    2017-01-01

    The identification of a single global model for a stochastic dynamical system operating under various conditions is considered. Each operating condition is assumed to have a pseudo-static effect on the dynamics and be characterized by a single measurable scheduling variable. Identification is accomplished within a recently introduced Functionally Pooled (FP) framework, which offers a number of advantages over Linear Parameter Varying (LPV) identification techniques. The focus of the work is on the extension of the framework to include the important FP-ARMAX model case. Compared to their simpler FP-ARX counterparts, FP-ARMAX models are much more general and offer improved flexibility in describing various types of stochastic noise, but at the same time lead to a more complicated, non-quadratic, estimation problem. Prediction Error (PE), Maximum Likelihood (ML), and multi-stage estimation methods are postulated, and the PE estimator optimality, in terms of consistency and asymptotic efficiency, is analytically established. The postulated estimators are numerically assessed via Monte Carlo experiments, while the effectiveness of the approach and its superiority over its FP-ARX counterpart are demonstrated via an application case study pertaining to simulated railway vehicle suspension dynamics under various mass loading conditions.

  10. Target identification performance as a function of spurious response: aliasing with respect to the half sample rate

    Science.gov (United States)

    Moyer, Steven K.; Driggers, Ronald G.; Vollmerhausen, Richard H.; Krapels, Keith A.

    2001-09-01

    The sampling limitations associated with focal plane array imagers caused an aliased signal that corrupts the image. The aliased signal is a function of pre-sample blur, sampling frequency, and post-blur or image reconstruction. Previous experiments at the U.S. Army Night Vision and Electronic Sensors Directorate have quantified the effect of aliasing on the task of infrared target identification. Based on data from these experiments, the MTF Squeeze model was developed. The degraded performance due to under- sampling was modeled as an increase in system blur or, equivalently, a contraction or `squeeze' in the MTF. This paper describes the results of numerous sampling experiments.

  11. Diversity and localization of bacterial symbionts in three whitefly species (Hemiptera: Aleyrodidae) from the east coast of the Adriatic Sea.

    Science.gov (United States)

    Skaljac, M; Zanić, K; Hrnčić, S; Radonjić, S; Perović, T; Ghanim, M

    2013-02-01

    Several whitefly species (Hemiptera: Aleyrodidae) are cosmopolitan phloem-feeders that cause serious damage in numerous agricultural crops. All whitefly species harbor a primary bacterial symbiont and a diverse array of secondary symbionts which may influence several aspects of the insect's biology. We surveyed infections by secondary symbionts in Bemisia tabaci (Gennadius), Trialeurodes vaporariorum (Westwood) and Siphoninus phillyreae (Haliday) from areas in the east cost of the Adriatic Sea. Both the Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) B. tabaci genetic groups were detected in Montenegro, whereas only the MED was confirmed in Croatia. Trialeurodes vaporariorum and S. phillyreae were found in all areas surveyed. MEAM1 and MED exhibited similarity to previously reported infections, while populations of T. vaporariorum from Montenegro harbored Rickettsia, Wolbachia and Cardinium in addition to previously reported Hamiltonella and Arsenopnohus. Siphoninus phillyreae harbored Hamiltonella, Wolbachia, Cardinium and Arsenophonus, with the latter appearing in two alleles. Multiple infections of all symbionts were common in the three insect species tested, with some reaching near fixation. Florescent in situ hybridization showed new localization patterns for Hamiltonella in S. phillyreae, and the morphology of the bacteriosome differed from that observed in other whitefly species. Our results show new infections with bacterial symbionts in the whitefly species studied. Infections with the same symbionts in reproductively isolated whitefly species confirm complex relationships between whiteflies and bacterial symbionts, and suggest possible horizontal transfer of some of these bacteria.

  12. Preferential allocation, physio-evolutionary feedbacks, and the stability and environmental patterns of mutualism between plants and their root symbionts.

    Science.gov (United States)

    Bever, James D

    2015-03-01

    The common occurrence of mutualistic interactions between plants and root symbionts is problematic. As the delivery of benefit to hosts involves costs to symbionts, symbionts that provide reduced benefit to their host are expected to increase in frequency. Plants have been shown to allocate preferentially to the most efficient symbiont and this preferential allocation may stabilize the mutualism. I construct a general model of the interactive feedbacks of host preferential allocation and the dynamics of root symbiont populations to evaluate the stability of nutritional mutualisms. Preferential allocation can promote the evolution of mutualism even when the cost to the symbiont is very large. Moreover, the physiological plasticity of preferential allocation likely leads to coexistence of beneficial and nonbeneficial symbionts. For arbuscular mycorrhizal fungi, which facilitate plant uptake of phosphorus (P), the model predicts greater P transfer from these fungi per unit carbon invested with decreasing concentrations of soil P and with increasing concentrations of atmospheric CO2 , patterns that have been observed in laboratory and field studies. This framework connects physiological plasticity in plant allocation to population processes that determine mutualism stability and, as such, represents a significant step in understanding the stability and environmental patterns in mutualism. © 2015 The Author. New Phytologist © 2015 New Phytologist Trust.

  13. Diversity, Bacterial Symbionts and Antibacterial Potential of Gut-Associated Fungi Isolated from the Pantala flavescens Larvae in China.

    Directory of Open Access Journals (Sweden)

    Ming-Wei Shao

    Full Text Available The diversity of fungi associated with the gut of Pantala flavescens larvae was investigated using a culture-dependent method and molecular identification based on an analysis of the internally transcribed spacer sequence. In total, 48 fungal isolates were obtained from P. flavescens larvae. Based on phylogenetic analyses, the fungal isolates were grouped in 5 classes and 12 different genera. Fourteen bacterial 16S rDNA sequences derived from total genomic DNA extractions of fungal mycelia were obtained. The majority of the sequences were associated with Proteobacteria (13/14, and one Bacillaceae (1/14 was included. Leclercia sp., Oceanobacillus oncorhynchi and Methylobacterium extorquens, were reported for the first time as bacterial endosymbionts in fungi. High-performance liquid chromatography (HPLC analysis indicated that bacterial symbionts produced specific metabolites and also exerted an inhibitory effect on fungal metabolites. The biological activity of the fungal culture extracts against the pathogenic bacteria Staphylococcus aureus (ATCC 6538, Bacillus subtilis (ATCC 6633 and Escherichia coli (ATCC 8739 was investigated, and 20 extracts (42% exhibited antibacterial activity against at least one of the tested bacterial strains. This study is the first report on the diversity and antibacterial activity of symbiotic fungi residing in the gut of P. flavescens larvae, and the results show that these fungi are highly diverse and could be exploited as a potential source of bioactive compounds.

  14. Parasitoids and dipteran predators exploit volatiles from microbial symbionts to locate bark beetles.

    Science.gov (United States)

    Boone, Celia K; Six, Diana L; Zheng, Yanbing; Raffa, Kenneth F

    2008-02-01

    Host location by parasitoids and dipteran predators of bark beetles is poorly understood. Unlike coleopteran predators that locate prey by orienting to prey pheromones, wasps and flies often attack life stages not present until after pheromone production ceases. Bark beetles have important microbial symbionts, which could provide sources of cues. We tested host trees, trees colonized by beetles and symbionts, and trees colonized by symbionts alone for attractiveness to hymenopteran parasitoids and dipteran predators. Field studies were conducted with Ips pini in Montana. Three pteromalid wasps were predominant. All were associated with the second and third instars of I. pini. Heydenia unica was more attracted to logs colonized by either I. pini or the fungus Ophiostoma ips than logs alone or blank controls (screen with no log). Rhopalicus pulchripennis was more attracted to logs colonized by I. pini than logs alone or blank controls. Dibrachys cavus was attracted to logs but did not distinguish whether or not they were colonized. Two dolichopodid predators were predominant. A Medetera species was more attracted to colonized than uncolonized logs and more attracted to logs than blank controls. It was also more attracted to logs colonized with the yeast Pichia scolyti than uncolonized logs, but attraction was less consistent. An unidentified dolichopodid was more attracted to logs colonized with I. pini, O. ips, and the bacteria Burkholderia sp., than to uncolonized logs. It was also attracted to uncolonized logs. Its responses were less consistent and pronounced than H. unica. These results suggest some parasitoids and dipteran predators exploit microbial symbionts of bark beetles to locate hosts. Overall, specialists showed strong attraction to fungal cues, whereas generalists were more attracted by plant volatiles. These results also show how microbial symbionts can have conflicting effects on host fitness.

  15. Root fungal symbionts interact with mammalian herbivory, soil nutrient availability and specific habitat conditions.

    Science.gov (United States)

    Ruotsalainen, Anna L; Eskelinen, Anu

    2011-07-01

    Herbivory, competition and soil fertility interactively shape plant communities and exhibit an important role in modifying conditions for host-dependent fungal symbionts. However, field studies on the combined impacts of natural herbivory, competition and soil fertility on root fungal symbionts are rare. We asked how mammalian herbivory, fertilization, liming and plant-plant competition affect the root colonization of arbuscular mycorrhizal fungi (AMF) and dark septate endophytic (DSE) fungi of the dicot herb, Solidago virgaurea. The 2-year full-factorial experiment was conducted in two contrasting habitats: non-acidic and acidic mountain tundra. We found that herbivory increased arbuscular colonization (i.e. the site of resource exchange) at fertile non-acidic sites, where vegetation was rich in species having AMF symbionts, whereas at infertile acidic sites, where plants having AMF symbiont are scarce, the response was the opposite. Herbivory of the host plant negatively affected DSE hyphal and sclerotial colonization in unfertilized plots, possibly due to reduced carbon flow from the host plant while there was no effect of herbivory in fertilized plots. DSE colonization was highest in unfertilized exclosures where soil nutrient concentrations were also lowest. Liming had a negative effect on DSE hyphal colonization, and its effect also interacted with herbivory and the habitat. Biomass removal of the neighboring plants did not affect the root colonization percent of either arbuscules or DSE. Our results show that the impacts of aboveground mammalian herbivory, soil nutrient availability and specific habitat conditions on belowground root fungal symbionts are highly dependent on each other. Arbuscule response to herbivory appeared to be regulated by specific habitat conditions possibly caused by differences in the AMF availability in the soil while DSE response was associated with availability of host-derived carbon. Our result of the relationship between

  16. Contrasting physiological plasticity in response to environmental stress within different cnidarians and their respective symbionts

    Science.gov (United States)

    Hoadley, Kenneth D.; Pettay, Daniel. T.; Dodge, Danielle; Warner, Mark E.

    2016-06-01

    Given concerns surrounding coral bleaching and ocean acidification, there is renewed interest in characterizing the physiological differences across the multiple host-algal symbiont combinations commonly found on coral reefs. Elevated temperature and CO2 were used to compare physiological responses within the scleractinian corals Montipora hirsuta ( Symbiodinium C15) and Pocillopora damicornis ( Symbiodinium D1), as well as the corallimorph (a non-calcifying anthozoan closely related to scleractinians) Discosoma nummiforme ( Symbiodinium C3). Several physiological proxies were affected more by temperature than CO2, including photochemistry, algal number and cellular chlorophyll a. Marked differences in symbiont number, chlorophyll and volume contributed to distinctive patterns of chlorophyll absorption among these animals. In contrast, carbon fixation either did not change or increased under elevated temperature. Also, the rate of photosynthetically fixed carbon translocated to each host did not change, and the percent of carbon translocated to the host increased in the corallimorph. Comparing all data revealed a significant negative correlation between photosynthetic rate and symbiont density that corroborates previous hypotheses about carbon limitation in these symbioses. The ratio of symbiont-normalized photosynthetic rate relative to the rate of symbiont-normalized carbon translocation (P:T) was compared in these organisms as well as the anemone, Exaiptasia pallida hosting Symbiodinium minutum, and revealed a P:T close to unity ( D. nummiforme) to a range of 2.0-4.5, with the lowest carbon translocation in the sea anemone. Major differences in the thermal responses across these organisms provide further evidence of a range of acclimation potential and physiological plasticity that highlights the need for continued study of these symbioses across a larger group of host taxa.

  17. Statistical identification of the confidence limits of open loop transfer functions obtained by MAR analysis

    International Nuclear Information System (INIS)

    Antonopoulos-Domis, M.; Mourtzanos, K.

    1996-01-01

    Estimators of the confidence limits of open loop transfer functions via Multivariate Auto-Regressive (MAR) modelling are not available in the literature. The statistics of open loop transfer functions obtained by MAR modelling are investigated via numerical experiments. A system of known open loop transfer functions is simulated digitally and excited by random number series. The digital signals of the simulated system are then MAR modelled and the open loop transfer functions are estimated. Performing a large number of realizations, mean values and variances of the open loop transfer functions are estimated. It is found that if the record length N of each realization is long enough then the estimates of open loop transfer functions follow normal distribution. The variance of the open loop transfer functions is proportional to 1/N. For MAR processes the asymptotic covariance matrix of the estimate of open loop transfer functions was found in agreement with theoretical prediction. (author)

  18. The PD-(D/EXK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto unknown function

    Directory of Open Access Journals (Sweden)

    Bujnicki Janusz M

    2005-07-01

    Full Text Available Abstract Background The PD-(D/EXK nuclease superfamily, initially identified in type II restriction endonucleases and later in many enzymes involved in DNA recombination and repair, is one of the most challenging targets for protein sequence analysis and structure prediction. Typically, the sequence similarity between these proteins is so low, that most of the relationships between known members of the PD-(D/EXK superfamily were identified only after the corresponding structures were determined experimentally. Thus, it is tempting to speculate that among the uncharacterized protein families, there are potential nucleases that remain to be discovered, but their identification requires more sensitive tools than traditional PSI-BLAST searches. Results The low degree of amino acid conservation hampers the possibility of identification of new members of the PD-(D/EXK superfamily based solely on sequence comparisons to known members. Therefore, we used a recently developed method HHsearch for sensitive detection of remote similarities between protein families represented as profile Hidden Markov Models enhanced by secondary structure. We carried out a comparison of known families of PD-(D/EXK nucleases to the database comprising the COG and PFAM profiles corresponding to both functionally characterized as well as uncharacterized protein families to detect significant similarities. The initial candidates for new nucleases were subsequently verified by sequence-structure threading, comparative modeling, and identification of potential active site residues. Conclusion In this article, we report identification of the PD-(D/EXK nuclease domain in numerous proteins implicated in interactions with DNA but with unknown structure and mechanism of action (such as putative recombinase RmuC, DNA competence factor CoiA, a DNA-binding protein SfsA, a large human protein predicted to be a DNA repair enzyme, predicted archaeal transcription regulators, and the head

  19. Identification of susceptible genes for complex chronic diseases based on disease risk functional SNPs and interaction networks.

    Science.gov (United States)

    Li, Wan; Zhu, Lina; Huang, Hao; He, Yuehan; Lv, Junjie; Li, Weimin; Chen, Lina; He, Weiming

    2017-10-01

    Complex chronic diseases are caused by the effects of genetic and environmental factors. Single nucleotide polymorphisms (SNPs), one common type of genetic variations, played vital roles in diseases. We hypothesized that disease risk functional SNPs in coding regions and protein interaction network modules were more likely to contribute to the identification of disease susceptible genes for complex chronic diseases. This could help to further reveal the pathogenesis of complex chronic diseases. Disease risk SNPs were first recognized from public SNP data for coronary heart disease (CHD), hypertension (HT) and type 2 diabetes (T2D). SNPs in coding regions that were classified into nonsense and missense by integrating several SNP functional annotation databases were treated as functional SNPs. Then, regions significantly associated with each disease were screened using random permutations for disease risk functional SNPs. Corresponding to these regions, 155, 169 and 173 potential disease susceptible genes were identified for CHD, HT and T2D, respectively. A disease-related gene product interaction network in environmental context was constructed for interacting gene products of both disease genes and potential disease susceptible genes for these diseases. After functional enrichment analysis for disease associated modules, 5 CHD susceptible genes, 7 HT susceptible genes and 3 T2D susceptible genes were finally identified, some of which had pleiotropic effects. Most of these genes were verified to be related to these diseases in literature. This was similar for disease genes identified from another method proposed by Lee et al. from a different aspect. This research could provide novel perspectives for diagnosis and treatment of complex chronic diseases and susceptible genes identification for other diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Identification of hidden failures in control systems: a functional modelling approach

    International Nuclear Information System (INIS)

    Jalashgar, A.; Modarres, M.

    1996-01-01

    This paper presents a model which encompasses knowledge about a process control system's functionalities in a function-oriented failure analysis task. The technique called Hybrid MFM-GTST, mainly utilizes two different function - oriented methods (MFM and GTST) to identify all functions of the system components, and hence possible sources of hidden failures in process control systems. Hidden failures are referred to incipient failures within the system that in long term may lead to loss of major functions. The features of the method are described and demonstrated by using an example of a process control system

  1. Inverse material identification in coupled acoustic-structure interaction using a modified error in constitutive equation functional

    Science.gov (United States)

    Warner, James E.; Diaz, Manuel I.; Aquino, Wilkins; Bonnet, Marc

    2014-09-01

    This work focuses on the identification of heterogeneous linear elastic moduli in the context of frequency-domain, coupled acoustic-structure interaction (ASI), using either solid displacement or fluid pressure measurement data. The approach postulates the inverse problem as an optimization problem where the solution is obtained by minimizing a modified error in constitutive equation (MECE) functional. The latter measures the discrepancy in the constitutive equations that connect kinematically admissible strains and dynamically admissible stresses, while incorporating the measurement data as additional quadratic error terms. We demonstrate two strategies for selecting the MECE weighting coefficient to produce regularized solutions to the ill-posed identification problem: 1) the discrepancy principle of Morozov, and 2) an error-balance approach that selects the weight parameter as the minimizer of another functional involving the ECE and the data misfit. Numerical results demonstrate that the proposed methodology can successfully recover elastic parameters in 2D and 3D ASI systems from response measurements taken in either the solid or fluid subdomains. Furthermore, both regularization strategies are shown to produce accurate reconstructions when the measurement data is polluted with noise. The discrepancy principle is shown to produce nearly optimal solutions, while the error-balance approach, although not optimal, remains effective and does not need a priori information on the noise level.

  2. Experimental evaluation of the parameter-based closed-loop transfer function identification for electro-hydraulic servo systems

    Directory of Open Access Journals (Sweden)

    Guang-Da Liu

    2016-12-01

    Full Text Available Closed-loop systems of an electro-hydraulic servo system including position, acceleration, and force closed-loop systems and their closed-loop transfer functions based on parameter model are adaptive identified using a recursive extended least-squares algorithm. The position and force closed-loop tracking controllers are designed by a proportional–integral–derivative controller and are tuned by the position and force step signals. The acceleration closed-loop tracking controller is designed by a three-variable controller and the three states include position, velocity, and acceleration. Experimental results of the estimated position, acceleration, and force closed-loop transfer functions are performed on an actual electro-hydraulic servo system using xPC rapid prototyping technology, which clearly demonstrate the benefit of the adaptive identification method.

  3. PhaR, a Negative Regulator of PhaP, Modulates the Colonization of a Burkholderia Gut Symbiont in the Midgut of the Host Insect, Riptortus pedestris.

    Science.gov (United States)

    Jang, Seong Han; Jang, Ho Am; Lee, Junbeom; Kim, Jong Uk; Lee, Seung Ah; Park, Kyoung-Eun; Kim, Byung Hyun; Jo, Yong Hun; Lee, Bok Luel

    2017-06-01

    Five genes encoding PhaP family proteins and one phaR gene have been identified in the genome of Burkholderia symbiont strain RPE75. PhaP proteins function as the surface proteins of polyhydroxyalkanoate (PHA) granules, and the PhaR protein acts as a negative regulator of PhaP biosynthesis. Recently, we characterized one phaP gene to understand the molecular cross talk between Riptortus insects and Burkholderia gut symbionts. In this study, we constructed four other phaP gene-depleted mutants (Δ phaP1 , Δ phaP2 , Δ phaP3 , and Δ phaP4 mutants), one phaR gene-depleted mutant, and a phaR -complemented mutant (Δ phaR/phaR mutant). To address the biological roles of four phaP family genes and the phaR gene during insect-gut symbiont interaction, these Burkholderia mutants were fed to the second-instar nymphs, and colonization ability and fitness parameters were examined. In vitro , the Δ phaP3 and Δ phaR mutants cannot make a PHA granule normally in a stressful environment. Furthermore, the Δ phaR mutation decreased the colonization ability in the host midgut and negatively affected the host insect's fitness compared with wild-type Burkholderia -infected insects. However, other phaP family gene-depleted mutants colonized well in the midgut of the fifth-instar nymph insects. However, in the case of females, the colonization rate of the Δ phaP3 mutant was decreased and the host's fitness parameters were decreased compared with the wild-type-infected host, suggesting that the environment of the female midgut may be more hostile than that of the male midgut. These results demonstrate that PhaR plays an important role in the biosynthesis of PHA granules and that it is significantly related to the colonization of the Burkholderia gut symbiont in the host insects' midgut. IMPORTANCE Bacterial polyhydroxyalkanoate (PHA) biosynthesis is a complex process requiring several enzymes. The biological roles of PHA granule synthesis enzymes and the surface proteins of PHA

  4. Identification of International Classification of Functioning, Disability and Health categories for patients with peripheral arterial disease.

    Science.gov (United States)

    Vyskocil, Erich; Gruther, Wolfgang; Steiner, Irene; Schuhfried, Othmar

    2014-07-01

    Disease-specific categories of the International Classification of Functioning, Disability and Health have not yet been described for patients with chronic peripheral arterial obstructive disease (PAD). The authors examined the relationship between the categories of the Brief Core Sets for ischemic heart diseases with the Peripheral Artery Questionnaire and the ankle-brachial index to determine which International Classification of Functioning, Disability and Health categories are most relevant for patients with PAD. This is a retrospective cohort study including 77 patients with verified PAD. Statistical analyses of the relationship between International Classification of Functioning, Disability and Health categories as independent variables and the endpoints Peripheral Artery Questionnaire or ankle-brachial index were carried out by simple and stepwise linear regression models adjusting for age, sex, and leg (left vs. right). The stepwise linear regression model with the ankle-brachial index as dependent variable revealed a significant effect of the variables blood vessel functions and muscle endurance functions. Calculating a stepwise linear regression model with the Peripheral Artery Questionnaire as dependent variable, a significant effect of age, emotional functions, energy and drive functions, carrying out daily routine, as well as walking could be observed. This study identifies International Classification of Functioning, Disability and Health categories in the Brief Core Sets for ischemic heart diseases that show a significant effect on the ankle-brachial index and the Peripheral Artery Questionnaire score in patients with PAD. These categories provide fundamental information on functioning of patients with PAD and patient-centered outcomes for rehabilitation interventions.

  5. Identification of optimal soil hydraulic functions and parameters for predicting soil moisture

    Science.gov (United States)

    We examined the accuracy of several commonly used soil hydraulic functions and associated parameters for predicting observed soil moisture data. We used six combined methods formed by three commonly used soil hydraulic functions – i.e., Brooks and Corey (1964) (BC), Campbell (19...

  6. Seismic margin reviews of nuclear power plants: Identification of important functions and systems

    International Nuclear Information System (INIS)

    Prassinos, P.G.; Moore, D.L.; Amico, P.J.

    1987-01-01

    The results from the review of the seven utility-sponsored seismic PRAs plus the Zion SSMRP have been used to develop some insights regarding the importance of various systems and functions to seismic margins. By taking this information and combining it with the fragility insights we can develop some functional/systemic screening guideline for margin studies. This screening approach will greatly reduce the scope of the analysis. It is possible only to come to conclusions regarding the importance of plant systems and safety functions for PWRs, for which six plants were studied. For PWRs, it is possible to categorize plant safety functions as belonging to one of two groups, one of which is important to the assessment of seismic margins and one of which is not. The important functional group involves only two functions that must be considered for estimating seismic margin. These two functions are shutting down the nuclear reaction and providing cooling to the reactor core in the time period immediately following the seismic event (that is, the injection phase or pre-residual heat removal time period). It is possible to reasonably estimate the seismic margin of the plant by performing a study only involving the analysis of the plant systems and structure which are required in order to perform the two functions. Such analysis must include an assessment of a complete set of seismic initiating events. (orig./HP)

  7. Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data

    Directory of Open Access Journals (Sweden)

    Li Min

    2012-05-01

    Full Text Available Abstract Background Identification of protein complexes and functional modules from protein-protein interaction (PPI networks is crucial to understanding the principles of cellular organization and predicting protein functions. In the past few years, many computational methods have been proposed. However, most of them considered the PPI networks as static graphs and overlooked the dynamics inherent within these networks. Moreover, few of them can distinguish between protein complexes and functional modules. Results In this paper, a new framework is proposed to distinguish between protein complexes and functional modules by integrating gene expression data into protein-protein interaction (PPI data. A series of time-sequenced subnetworks (TSNs is constructed according to the time that the interactions were activated. The algorithm TSN-PCD was then developed to identify protein complexes from these TSNs. As protein complexes are significantly related to functional modules, a new algorithm DFM-CIN is proposed to discover functional modules based on the identified complexes. The experimental results show that the combination of temporal gene expression data with PPI data contributes to identifying protein complexes more precisely. A quantitative comparison based on f-measure reveals that our algorithm TSN-PCD outperforms the other previous protein complex discovery algorithms. Furthermore, we evaluate the identified functional modules by using “Biological Process” annotated in GO (Gene Ontology. The validation shows that the identified functional modules are statistically significant in terms of “Biological Process”. More importantly, the relationship between protein complexes and functional modules are studied. Conclusions The proposed framework based on the integration of PPI data and gene expression data makes it possible to identify protein complexes and functional modules more effectively. Moveover, the proposed new framework and

  8. The Dictyostelium discoideum cellulose synthase: Structure/function analysis and identification of interacting proteins

    Energy Technology Data Exchange (ETDEWEB)

    Richard L. Blanton

    2004-02-19

    OAK-B135 The major accomplishments of this project were: (1) the initial characterization of dcsA, the gene for the putative catalytic subunit of cellulose synthase in the cellular slime mold Dictyostelium discoideum; (2) the detection of a developmentally regulated event (unidentified, but perhaps a protein modification or association with a protein partner) that is required for cellulose synthase activity (i.e., the dcsA product is necessary, but not sufficient for cellulose synthesis); (3) the continued exploration of the developmental context of cellulose synthesis and DcsA; (4) the isolation of a GFP-DcsA-expressing strain (work in progress); and (5) the identification of Dictyostelium homologues for plant genes whose products play roles in cellulose biosynthesis. Although our progress was slow and many of our results negative, we did develop a number of promising avenues of investigation that can serve as the foundation for future projects.

  9. A novel fiber-optical vibration defending system with on-line intelligent identification function

    Science.gov (United States)

    Wu, Huijuan; Xie, Xin; Li, Hanyu; Li, Xiaoyu; Wu, Yu; Gong, Yuan; Rao, Yunjiang

    2013-09-01

    Capacity of the sensor network is always a bottleneck problem for the novel FBG-based quasi-distributed fiberoptical defending system. In this paper, a highly sensitive sensing network with FBG vibration sensors is presented to relieve stress of the capacity and the system cost. However, higher sensitivity may cause higher Nuisance Alarm Rates (NARs) in practical uses. It is necessary to further classify the intrusion pattern or threat level and determine the validity of an unexpected event. Then an intelligent identification method is proposed by extracting the statistical features of the vibration signals in the time domain, and inputting them into a 3-layer Back-Propagation(BP) Artificial Neural Network to classify the events of interest. Experiments of both simulation and field tests are carried out to validate its effectiveness. The results show the recognition rate can be achieved up to 100% for the simulation signals and as high as 96.03% in the real tests.

  10. Chemical identification and functional analysis of apocarotenoids involved in the development of arbuscular mycorrhizal symbiosis.

    Science.gov (United States)

    Akiyama, Kohki

    2007-06-01

    Arbuscular mycorrhizae formed between more than 80% of land plants and arbuscular mycorrhizal (AM) fungi represent the most widespread symbiosis on the earth. AM fungi facilitate the uptake of soil nutrients, especially phosphate, by plants, and in return obtain carbohydrates from hosts. Apocarotenoids, oxidative cleavage products of carotenoids, have been found to play a critical role in the establishment of AM symbiosis. Strigolactones previously isolated as seed-germination stimulants for root parasitic weeds act as a chemical signal for AM fungi during presymbiotic stages. Stimulation of carotenoid metabolism, leading to massive accumulation of mycorradicin and cyclohexenone derivatives, occurs during root colonization by AM fungi. This review highlights research into the chemical identification of arbuscular mycorrhiza-related apocarotenoids and their role in the regulation and establishment of AM symbiosis conducted in the past 10 years.

  11. Identification of Functions Affecting Predator-Prey Interactions between Myxococcus xanthus and Bacillus subtilis.

    Science.gov (United States)

    Müller, Susanne; Strack, Sarah N; Ryan, Sarah E; Shawgo, Mary; Walling, Abigail; Harris, Susanna; Chambers, Chris; Boddicker, Jennifer; Kirby, John R

    2016-12-15

    Soil bacteria engage each other in competitive and cooperative ways to determine their microenvironments. In this study, we report the identification of a large number of genes required for Myxococcus xanthus to engage Bacillus subtilis in a predator-prey relationship. We generated and tested over 6,000 individual transposon insertion mutants of M. xanthus and found many new factors required to promote efficient predation, including the specialized metabolite myxoprincomide, an ATP-binding cassette (ABC) transporter permease, and a clustered regularly interspaced short palindromic repeat (CRISPR) locus encoding bacterial immunity. We also identified genes known to be involved in predation, including those required for the production of exopolysaccharides and type IV pilus (T4P)-dependent motility, as well as chemosensory and two-component systems. Furthermore, deletion of these genes confirmed their role during predation. Overall, M. xanthus predation appears to be a multifactorial process, with multiple determinants enhancing predation capacity. Soil bacteria engage each other in complex environments and utilize multiple traits to ensure survival. Here, we report the identification of multiple traits that enable a common soil organism, Myxococcus xanthus, to prey upon and utilize nutrients from another common soil organism, Bacillus subtilis We mutagenized the predator and carried out a screen to identify genes that were required to either enhance or diminish capacity to consume prey. We identified dozens of genes encoding factors that contribute to the overall repertoire for the predator to successfully engage its prey in the natural environment. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  12. Development of functional markers associated with phenotypic characteristics for identification of soy variety

    International Nuclear Information System (INIS)

    Ibarra, M.; Castro, A; Capdevielle, F.

    2013-01-01

    The organization of agricultural systems requires the verification of the genetic identity and purity of cultivars. The increase in the number of soy varieties to be evaluated, and the narrow genetic base of soybean cultivars, make the identification using phenotypic descriptors very difficult. The International Union for the Protection of New Varieties of Plants (UPOV) has recognized the utility of molecular markers associated with descriptive phenotypic characteristics. With the goal of developing this kind of markers, six genic or genomic S SR were selected in silico (Sat286, Satt229, GmPrx1, GMES1173, Satt571 and Gm Hi), plus two previously reported markers (GmF35H and SoyF3H). All were evaluated in 35 soybean cultivars. The SSRs GmPrx1 and Gm Hi selected for seed coat peroxidase and hilum color respectively were monomorphic. The mean Polymorphism Information Content (PI C) value within the selected group of polymorphic markers was 0.48 with an average of 3.12 allele per locus. GmF35H discriminated the soybean varieties according to the flower color (white and purple). Discrimination tests showed a high percentage of accurate classification of growth habit (95.8%) and pubescence color (80.6%) with Sat286 and Soy F3H, respectively. The classification values for pod color (74.2%) and leaflet size (73.5%) were intermediate using GMES1173 and Satt571, respectively. The marker Satt229 was not discriminating for flowering time (50%) and maturity (42.8%). Molecular markers selected in or close to sequences of interest can be integrated into a genetic identification system as complementary markers to the classic phenotypic descriptors of soybean varieties

  13. Identification of interphase functions for the NIMA kinase involving microtubules and the ESCRT pathway.

    Directory of Open Access Journals (Sweden)

    Meera Govindaraghavan

    2014-03-01

    Full Text Available The Never in Mitosis A (NIMA kinase (the founding member of the Nek family of kinases has been considered a mitotic specific kinase with nuclear restricted roles in the model fungus Aspergillus nidulans. By extending to A. nidulans the results of a synthetic lethal screen performed in Saccharomyces cerevisiae using the NIMA ortholog KIN3, we identified a conserved genetic interaction between nimA and genes encoding proteins of the Endosomal Sorting Complex Required for Transport (ESCRT pathway. Absence of ESCRT pathway functions in combination with partial NIMA function causes enhanced cell growth defects, including an inability to maintain a single polarized dominant cell tip. These genetic insights suggest NIMA potentially has interphase functions in addition to its established mitotic functions at nuclei. We therefore generated endogenously GFP-tagged NIMA (NIMA-GFP which was fully functional to follow its interphase locations using live cell spinning disc 4D confocal microscopy. During interphase some NIMA-GFP locates to the tips of rapidly growing cells and, when expressed ectopically, also locates to the tips of cytoplasmic microtubules, suggestive of non-nuclear interphase functions. In support of this, perturbation of NIMA function either by ectopic overexpression or through partial inactivation results in marked cell tip growth defects with excess NIMA-GFP promoting multiple growing cell tips. Ectopic NIMA-GFP was found to locate to the plus ends of microtubules in an EB1 dependent manner, while impairing NIMA function altered the dynamic localization of EB1 and the cytoplasmic microtubule network. Together, our genetic and cell biological analyses reveal novel non-nuclear interphase functions for NIMA involving microtubules and the ESCRT pathway for normal polarized fungal cell tip growth. These insights extend the roles of NIMA both spatially and temporally and indicate that this conserved protein kinase could help integrate cell

  14. Functionality of road safety devices – identification and analysis of factors

    Directory of Open Access Journals (Sweden)

    Jeliński Łukasz

    2017-01-01

    Full Text Available Road safety devices are designed to protect road users from the risk of injury or death. The principal type of restraint is the safety barrier. Deployed on sites with the highest risk of run-off-road accidents, safety barriers are mostly found on bridges, flyovers, central reservations, and on road edges which have fixed obstacles next to them. If properly designed and installed, safety barriers just as other road safety devices, should meet a number of functional features. This report analyses factors which may deteriorate functionality, ways to prevent this from happening and the thresholds for loss of road safety device functionality.

  15. BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors.

    Science.gov (United States)

    Dong, Xiaobao; Lu, Xiaotian; Zhang, Ziding

    2015-01-01

    Gram-negative pathogenic bacteria inject type III secreted effectors (T3SEs) into host cells to sabotage their immune signaling networks. Because T3SEs constitute a meeting-point of pathogen virulence and host defense, they are of keen interest to host-pathogen interaction research community. To accelerate the identification and functional understanding of T3SEs, we present BEAN 2.0 as an integrated web resource to predict, analyse and store T3SEs. BEAN 2.0 includes three major components. First, it provides an accurate T3SE predictor based on a hybrid approach. Using independent testing data, we show that BEAN 2.0 achieves a sensitivity of 86.05% and a specificity of 100%. Second, it integrates a set of online sequence analysis tools. Users can further perform functional analysis of putative T3SEs in a seamless way, such as subcellular location prediction, functional domain scan and disorder region annotation. Third, it compiles a database covering 1215 experimentally verified T3SEs and constructs two T3SE-related networks that can be used to explore the relationships among T3SEs. Taken together, by presenting a one-stop T3SE bioinformatics resource, we hope BEAN 2.0 can promote comprehensive understanding of the function and evolution of T3SEs. © The Author(s) 2015. Published by Oxford University Press.

  16. Functionality of veterinary identification microchips following low- (0.5 tesla) and high-field (3 tesla) magnetic resonance imaging.

    Science.gov (United States)

    Piesnack, Susann; Frame, Mairi E; Oechtering, Gerhard; Ludewig, Eberhard

    2013-01-01

    The ability to read patient identification microchips relies on the use of radiofrequency pulses. Since radiofrequency pulses also form an integral part of the magnetic resonance imaging (MRI) process, the possibility of loss of microchip function during MRI scanning is of concern. Previous clinical trials have shown microchip function to be unaffected by MR imaging using a field strength of 1 Tesla and 1.5. As veterinary MRI scanners range widely in field strength, this study was devised to determine whether exposure to lower or higher field strengths than 1 Tesla would affect the function of different types of microchip. In a phantom study, a total of 300 International Standards Organisation (ISO)-approved microchips (100 each of three different types: ISO FDX-B 1.4 × 9 mm, ISO FDX-B 2.12 × 12 mm, ISO HDX 3.8 × 23 mm) were tested in a low field (0.5) and a high field scanner (3.0 Tesla). A total of 50 microchips of each type were tested in each scanner. The phantom was composed of a fluid-filled freezer pack onto which a plastic pillow and a cardboard strip with affixed microchips were positioned. Following an MRI scan protocol simulating a head study, all of the microchips were accurately readable. Neither 0.5 nor 3 Tesla imaging affected microchip function in this study. © 2013 Veterinary Radiology & Ultrasound.

  17. Structural and resting state functional connectivity of the subthalamic nucleus: identification of motor STN parts and the hyperdirect pathway.

    Directory of Open Access Journals (Sweden)

    Ellen J L Brunenberg

    Full Text Available Deep brain stimulation (DBS for Parkinson's disease often alleviates the motor symptoms, but causes cognitive and emotional side effects in a substantial number of cases. Identification of the motor part of the subthalamic nucleus (STN as part of the presurgical workup could minimize these adverse effects. In this study, we assessed the STN's connectivity to motor, associative, and limbic brain areas, based on structural and functional connectivity analysis of volunteer data. For the structural connectivity, we used streamline counts derived from HARDI fiber tracking. The resulting tracks supported the existence of the so-called "hyperdirect" pathway in humans. Furthermore, we determined the connectivity of each STN voxel with the motor cortical areas. Functional connectivity was calculated based on functional MRI, as the correlation of the signal within a given brain voxel with the signal in the STN. Also, the signal per STN voxel was explained in terms of the correlation with motor or limbic brain seed ROI areas. Both right and left STN ROIs appeared to be structurally and functionally connected to brain areas that are part of the motor, associative, and limbic circuit. Furthermore, this study enabled us to assess the level of segregation of the STN motor part, which is relevant for the planning of STN DBS procedures.

  18. IDENTIFICATION AND ASSESSMENT OF THE AIRCRAFT FUNCTIONAL SYSTEMS IN THE FLIGHT SAFETY MANAGEMENT SYSTEMS

    Directory of Open Access Journals (Sweden)

    I. D. Dashkov

    2014-01-01

    Full Text Available The article discusses issues related to determining the technical states of aircraft functional systems (FS. Mathematical formulas are given for expressing the relationship between the main parameters characterizing the model.

  19. Identification of the Types Properties and Functional Characteristics of Telomerase Expressing Cells in Breast Cancer

    National Research Council Canada - National Science Library

    Hines, William

    2003-01-01

    ... biochemical and functional properties may be characterized. Through examining the role of telomerase in cancer, this project also fosters the education of the candidate through the interaction with several experts in breast cancer pathology, epidemiology, bio...

  20. Identification of the Types, Properties, and Functional Characteristics of Telomerase Expressing Cells in Breast Cancer

    National Research Council Canada - National Science Library

    Hines, William C; Griffith, Jeffrey K

    2005-01-01

    ... biochemical and functional properties may be characterized. Through examining the role of telomerase in cancer, this project also fosters the education of the candidate through the interaction with several experts in breast cancer pathology, epidemiology, bio...

  1. Case study of the identification, assessment and early intervention of executive function deficits

    OpenAIRE

    Vakil, Lynn A. Ciccantelli and Shernavaz

    2011-01-01

    Educators recognize the need to identify young children who may require intervention because the sooner intervention is initiated, the greater the possibility for remediating a problem. It is imperative that teachers be provided with timely and sufficient information about their students in order to begin to help child become successful learners. Executive functions play a fundamental role in a child's cognitive and social-emotional/behavioral functioning; hence the importance of early...

  2. Case study of the identification, assessment and early intervention of executive function deficits

    OpenAIRE

    Vakil, Lynn A. Ciccantelli and Shernavaz; Vakil, Shernavaz

    2014-01-01

    Educators recognize the need to identify young children who may require intervention because the sooner intervention is initiated, the greater the possibility for remediating a problem. It is imperative that teachers be provided with timely and sufficient information about their students in order to begin to help child become successful learners. Executive functions play a fundamental role in a child's cognitive and social-emotional/behavioral functioning; hence the importance of e...

  3. Ontogenetic Changes in the Bacterial Symbiont Community of the Tropical Demosponge Amphimedon queenslandica: Metamorphosis Is a New Beginning

    OpenAIRE

    Fieth, Rebecca A.; Gauthier, Marie-Emilie A.; Bayes, Joanne; Green, Kathryn M.; Degnan, Sandie M.

    2016-01-01

    Vertical transmission of bacterial symbionts, which is known in many species of sponge (Porifera), is expected to promote strong fidelity between the partners. Combining 16S rRNA gene amplicon sequencing and electron microscopy, we have assayed the relative abundance of vertically-inherited bacterial symbionts in several stages of the life cycle of Amphimedon queenslandica, a tropical coral reef sponge. We reveal that adult A. queenslandica house a low diversity microbiome dominated by just t...

  4. Transcriptomic immune response of the cotton stainer Dysdercus fasciatus to experimental elimination of vitamin-supplementing intestinal symbionts.

    Directory of Open Access Journals (Sweden)

    Eugen Bauer

    Full Text Available The acquisition and vertical transmission of bacterial symbionts plays an important role in insect evolution and ecology. However, the molecular mechanisms underlying the stable maintenance and control of mutualistic bacteria remain poorly understood. The cotton stainer Dysdercus fasciatus harbours the actinobacterial symbionts Coriobacterium glomerans and Gordonibacter sp. in its midgut. The symbionts supplement limiting B vitamins and thereby significantly contribute to the host's fitness. In this study, we experimentally disrupted the symbionts' vertical transmission route and performed comparative transcriptomic analyses of genes expressed in the gut of aposymbiotic (symbiont-free and control individuals to study the host immune response in presence and absence of the mutualists. Annotation of assembled cDNA reads identified a considerable number of genes involved in the innate immune system, including different protein isoforms of several immune effector proteins (specifically i-type lysozyme, defensin, hemiptericin, and pyrrhocoricin, suggesting the possibility for a highly differentiated response towards the complex resident microbial community. Gene expression analyses revealed a constitutive expression of transcripts involved in signal transduction of the main insect immune pathways, but differential expression of certain antimicrobial peptide genes. Specifically, qPCRs confirmed the significant down-regulation of c-type lysozyme and up-regulation of hemiptericin in aposymbiotic individuals. The high expression of c-type lysozyme in symbiont-containing bugs may serve to lyse symbiont cells and thereby harvest B-vitamins that are necessary for subsistence on the deficient diet of Malvales seeds. Our findings suggest a sophisticated host response to perturbation of the symbiotic gut microbiota, indicating that the innate immune system not only plays an important role in combating pathogens, but also serves as a communication interface

  5. Identification of small molecules that disrupt vacuolar function in the pathogen Candida albicans.

    Directory of Open Access Journals (Sweden)

    Helene Tournu

    Full Text Available The fungal vacuole is a large acidified organelle that performs a variety of cellular functions. At least a sub-set of these functions are crucial for pathogenic species of fungi, such as Candida albicans, to survive within and invade mammalian tissue as mutants with severe defects in vacuolar biogenesis are avirulent. We therefore sought to identify chemical probes that disrupt the normal function and/or integrity of the fungal vacuole to provide tools for the functional analysis of this organelle as well as potential experimental therapeutics. A convenient indicator of vacuolar integrity based upon the intracellular accumulation of an endogenously produced pigment was adapted to identify Vacuole Disrupting chemical Agents (VDAs. Several chemical libraries were screened and a set of 29 compounds demonstrated to reproducibly cause loss of pigmentation, including 9 azole antifungals, a statin and 3 NSAIDs. Quantitative analysis of vacuolar morphology revealed that (excluding the azoles a sub-set of 14 VDAs significantly alter vacuolar number, size and/or shape. Many C. albicans mutants with impaired vacuolar function are deficient in the formation of hyphal elements, a process essential for its pathogenicity. Accordingly, all 14 VDAs negatively impact C. albicans hyphal morphogenesis. Fungal selectivity was observed for approximately half of the VDA compounds identified, since they did not alter the morphology of the equivalent mammalian organelle, the lysosome. Collectively, these compounds comprise of a new collection of chemical probes that directly or indirectly perturb normal vacuolar function in C. albicans.

  6. Identification of subject specific and functional consistent ROIs using semi-supervised learning

    Science.gov (United States)

    Du, Yuhui; Li, Hongming; Wu, Hong; Fan, Yong

    2012-02-01

    Regions of interests (ROIs) for defining nodes of brain network are of great importance in brain network analysis of fMRI data. The ROIs are typically identified using prior anatomical information, seed region based correlation analysis, clustering analysis, region growing or ICA based methods. In this paper, we propose a novel method to identify subject specific and functional consistent ROIs for brain network analysis using semi-supervised learning. Specifically, a graph theory based semi-supervised learning method is adopted to optimize ROIs defined using prior knowledge with a constraint of local and global functional consistency, yielding subject specific ROIs with enhanced functional connectivity. Experiments using simulated fMRI data have demonstrated that functional consistent ROIs can be identified effectively from data with different signal to noise ratios (SNRs). Experiments using resting state fMRI data of 25 normal subjects for identifying ROIs of the default mode network have demonstrated that the proposed method is capable of identifying subject specific ROIs with stronger functional connectivity and higher consistency across subjects than existing alternative techniques, indicating that the proposed method can better identify brain network ROIs with intrinsic functional connectivity.

  7. Identification of Success Criteria for Automated Function Using Feed and Bleed Operation

    International Nuclear Information System (INIS)

    Kim, Bo Gyung; Kim, Sang Ho; Kang, Hyun Gook; Yoon, Ho Joon

    2013-01-01

    Since NPP has lots of functions and systems, operated procedure is much complicated and the chance of human error to operate the safety systems is quite high. In the case of large break loss of coolant accident (LBLOCA) and station black out (SBO), the dependency of operator is very low. However, when many mitigation systems are still available, operators have several choices to mitigate the accident and the human error can be increased more. To reduce the operator's workload and perform the operation accurate after the accident, automated function for safe cooldown based on the feed and bleed (F and B) operation was suggested. The automated function can predict whether the plant will be safe after the automated function is initiated, and perform the safety functions automatically. To expect the success of cooldown, success criteria should be identified. To perform the operation accurately after the accident, the automated function for safe cooldown based on the F and B operation is suggested. To expect the success of cooldown, sequence of RCS situation when heat removal by secondary system fails is identified. Based on the sequence of RCS situation, four levels of necessity of F and B operation are classified. To obtain the boundary of levels, the TH analysis will be performed

  8. Identification and Functional Characterization of Genes Encoding Omega-3 Polyunsaturated Fatty Acid Biosynthetic Activities from Unicellular Microalgae

    Directory of Open Access Journals (Sweden)

    Royah Vaezi

    2013-12-01

    Full Text Available In order to identify novel genes encoding enzymes involved in the biosynthesis of nutritionally important omega-3 long chain polyunsaturated fatty acids, a database search was carried out in the genomes of the unicellular photoautotrophic green alga Ostreococcus RCC809 and cold-water diatom Fragilariopsis cylindrus. The search led to the identification of two putative “front-end” desaturases (Δ6 and Δ4 from Ostreococcus RCC809 and one Δ6-elongase from F. cylindrus. Heterologous expression of putative open reading frames (ORFs in yeast revealed that the encoded enzyme activities efficiently convert their respective substrates: 54.1% conversion of α-linolenic acid for Δ6-desaturase, 15.1% conversion of 22:5n-3 for Δ4-desaturase and 38.1% conversion of γ-linolenic acid for Δ6-elongase. The Δ6-desaturase from Ostreococcus RCC809 displays a very strong substrate preference resulting in the predominant synthesis of stearidonic acid (C18:4Δ6,9,12,15. These data confirm the functional characterization of omega-3 long chain polyunsaturated fatty acid biosynthetic genes from these two species which have until now not been investigated for such activities. The identification of these new genes will also serve to expand the repertoire of activities available for metabolically engineering the omega-3 trait in heterologous hosts as well as providing better insights into the synthesis of eicosapentaenoic acid (EPA and docosahexaenoic acid (DHA in marine microalgae.

  9. Examining the effectiveness of discriminant function analysis and cluster analysis in species identification of male field crickets based on their calling songs.

    Science.gov (United States)

    Jaiswara, Ranjana; Nandi, Diptarup; Balakrishnan, Rohini

    2013-01-01

    Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA) and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6-7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species classification and

  10. Examining the effectiveness of discriminant function analysis and cluster analysis in species identification of male field crickets based on their calling songs.

    Directory of Open Access Journals (Sweden)

    Ranjana Jaiswara

    Full Text Available Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6-7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species

  11. Pattern classification of large-scale functional brain networks: identification of informative neuroimaging markers for epilepsy.

    Directory of Open Access Journals (Sweden)

    Jie Zhang

    Full Text Available The accurate prediction of general neuropsychiatric disorders, on an individual basis, using resting-state functional magnetic resonance imaging (fMRI is a challenging task of great clinical significance. Despite the progress to chart the differences between the healthy controls and patients at the group level, the pattern classification of functional brain networks across individuals is still less developed. In this paper we identify two novel neuroimaging measures that prove to be strongly predictive neuroimaging markers in pattern classification between healthy controls and general epileptic patients. These measures characterize two important aspects of the functional brain network in a quantitative manner: (i coordinated operation among spatially distributed brain regions, and (ii the asymmetry of bilaterally homologous brain regions, in terms of their global patterns of functional connectivity. This second measure offers a unique understanding of brain asymmetry at the network level, and, to the best of our knowledge, has not been previously used in pattern classification of functional brain networks. Using modern pattern-recognition approaches like sparse regression and support vector machine, we have achieved a cross-validated classification accuracy of 83.9% (specificity: 82.5%; sensitivity: 85% across individuals from a large dataset consisting of 180 healthy controls and epileptic patients. We identified significantly changed functional pathways and subnetworks in epileptic patients that underlie the pathophysiological mechanism of the impaired cognitive functions. Specifically, we find that the asymmetry of brain operation for epileptic patients is markedly enhanced in temporal lobe and limbic system, in comparison with healthy individuals. The present study indicates that with specifically designed informative neuroimaging markers, resting-state fMRI can serve as a most promising tool for clinical diagnosis, and also shed light onto

  12. Pattern classification of large-scale functional brain networks: identification of informative neuroimaging markers for epilepsy.

    Science.gov (United States)

    Zhang, Jie; Cheng, Wei; Wang, ZhengGe; Zhang, ZhiQiang; Lu, WenLian; Lu, GuangMing; Feng, Jianfeng

    2012-01-01

    The accurate prediction of general neuropsychiatric disorders, on an individual basis, using resting-state functional magnetic resonance imaging (fMRI) is a challenging task of great clinical significance. Despite the progress to chart the differences between the healthy controls and patients at the group level, the pattern classification of functional brain networks across individuals is still less developed. In this paper we identify two novel neuroimaging measures that prove to be strongly predictive neuroimaging markers in pattern classification between healthy controls and general epileptic patients. These measures characterize two important aspects of the functional brain network in a quantitative manner: (i) coordinated operation among spatially distributed brain regions, and (ii) the asymmetry of bilaterally homologous brain regions, in terms of their global patterns of functional connectivity. This second measure offers a unique understanding of brain asymmetry at the network level, and, to the best of our knowledge, has not been previously used in pattern classification of functional brain networks. Using modern pattern-recognition approaches like sparse regression and support vector machine, we have achieved a cross-validated classification accuracy of 83.9% (specificity: 82.5%; sensitivity: 85%) across individuals from a large dataset consisting of 180 healthy controls and epileptic patients. We identified significantly changed functional pathways and subnetworks in epileptic patients that underlie the pathophysiological mechanism of the impaired cognitive functions. Specifically, we find that the asymmetry of brain operation for epileptic patients is markedly enhanced in temporal lobe and limbic system, in comparison with healthy individuals. The present study indicates that with specifically designed informative neuroimaging markers, resting-state fMRI can serve as a most promising tool for clinical diagnosis, and also shed light onto the physiology

  13. Location of Symbionts in the Whitefly Bemisia tabaci Affects Their Densities during Host Development and Environmental Stress

    Science.gov (United States)

    Su, Qi; Xie, Wen; Wang, Shaoli; Wu, Qingjun; Ghanim, Murad; Zhang, Youjun

    2014-01-01

    Bacterial symbionts often enhance the physiological capabilities of their arthropod hosts and enable their hosts to expand into formerly unavailable niches, thus leading to biological diversification. Many arthropods, including the worldwide invasive whitefly Bemisia tabaci, have individuals simultaneously infected with symbionts of multiple genera that occur in different locations in the host. This study examined the population dynamics of symbionts that are located in different areas within B. tabaci. While densities of Portiera and Hamiltonella (which are located in bacteriocytes) appeared to be well-regulated during host development, densities of Rickettsia (which are not located in bacteriocytes) were highly variable among individual hosts during host development. Host mating did not significantly affect symbiont densities. Infection by Tomato yellow leaf curl virus did not affect Portiera and Hamiltonella densities in either sex, but increased Rickettsia densities in females. High and low temperatures did not affect Portiera and Hamiltonella densities, but low temperature (15°C) significantly suppressed Rickettsia densities whereas high temperature (35°C) had little effect on Rickettsia densities. The results are consistent with the view that the population dynamics of bacterial symbionts in B. tabaci are regulated by symbiont location within the host and that the regulation reflects adaptation between the bacteria and insect. PMID:24632746

  14. Identification of functional candidates amongst hypothetical proteins of Treponema pallidum ssp. pallidum.

    Science.gov (United States)

    Naqvi, Ahmad Abu Turab; Shahbaaz, Mohd; Ahmad, Faizan; Hassan, Md Imtaiyaz

    2015-01-01

    Syphilis is a globally occurring venereal disease, and its infection is propagated through sexual contact. The causative agent of syphilis, Treponema pallidum ssp. pallidum, a Gram-negative sphirochaete, is an obligate human parasite. Genome of T. pallidum ssp. pallidum SS14 strain (RefSeq NC_010741.1) encodes 1,027 proteins, of which 444 proteins are known as hypothetical proteins (HPs), i.e., proteins of unknown functions. Here, we performed functional annotation of HPs of T. pallidum ssp. pallidum using various database, domain architecture predictors, protein function annotators and clustering tools. We have analyzed the sequences of 444 HPs of T. pallidum ssp. pallidum and subsequently predicted the function of 207 HPs with a high level of confidence. However, functions of 237 HPs are predicted with less accuracy. We found various enzymes, transporters, binding proteins in the annotated group of HPs that may be possible molecular targets, facilitating for the survival of pathogen. Our comprehensive analysis helps to understand the mechanism of pathogenesis to provide many novel potential therapeutic interventions.

  15. Identification of intrinsically disordered regions in PTEN and delineation of its function via a network approach.

    Science.gov (United States)

    Malaney, Prerna; Uversky, Vladimir N; Davé, Vrushank

    2015-05-01

    Intrinsically disordered proteins (IDPs) are proteins that lack stable higher order structures for the entire protein molecule or a significant portion of it. The discovery of IDPs evolved as an antithesis to the conventional structure-function paradigm wherein a higher order structure dictates protein function. Over the last decade, a number of proteins with functionally relevant unstructured regions have been discovered, which includes tumor suppressor PTEN. The protein domains that lack structure provide "hot-spots" for post-translational modifications (PTMs) and protein-protein interactions (PPIs), which facilitate their regulation and participation in multiple cellular processes. Consequently, dysregulation in IDPs contribute to aberrant cellular pathophysiology. Herein, we present PTEN and its translational isoform PTEN-L as a hybrid protein possessing ordered domain and intrinsically disordered C-terminal and an N-terminal tails. We review the role of intrinsic disorder in PTEN function and propose a methodology for the use of intrinsic disorder to study PTEN-regulated higher order protein-networks by associating basic principles of network biology to functional pathway analysis at the systems level. Published by Elsevier Inc.

  16. Symbiont recognition of mutualistic bacteria by Acromyrmex leaf-cutting ants

    DEFF Research Database (Denmark)

    Zhang, Mingzi; Poulsen, Michael; Currie, Cameron R

    2007-01-01

    Symbiont choice has been proposed to play an important role in shaping many symbiotic relationships, including the fungus-growing ant-microbe mutualism. Over millions of years, fungus-growing ants have defended their fungus gardens from specialized parasites with antibiotics produced...... by an actinomycete bacterial mutualist (genus Pseudonocardia). Despite the potential of being infected by phylogenetically diverse strains of parasites, each ant colony maintains only a single Pseudonocardia symbiont strain, which is primarily vertically transmitted between colonies by the founding queens....... In this study, we show that Acromyrmex leaf-cutter ants are able to differentiate between their native actinomycete strain and a variety of foreign strains isolated from sympatric and allopatric Acromyrmex species, in addition to strains originating from other fungus-growing ant genera. The recognition...

  17. Rhizobium laguerreae is the main nitrogen-fixing symbiont of cultivated lentil (Lens culinaris) in Morocco.

    Science.gov (United States)

    Taha, Kaoutar; Berraho, El Bekkay; El Attar, Imane; Dekkiche, Samia; Aurag, Jamal; Béna, Gilles

    2018-03-01

    Genetic diversity and population structure of 268 Lens culinaris symbiotic rhizobia collected from 40 cultivated fields in the main lentil production regions in Morocco were estimated. Three chromosomal housekeeping genes (recA, glnII and atpD) and one common symbiotic gene (nodC) were sequenced and analyzed in order to identify the local symbionts of lentil. The molecular phylogeny of the concatenated housekeeping genes clustered more than 95% of the isolates in one main clade together with Rhizobium laguerreae species. R. laguerreae represents the main symbiont of cultivated lentil in Morocco and, for the first time, a large sample of individuals is obtained for this species. There is a significant and high genetic differentiation of bacterial populations among the four regions for their symbiotic gene, and much lower for their housekeeping genes. The reasons why R. laguerreae is so frequently recovered in our study is discussed. Copyright © 2018 Elsevier GmbH. All rights reserved.

  18. Farming termites determine the genetic population structure of Termitomyces fungal symbionts

    DEFF Research Database (Denmark)

    Nobre, Tânia; Fernandes, Cecília; Boomsma, Jacobus J

    2011-01-01

    population structure of Termitomyces fungus gardens across 74 colonies of Macrotermes bellicosus in four west and central African countries. We confirm earlier, more limited, studies showing that the Termitomyces symbionts of M. bellicosus are normally transmitted vertically and clonally by dispersing males....... We also document that the symbionts associated with this termite species belong to three main lineages that do not constitute a monophyletic group. The most common lineage occurs over the entire geographical region that we studied, including west, central and southern Africa, where it is also...... associated with the alternative termite hosts Macrotermes subhyalinus and Macrotermes natalensis. While Termitomyces associated with these alternative hosts are horizontally transmitted and recombine freely, the genetic population structure of the same Termitomyces associated with M. bellicosus is consistent...

  19. Identification of Functional Peptide Sequences to Lead the Design of Precision Polymers.

    Science.gov (United States)

    Ten Brummelhuis, Niels; Wilke, Patrick; Börner, Hans G

    2017-12-01

    Peptide sciences developed dramatically as a result of routine use of solid-phase peptide synthesis and nowadays offer a rich set of well-established strategies to design and identify functional peptide sequences for advanced applications in materials sciences. Appropriate sequences for a wide range of interesting material targets, ranging from molecules to materials surfaces and internal interfaces, can be selected via combinatorial means, and sequence specificities within the resulting peptide-target interactions can be routinely investigated. Based on this understanding, macromolecular sciences can define new polymer structures that meet required functionalities or functional sequences with fully synthetic, nonpeptidic precision polymers to endeavor toward information-based design of next-generation, purpose-adapted macromolecules. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Identification of functional elements and regulatory circuits by Drosophila modENCODE.

    Science.gov (United States)

    Roy, Sushmita; Ernst, Jason; Kharchenko, Peter V; Kheradpour, Pouya; Negre, Nicolas; Eaton, Matthew L; Landolin, Jane M; Bristow, Christopher A; Ma, Lijia; Lin, Michael F; Washietl, Stefan; Arshinoff, Bradley I; Ay, Ferhat; Meyer, Patrick E; Robine, Nicolas; Washington, Nicole L; Di Stefano, Luisa; Berezikov, Eugene; Brown, Christopher D; Candeias, Rogerio; Carlson, Joseph W; Carr, Adrian; Jungreis, Irwin; Marbach, Daniel; Sealfon, Rachel; Tolstorukov, Michael Y; Will, Sebastian; Alekseyenko, Artyom A; Artieri, Carlo; Booth, Benjamin W; Brooks, Angela N; Dai, Qi; Davis, Carrie A; Duff, Michael O; Feng, Xin; Gorchakov, Andrey A; Gu, Tingting; Henikoff, Jorja G; Kapranov, Philipp; Li, Renhua; MacAlpine, Heather K; Malone, John; Minoda, Aki; Nordman, Jared; Okamura, Katsutomo; Perry, Marc; Powell, Sara K; Riddle, Nicole C; Sakai, Akiko; Samsonova, Anastasia; Sandler, Jeremy E; Schwartz, Yuri B; Sher, Noa; Spokony, Rebecca; Sturgill, David; van Baren, Marijke; Wan, Kenneth H; Yang, Li; Yu, Charles; Feingold, Elise; Good, Peter; Guyer, Mark; Lowdon, Rebecca; Ahmad, Kami; Andrews, Justen; Berger, Bonnie; Brenner, Steven E; Brent, Michael R; Cherbas, Lucy; Elgin, Sarah C R; Gingeras, Thomas R; Grossman, Robert; Hoskins, Roger A; Kaufman, Thomas C; Kent, William; Kuroda, Mitzi I; Orr-Weaver, Terry; Perrimon, Norbert; Pirrotta, Vincenzo; Posakony, James W; Ren, Bing; Russell, Steven; Cherbas, Peter; Graveley, Brenton R; Lewis, Suzanna; Micklem, Gos; Oliver, Brian; Park, Peter J; Celniker, Susan E; Henikoff, Steven; Karpen, Gary H; Lai, Eric C; MacAlpine, David M; Stein, Lincoln D; White, Kevin P; Kellis, Manolis

    2010-12-24

    To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.

  1. Complete identification of E-selectin ligands on neutrophils reveals distinct functions of PSGL-1, ESL-1, and CD44.

    Science.gov (United States)

    Hidalgo, Andrés; Peired, Anna J; Wild, Martin; Vestweber, Dietmar; Frenette, Paul S

    2007-04-01

    The selectins and their ligands are required for leukocyte extravasation during inflammation. Several glycoproteins have been suggested to bind to E-selectin in vitro, but the complete identification of its physiological ligands has remained elusive. Here, we showed that E-selectin ligand-1 (ESL-1), P-selectin glycoprotein ligand-1 (PSGL-1), and CD44 encompassed all endothelial-selectin ligand activity on neutrophils by using gene- and RNA-targeted loss of function. PSGL-1 played a major role in the initial leukocyte capture, whereas ESL-1 was critical for converting initial tethers into steady slow rolling. CD44 controlled rolling velocity and mediated E-selectin-dependent redistribution of PSGL-1 and L-selectin to a major pole on slowly rolling leukocytes through p38 signaling. These results suggest distinct and dynamic contributions of these three glycoproteins in selectin-mediated neutrophil adhesion and signaling.

  2. Phenotype Analysis Method for Identification of Gene Functions Involved in Asymmetric Division of Caenorhabditis elegans.

    Science.gov (United States)

    Yang, Sihai; Han, Xianhua; Tohsato, Yukako; Kyoda, Koji; Onami, Shuichi; Nishikawa, Ikuko; Chen, Yenwei

    2017-05-01

    In gene function analysis, it is arduous to identify gene function individually, and the way to screen out all involved genes according to a particular phenotype or disease usually shows us little information for a specific problem. We present a data-driven analysis system based on wild type (WT) embryos to study the concrete function of each gene associated with certain category of abnormal phenotypes. It can be applied to genes with very few RNAi embryos. Instead of presupposing the particular function of a gene, its function is confirmed by the statistical testing of built models. The scheme includes the following five: first, verify the to be detected genes and determine related recognized features according to the given category; second, compute the value of each feature based on WT embryos and merge them by principal component analysis (PCA); third, for each of the selected components of PCA, build a normal distribution and verify its normality; fourth, project the RNAi embryos to each component and probe them; and finally, analyze the more detailed functions of each gene based on the physical or biological meaning of each component. Choosing the first-round asymmetric division process of Caenorhabditis elegans as the phenotype, experimental results show that on the different aspects of the asymmetric division process, par-2, par-3, and let-754 are related to scalar differences; dcn-1 and mcm-5 are associated with the divergences of scalar variation, which may reflect the disaccord in development; and dcn-1, par-2, and par-3 are involved with morphological discrepancies.

  3. Identification of antibody glycosylation structures that predict monoclonal antibody Fc-effector function.

    Science.gov (United States)

    Chung, Amy W; Crispin, Max; Pritchard, Laura; Robinson, Hannah; Gorny, Miroslaw K; Yu, Xiaojie; Bailey-Kellogg, Chris; Ackerman, Margaret E; Scanlan, Chris; Zolla-Pazner, Susan; Alter, Galit

    2014-11-13

    To determine monoclonal antibody (mAb) features that predict fragment crystalizable (Fc)-mediated effector functions against HIV. Monoclonal antibodies, derived from Chinese hamster ovary cells or Epstein-Barr virus-immortalized mouse heteromyelomas, with specificity to key regions of the HIV envelope including gp120-V2, gp120-V3 loop, gp120-CD4(+) binding site, and gp41-specific antibodies, were functionally profiled to determine the relative contribution of the variable and constant domain features of the antibodies in driving robust Fc-effector functions. Each mAb was assayed for antibody-binding affinity to gp140(SR162), antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP) and for the ability to bind to FcγRIIa, FcγRIIb and FcγRIIIa receptors. Antibody glycan profiles were determined by HPLC. Neither the specificity nor the affinity of the mAbs determined the potency of Fc-effector function. FcγRIIIa binding strongly predicted ADCC and decreased galactose content inversely correlated with ADCP, whereas N-glycolylneuraminic acid-containing structures exhibited enhanced ADCP. Additionally, the bi-antenary glycan arm onto which galactose was added predicted enhanced binding to FcγRIIIa and ADCC activity, independent of the specificity of the mAb. Our studies point to the specific Fc-glycan structures that can selectively promote Fc-effector functions independently of the antibody specificity. Furthermore, we demonstrated antibody glycan structures associated with enhanced ADCP activity, an emerging Fc-effector function that may aid in the control and clearance of HIV infection.

  4. Identification of a functional hepatocyte nuclear factor 4 binding site in the neutral ceramidase promoter

    DEFF Research Database (Denmark)

    Maltesen, Henrik R; Troelsen, Jesper T; Olsen, Jørgen

    2010-01-01

    in ceramide digestion. It was the purpose of the present work to experimentally verify the functional importance of a HNF-4a binding site predicted by bioinformatic analysis to be present in the Asah2 promoter. Using supershift analysis, HNF-4a overexpression, and HNF-4a knockdown experiments it was confirmed...... that the predicted HNF-4a binding site identified in the Asah2 promoter is functional. The results support the hypothesis that HNF-4a might be important for intestinal glycolipid metabolism....

  5. Identification and characterization of two functional variants in the human longevity gene FOXO3

    DEFF Research Database (Denmark)

    Flachsbart, Friederike; Dose, Janina; Gentschew, Liljana

    2017-01-01

    FOXO3 is consistently annotated as a human longevity gene. However, functional variants and underlying mechanisms for the association remain unknown. Here, we perform resequencing of the FOXO3 locus and single-nucleotide variant (SNV) genotyping in three European populations. We find two FOXO3 SNVs......, rs12206094 and rs4946935, to be most significantly associated with longevity and further characterize them functionally. We experimentally validate the in silico predicted allele-dependent binding of transcription factors (CTCF, SRF) to the SNVs. Specifically, in luciferase reporter assays...

  6. The distribution of intra-genomically variable dinoflagellate symbionts at Lord Howe Island, Australia

    Science.gov (United States)

    Wilkinson, Shaun P.; Pontasch, Stefanie; Fisher, Paul L.; Davy, Simon K.

    2016-06-01

    The symbiotic dinoflagellates of corals and other marine invertebrates ( Symbiodinium) are essential to the development of shallow-water coral reefs. This genus contains considerable genetic diversity and a corresponding range of physiological and ecological traits. Most genetic variation arises through the accumulation of somatic mutations that arise during asexual reproduction. Yet growing evidence suggests that occasional sexual reproductive events also occur within, and perhaps between, Symbiodinium lineages, further contributing to the pool of genetic variation available for evolutionary adaptation. Intra-genomic variation can therefore arise from both sexual and asexual reproductive processes, making it difficult to discern its underlying causes and consequences. We used quantitative PCR targeting the ITS2 locus to estimate proportions of genetically homogeneous symbionts and intra-genomically variable Symbiodinium (IGV Symbiodinium) in the reef-building coral Pocillopora damicornis at Lord Howe Island, Australia. We then sampled colonies through time and at a variety of spatial scales to find out whether the distribution of these symbionts followed patterns consistent with niche partitioning. Estimated ratios of homogeneous to IGV Symbiodinium varied between colonies within sites (metres to tens of metres) and between sites separated by hundreds to thousands of metres, but remained stable within colonies through time. Symbiont ratios followed a temperature gradient, with the local thermal maximum emerging as a negative predictor for the estimated proportional abundance of IGV Symbiodinium. While this pattern may result from fine-scale spatial population structure, it is consistent with an increased susceptibility to thermal stress, suggesting that the evolutionary processes that generate IGV (such as inter-lineage recombination and the accumulation of somatic mutations at the ITS2 locus) may have important implications for the fitness of the symbiont and

  7. Aphid symbionts and endogenous resistance traits mediate competition between rival parasitoids.

    Science.gov (United States)

    Kraft, Laura J; Kopco, James; Harmon, Jason P; Oliver, Kerry M

    2017-01-01

    Insects use endogenous mechanisms and infection with protective symbionts to thwart attacks from natural enemies. Defenses that target specific enemies, however, potentially mediate competition between rivals and thereby impact community composition. Following its introduction to North America to control pea aphids (Acyrthosiphon pisum), the parasitoid Aphidius ervi competitively displaced other parasitoids, except for the native Praon pequodorum. The pea aphid exhibits tremendous clonal variation in resistance to A. ervi, primarily through infection with the heritable bacterial symbiont Hamiltonella defensa, although some symbiont-free aphid genotypes encode endogenous resistance. Interestingly, H. defensa strains and aphid genotypes that protect against A. ervi, provide no protection against the closely related, P. pequodorum. Given the specificity of aphid defenses, we hypothesized that aphid resistance traits may contribute to the continued persistence of P. pequodorum. We conducted multiparasitism assays to determine whether aphid resistance traits mediate internal competition between these two solitary parasitoid species, but found this was not the case; P. pequodorum was the successful internal competitor across lines varying in susceptibility to A. ervi. Next, to determine whether resistance traits influence competitive interactions resulting in the stable persistence of P. pequodorum, we established replicated cages varying in the proportion of resistant aphids and recorded successful parasitism for each wasp species over time. As expected, A. ervi outcompeted P. pequodorum in cages containing only susceptible aphids. However, P. pequodorum not only persisted, but was the superior competitor in populations containing any proportion (20-100%) of resistant aphids (20-100%). Smaller scale, better replicated competition cage studies corroborated this finding, and no-competition and behavioral assays provide insight into the processes mediating competition

  8. Genetic connectivity between north and south Mid-Atlantic Ridge chemosynthetic bivalves and their symbionts.

    Directory of Open Access Journals (Sweden)

    Karina van der Heijden

    Full Text Available Transform faults are geological structures that interrupt the continuity of mid-ocean ridges and can act as dispersal barriers for hydrothermal vent organisms. In the equatorial Atlantic Ocean, it has been hypothesized that long transform faults impede gene flow between the northern and the southern Mid-Atlantic Ridge (MAR and disconnect a northern from a southern biogeographic province. To test if there is a barrier effect in the equatorial Atlantic, we examined phylogenetic relationships of chemosynthetic bivalves and their bacterial symbionts from the recently discovered southern MAR hydrothermal vents at 5°S and 9°S. We examined Bathymodiolus spp. mussels and Abyssogena southwardae clams using the mitochondrial cytochrome c oxidase subunit I (COI gene as a phylogenetic marker for the hosts and the bacterial 16S rRNA gene as a marker for the symbionts. Bathymodiolus spp. from the two southern sites were genetically divergent from the northern MAR species B. azoricus and B. puteoserpentis but all four host lineages form a monophyletic group indicating that they radiated after divergence from their northern Atlantic sister group, the B. boomerang species complex. This suggests dispersal of Bathymodiolus species from north to south across the equatorial belt. 16S rRNA genealogies of chemoautotrophic and methanotrophic symbionts of Bathymodiolus spp. were inconsistent and did not match the host COI genealogy indicating disconnected biogeography patterns. The vesicomyid clam Abyssogena southwardae from 5°S shared an identical COI haplotype with A. southwardae from the Logatchev vent field on the northern MAR and their symbionts shared identical 16S phylotypes, suggesting gene flow across the Equator. Our results indicate genetic connectivity between the northern and southern MAR and suggest that a strict dispersal barrier does not exist.

  9. Comparative sequence analysis of bacterial symbionts from the marine sponges Geodia cydonium and Ircinia muscarum

    OpenAIRE

    Zuppa, Antonio; Costantini, Susan; Costantini, Maria

    2014-01-01

    Marine sponges (Porifera) live in a symbiotic relationship with microorganisms, primarily bacteria. Recently, several studies indicated that sponges are the most prolific source of biologically-active compounds produced by symbiotic microorganisms rather than by the sponges themselves. In the present study we characterized the bacterial symbionts from two Demospongiae, Ircinia muscarum and Geodia cydonium. We amplified 16S rRNA by PCR, using specific bacterial-primers. The phylogenetic analys...

  10. Nocturnal Production of Endospores in Natural Populations of Epulopiscium-Like Surgeonfish Symbionts

    OpenAIRE

    Flint, Joseph F.; Drzymalski, Dan; Montgomery, W. Linn; Southam, Gordon; Angert, Esther R.

    2005-01-01

    Prior studies have described a morphologically diverse group of intestinal microorganisms associated with surgeonfish. Despite their diversity of form, 16S rRNA gene surveys and fluorescent in situ hybridizations indicate that these bacteria are low-G+C gram-positive bacteria related to Epulopiscium spp. Many of these bacteria exhibit an unusual mode of reproduction, developing multiple offspring intracellularly. Previous reports have suggested that some Epulopiscium-like symbionts produce do...

  11. Identification of functional elements and regulatory circuits by Drosophila modENCODE

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Sushmita; Ernst, Jason; Kharchenko, Peter V.; Kheradpour, Pouya; Negre, Nicolas; Eaton, Matthew L.; Landolin, Jane M.; Bristow, Christopher A.; Ma, Lijia; Lin, Michael F.; Washietl, Stefan; Arshinoff, Bradley I.; Ay, Ferhat; Meyer, Patrick E.; Robine, Nicolas; Washington, Nicole L.; Stefano, Luisa Di; Berezikov, Eugene; Brown, Christopher D.; Candeias, Rogerio; Carlson, Joseph W.; Carr, Adrian; Jungreis, Irwin; Marbach, Daniel; Sealfon, Rachel; Tolstorukov, Michael Y.; Will, Sebastian; Alekseyenko, Artyom A.; Artieri, Carlo; Booth, Benjamin W.; Brooks, Angela N.; Dai, Qi; Davis, Carrie A.; Duff, Michael O.; Feng, Xin; Gorchakov, Andrey A.; Gu, Tingting; Henikoff, Jorja G.; Kapranov, Philipp; Li, Renhua; MacAlpine, Heather K.; Malone, John; Minoda, Aki; Nordman, Jared; Okamura, Katsutomo; Perry, Marc; Powell, Sara K.; Riddle, Nicole C.; Sakai, Akiko; Samsonova, Anastasia; Sandler, Jeremy E.; Schwartz, Yuri B.; Sher, Noa; Spokony, Rebecca; Sturgill, David; van Baren, Marijke; Wan, Kenneth H.; Yang, Li; Yu, Charles; Feingold, Elise; Good, Peter; Guyer, Mark; Lowdon, Rebecca; Ahmad, Kami; Andrews, Justen; Berger, Bonnie; Brenner, Steven E.; Brent, Michael R.; Cherbas, Lucy; Elgin, Sarah C. R.; Gingeras, Thomas R.; Grossman, Robert; Hoskins, Roger A.; Kaufman, Thomas C.; Kent, William; Kuroda, Mitzi I.; Orr-Weaver, Terry; Perrimon, Norbert; Pirrotta, Vincenzo; Posakony, James W.; Ren, Bing; Russell, Steven; Cherbas, Peter; Graveley, Brenton R.; Lewis, Suzanna; Micklem, Gos; Oliver, Brian; Park, Peter J.; Celniker, Susan E.; Henikoff, Steven; Karpen, Gary H.; Lai, Eric C.; MacAlpine, David M.; Stein, Lincoln D.; White, Kevin P.; Kellis, Manolis

    2010-12-22

    To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation. Several years after the complete genetic sequencing of many species, it is still unclear how to translate genomic information into a functional map of cellular and developmental programs. The Encyclopedia of DNA Elements (ENCODE) (1) and model organism ENCODE (modENCODE) (2) projects use diverse genomic assays to comprehensively annotate the Homo sapiens (human), Drosophila melanogaster (fruit fly), and Caenorhabditis elegans (worm) genomes, through systematic generation and computational integration of functional genomic data sets. Previous genomic studies in flies have made seminal contributions to our understanding of basic biological mechanisms and genome functions, facilitated by genetic, experimental, computational, and manual annotation of the euchromatic and heterochromatic genome (3), small genome size, short life cycle, and a deep knowledge of development, gene function, and chromosome biology. The functions

  12. Cyclic nucleotide gated channel gene family in tomato: genome-wide identification and functional analyses in disease resistance

    Directory of Open Access Journals (Sweden)

    Mumtaz Ali Saand

    2015-05-01

    Full Text Available The cyclic nucleotide gated channel (CNGC is suggested to be one of the important calcium conducting channels. Nevertheless, genome-wide identification and systemic functional analysis of CNGC gene family in crop plant species have not yet been conducted. In this study, we performed genome-wide identification of CNGC gene family in the economically important crop tomato (Solanum lycopersicum L. and analyzed function of the group IVb SlCNGC genes in disease resistance. Eighteen CNGC genes were identified in tomato genome, and four CNGC loci that were misannotated at database were corrected by cloning and sequencing. Detailed bioinformatics analyses on gene structure, domain composition and phylogenetic relationship of the SlCNGC gene family were conducted and the group-specific feature was revealed. Comprehensive expression analyses demonstrated that SlCNGC genes were highly and widely responsive to diverse stimuli and the expression profile was gene-dependent. Pharmacological assays showed that the putative CNGC activators cGMP and cAMP enhanced resistance against Sclerotinia sclerotiorum. Silencing of group IVb SlCNGC genes significantly enhanced resistance to fungal pathogens Pythium aphanidermatum and S. sclerotiorum, strongly reduced resistance to viral pathogen Tobacco rattle virus, while attenuated PAMP- and DAMP-triggered immunity as shown by obvious decrease of the flg22- and AtPep1-elicited hydrogen peroxide accumulation in SlCNGC-silenced plants. Additionally, silencing of these SlCNGC genes significantly altered expression of a set of Ca2+ signaling genes including SlCaMs, SlCDPKs and SlCAMTA3. Collectively, our results reveal that group IV SlCNGC genes regulate a wide range of resistance in tomato probably by affecting Ca2+ signaling.

  13. Consumer versus expert hazard identification: A mental models study of a functional food ingredient

    DEFF Research Database (Denmark)

    Hagemann, Kit; Scholderer, Joachim

    Objectives: The consumer part of the EU project NOFORISK compares laypeople and experts' understanding of benefits and risks associated with the functional food ingredient Phytosterol. The Council of the European Union has recently authorised the marketing of Phytosterol-enriched rye bread...

  14. Identification of a functional nuclear localization signal within the human USP22 protein

    International Nuclear Information System (INIS)

    Xiong, Jianjun; Wang, Yaqin; Gong, Zhen; Liu, Jianyun; Li, Weidong

    2014-01-01

    Highlights: • USP22 was accumulated in nucleus. • We identified of a functional USP22 NLS. • The KRRK amino acid residues are indispensable in NLS. • The KRRK motif is conserved in USP22 homologues. - Abstract: Ubiquitin-specific processing enzyme 22 (USP22), a member of the deubiquitinase family, is over-expressed in most human cancers and has been implicated in tumorigenesis. Because it is an enzymatic subunit of the human SAGA transcriptional cofactor, USP22 deubiquitylates histone H2A and H2B in the nucleus, thus participating in gene regulation and cell-cycle progression. However, the mechanisms regulating its nuclear translocation have not yet been elucidated. It was here demonstrated that USP22 is imported into the nucleus through a mechanism mediated by nuclear localization signal (NLS). The bipartite NLS sequence KRELELLKHNPKRRKIT (aa152–168), was identified as the functional NLS for its nuclear localization. Furthermore, a short cluster of basic amino acid residues KRRK within this bipartite NLS plays the primary role in nuclear localization and is evolutionarily conserved in USP22 homologues. In the present study, a functional NLS and the minimal sequences required for the active targeting of USP22 to the nucleus were identified. These findings may provide a molecular basis for the mechanism underlying USP22 nuclear trafficking and function

  15. PROFSS : A screening tool for early identification of functional somatic symptoms

    NARCIS (Netherlands)

    Gol, Janna M; Burger, Huibert; Janssens, Karin A M; Slaets, Joris P J; Gans, Rijk O B; Rosmalen, Judith G M

    2014-01-01

    Objective: To develop and validate a brief screening tool for predicting functional somatic symptoms (FSS) based on clinical and non-clinical information from the general practitioner referral letter, and to assess its inter-rater reliability. Methods: The-derivation sample consisted of 357

  16. Protein profile of human hepatocarcinoma cell line SMMC-7721: Identification and functional analysis

    OpenAIRE

    Feng, Yi; Tian, Zhong-Min; Wan, Ming-Xi; Zheng, Zhao-Bin

    2007-01-01

    AIM: To investigate the protein profile of human hepatocarcinoma cell line SMMC-7721, to analyze the specific functions of abundant expressed proteins in the processes of hepatocarcinoma genesis, growth and metastasis, to identify the hepatocarcinoma-specific biomarkers for the early prediction in diagnosis, and to explore the new drug targets for liver cancer therapy.

  17. Identification of a functional nuclear localization signal within the human USP22 protein

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Jianjun [Key Laboratory of Jiangxi Province for the Systems Bio-Medicine, Jiujiang, Jiangxi Province 332000 (China); College of Basic Medical Science, Jiujiang University, Jiujiang, Jiangxi Province 332000 (China); Wang, Yaqin [Reproductive Medical Center, Renmin Hospital of Wuhan University, Wuhan, Hubei Province 430060 (China); Gong, Zhen [Key Laboratory of Jiangxi Province for the Systems Bio-Medicine, Jiujiang, Jiangxi Province 332000 (China); Liu, Jianyun [College of Basic Medical Science, Jiujiang University, Jiujiang, Jiangxi Province 332000 (China); Li, Weidong, E-mail: lwd626518@163.com [College of Basic Medical Science, Jiujiang University, Jiujiang, Jiangxi Province 332000 (China)

    2014-06-20

    Highlights: • USP22 was accumulated in nucleus. • We identified of a functional USP22 NLS. • The KRRK amino acid residues are indispensable in NLS. • The KRRK motif is conserved in USP22 homologues. - Abstract: Ubiquitin-specific processing enzyme 22 (USP22), a member of the deubiquitinase family, is over-expressed in most human cancers and has been implicated in tumorigenesis. Because it is an enzymatic subunit of the human SAGA transcriptional cofactor, USP22 deubiquitylates histone H2A and H2B in the nucleus, thus participating in gene regulation and cell-cycle progression. However, the mechanisms regulating its nuclear translocation have not yet been elucidated. It was here demonstrated that USP22 is imported into the nucleus through a mechanism mediated by nuclear localization signal (NLS). The bipartite NLS sequence KRELELLKHNPKRRKIT (aa152–168), was identified as the functional NLS for its nuclear localization. Furthermore, a short cluster of basic amino acid residues KRRK within this bipartite NLS plays the primary role in nuclear localization and is evolutionarily conserved in USP22 homologues. In the present study, a functional NLS and the minimal sequences required for the active targeting of USP22 to the nucleus were identified. These findings may provide a molecular basis for the mechanism underlying USP22 nuclear trafficking and function.

  18. The identification and functional annotation of RNA structures conserved in vertebrates

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Mirza, Aashiq Hussain; Hansen, Claus

    2017-01-01

    Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure-b...

  19. [Early identification of impaired renal function in obese children with non-alcoholic fatty liver disease].

    Science.gov (United States)

    Lin, Hu; Fu, Junfen; Chen, Xuefeng; Huang, Ke; Wu, Wei; Liang, Li

    2013-07-01

    To early assess the impaired renal function in the obese children with non-alcoholic fatty liver disease (NAFLD) and to identify the relationship between NAFLD and impairment of renal function. Three hundred and eighty-six obese children were enrolled and divided into NAFLD group and simple obesity group (control) according to the diagnostic criteria. Clinical biochemical parameters and early impaired renal functions were evaluated and compared. Among all patients 234 obese children aged over 10 y were subdivided into 3 groups: NAFLD combined with metabolic syndrome (NAFLD+MS) group, NAFLD group and simple obesity group (control), and the above indexes were compared among 3 groups. The urinary microalbumin levels in NAFLD, NAFLD+MS (>10y) and NAFLD groups (>10y) were significantly higher than those in controls. Additionally, the positive correlations of urinary microalbumin with systolic pressure, triglyceride and 2h-postprandial blood glucose were found. There is early renal dysfunction in children with NAFLD and those accompanied with MS, which may be associated with hypertension and glucose-lipid metabolic disorder. The results indicate that NAFLD is not only an early sign of early impaired renal function but also an early stage of chronic kidney disease (CKD) in obese children.

  20. The Different Potential of Sponge Bacterial Symbionts in N2 Release Indicated by the Phylogenetic Diversity and Abundance Analyses of Denitrification Genes, nirK and nosZ

    Science.gov (United States)

    Zhang, Xia; He, Liming; Zhang, Fengli; Sun, Wei; Li, Zhiyong

    2013-01-01

    Nitrogen cycle is a critical biogeochemical process of the oceans. The nitrogen fixation by sponge cyanobacteria was early observed. Until recently, sponges were found to be able to release nitrogen gas. However the gene-level evidence for the role of bacterial symbionts from different species sponges in nitrogen gas release is limited. And meanwhile, the quanitative analysis of nitrogen cycle-related genes of sponge microbial symbionts is relatively lacking. The nirK gene encoding nitrite reductase which catalyzes soluble nitrite into gas NO and nosZ gene encoding nitrous oxide reductase which catalyzes N2O into N2 are two key functional genes in the complete denitrification pathway. In this study, using nirK and nosZ genes as markers, the potential of bacterial symbionts in six species of sponges in the release of N2 was investigated by phylogenetic analysis and real-time qPCR. As a result, totally, 2 OTUs of nirK and 5 OTUs of nosZ genes were detected by gene library-based saturated sequencing. Difference phylogenetic diversity of nirK and nosZ genes were observed at OTU level in sponges. Meanwhile, real-time qPCR analysis showed that Xestospongia testudinaria had the highest abundance of nosZ gene, while Cinachyrella sp. had the greatest abundance of nirK gene. Phylogenetic analysis showed that the nirK and nosZ genes were probably of Alpha-, Beta-, and Gammaproteobacteria origin. The results from this study suggest that the denitrification potential of bacteria varies among sponges because of the different phylogenetic diversity and relative abundance of nosZ and nirK genes in sponges. Totally, both the qualitative and quantitative analyses of nirK and nosZ genes indicated the different potential of sponge bacterial symbionts in the release of nitrogen gas. PMID:23762300

  1. Impacts of Antibiotic and Bacteriophage Treatments on the Gut-Symbiont-Associated Blissus insularis (Hemiptera: Blissidae

    Directory of Open Access Journals (Sweden)

    Yao Xu

    2016-11-01

    Full Text Available The Southern chinch bug, Blissus insularis, possesses specialized midgut crypts that harbor dense populations of the exocellular symbiont Burkholderia. Oral administration of antibiotics suppressed the gut symbionts in B. insularis and negatively impacted insect host fitness, as reflected by retarded development, smaller body size, and higher susceptibility to an insecticide, bifenthrin. Considering that the antibiotics probably had non-lethal but toxic effects on host fitness, attempts were conducted to reduce gut symbionts using bacteriophage treatment. Soil-lytic phages active against the cultures of specific Burkholderia ribotypes were successfully isolated using a soil enrichment protocol. Characterization of the BiBurk16MC_R phage determined its specificity to the Bi16MC_R_vitro ribotype and placed it within the family Podoviridae. Oral administration of phages to fifth-instar B. insularis, inoculated with Bi16MC_R_vitro as neonates had no deleterious effects on host fitness. However, the ingested phages failed to impact the crypt-associated Burkholderia. The observed inactivity of the phage was likely due to the blockage of the connection between the anterior and posterior midgut regions. These findings suggest that the initial colonization by Burkholderia programs the ontogeny of the midgut, providing a sheltered residence protected from microbial antagonists.

  2. Facultative symbiont Hamiltonella confers benefits to Bemisia tabaci (Hemiptera: Aleyrodidae), an invasive agricultural pest worldwide.

    Science.gov (United States)

    Su, Qi; Oliver, Kerry M; Pan, Huipeng; Jiao, Xiaoguo; Liu, Baiming; Xie, Wen; Wang, Shaoli; Wu, Qingjun; Xu, Baoyun; White, Jennifer A; Zhou, Xuguo; Zhang, Youjun

    2013-12-01

    Bacterial symbionts infect most insect species, including important pests such as whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), and often exert important effects on host ecology. The facultative symbiont Hamiltonella is found at high frequencies in the B. tabaci MED (type: Mediterranean-MED) in China. The prevalence of this symbiont in natural populations suggests beneficial effects of infection or manipulation of host reproduction. To date, however, no empirical studies on the biological role of Hamiltonella on the host B. tabaci have been reported. Here, we investigated the effects of Hamiltonella infection on the sex ratio and several fitness parameters in B. tabaci MED by comparing Hamiltonella-infected whiteflies with Hamiltonella-free ones. We found that Hamiltonella-infected whiteflies produced significantly more eggs, exhibited significantly higher nymphal survival, faster development times, and larger adult body size in comparison with Hamiltonella-free whiteflies, while no evidence of reproductive manipulation by Hamiltonella were found in B. tabaci MED. In conclusion, Hamiltonella infection substantially enhanced B. tabaci MED performance. This beneficial role may, at least partially, explain the high prevalence of Hamiltonella in B. tabaci MED populations and may also contribute to their effectiveness in spread of the plant pathogens tomato yellow leaf curl virus.

  3. Exploring the Symbiodinium rare biosphere provides evidence for symbiont switching in reef-building corals.

    Science.gov (United States)

    Boulotte, Nadine M; Dalton, Steven J; Carroll, Andrew G; Harrison, Peter L; Putnam, Hollie M; Peplow, Lesa M; van Oppen, Madeleine Jh

    2016-11-01

    Reef-building corals possess a range of acclimatisation and adaptation mechanisms to respond to seawater temperature increases. In some corals, thermal tolerance increases through community composition changes of their dinoflagellate endosymbionts (Symbiodinium spp.), but this mechanism is believed to be limited to the Symbiodinium types already present in the coral tissue acquired during early life stages. Compelling evidence for symbiont switching, that is, the acquisition of novel Symbiodinium types from the environment, by adult coral colonies, is currently lacking. Using deep sequencing analysis of Symbiodinium rDNA internal transcribed spacer 2 (ITS2) PCR amplicons from two pocilloporid coral species, we show evidence consistent with de novo acquisition of Symbiodinium types from the environment by adult corals following two consecutive bleaching events. Most of these newly detected symbionts remained in the rare biosphere (background types occurring below 1% relative abundance), but one novel type reached a relative abundance of ~33%. Two de novo acquired Symbiodinium types belong to the thermally resistant clade D, suggesting that this switching may have been driven by consecutive thermal bleaching events. Our results are particularly important given the maternal mode of Symbiodinium transmission in the study species, which generally results in high symbiont specificity. These findings will cause a paradigm shift in our understanding of coral-Symbiodinium symbiosis flexibility and mechanisms of environmental acclimatisation in corals.

  4. Unraveling the role of fungal symbionts in plant abiotic stress tolerance

    Science.gov (United States)

    Singh, Lamabam Peter

    2011-01-01

    Fungal symbionts have been found to be associated with every plant studied in the natural ecosystem, where they colonize and reside entirely or partially in the internal tissues of their host plant. Fungal endophytes can express/form a range of different lifestyle/relationships with different host including symbiotic, mutualistic, commensalistic and parasitic in response to host genotype and environmental factors. In mutualistic association fungal endophyte can enhance growth, increase reproductive success and confer biotic and abiotic stress tolerance to its host plant. Since abiotic stress such as, drought, high soil salinity, heat, cold, oxidative stress and heavy metal toxicity is the common adverse environmental conditions that affect and limit crop productivity worldwide. It may be a promising alternative strategy to exploit fungal endophytes to overcome the limitations to crop production brought by abiotic stress. There is an increasing interest in developing the potential biotechnological applications of fungal endophytes for improving plant stress tolerance and sustainable production of food crops. Here we have described the fungal symbioses, fungal symbionts and their role in abiotic stress tolerance. A putative mechanism of stress tolerance by symbionts has also been covered. PMID:21512319

  5. Nocturnal production of endospores in natural populations of epulopiscium-like surgeonfish symbionts.

    Science.gov (United States)

    Flint, Joseph F; Drzymalski, Dan; Montgomery, W Linn; Southam, Gordon; Angert, Esther R

    2005-11-01

    Prior studies have described a morphologically diverse group of intestinal microorganisms associated with surgeonfish. Despite their diversity of form, 16S rRNA gene surveys and fluorescent in situ hybridizations indicate that these bacteria are low-G+C gram-positive bacteria related to Epulopiscium spp. Many of these bacteria exhibit an unusual mode of reproduction, developing multiple offspring intracellularly. Previous reports have suggested that some Epulopiscium-like symbionts produce dormant or phase-bright intracellular offspring. Close relatives of Epulopiscium, such as Metabacterium polyspora and Clostridium lentocellum, are endospore-forming bacteria, which raises the possibility that the phase-bright offspring are endospores. Structural evidence and the presence of dipicolinic acid demonstrate that phase-bright offspring of Epulopiscium-like bacteria are true endospores. In addition, endospores are formed as part of the normal daily life cycle of these bacteria. In the populations studied, mature endospores were seen only at night and the majority of cells in a given population produced one or two endospores per mother cell. Phylogenetic analyses confirmed the close relationship between the endospore-forming surgeonfish symbionts characterized here and previously described Epulopiscium spp. The broad distribution of endospore formation among the Epulopiscium phylogenetic group raises the possibility that sporulation is a characteristic of the group. We speculate that spore formation in Epulopiscium-like symbionts may be important for dispersal and may also enhance survival in the changing conditions of the fish intestinal tract.

  6. Verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny).

    Science.gov (United States)

    Pinel, Nicolás; Davidson, Seana K; Stahl, David A

    2008-09-01

    A Gram-negative, flagellated, heterotrophic, catalase-negative, rod-shaped bacterium previously identified as an earthworm symbiont was isolated from nephridia of the earthworm Eisenia foetida. Comparisons of 16S rRNA gene sequences indicated its relatedness to the betaproteobacterial genus Acidovorax and the novel isolates shared 92-94% sequence similarity with recognized species of this genus. Gene sequence phylogenies revealed that the group of earthworm symbionts formed a cohesive and independent clade. The DNA G+C content was 67.0+/-0.2 mol%. Major fatty acids were C(16:0), C(16:1)omega7c and C(17:0) cyclo. While capable of growing in fully aerated media, all isolates favoured low oxygen concentrations and all required biotin or a mix of amino acids in order to grow on defined mineral media. Based on phylogenies inferred from three housekeeping gene sequences (gap, recA and rpoC), DNA-DNA hybridization values, the unique ecology and the distinct physiology of the novel strains, the new genus Verminephrobacter gen. nov. is proposed for the earthworm nephridial symbionts. The name Verminephrobacter eiseniae sp. nov. is proposed for the type species with strain EF01-2(T) (=ATCC BAA-1489(T)=DSM 19286(T)) as the type strain of the type species.

  7. Gene expression in gut symbiotic organ of stinkbug affected by extracellular bacterial symbiont.

    Directory of Open Access Journals (Sweden)

    Ryo Futahashi

    Full Text Available The bean bug Riptortus pedestris possesses a specialized symbiotic organ in a posterior region of the midgut, where numerous crypts harbor extracellular betaproteobacterial symbionts of the genus Burkholderia. Second instar nymphs orally acquire the symbiont from the environment, and the symbiont infection benefits the host by facilitating growth and by occasionally conferring insecticide resistance. Here we performed comparative transcriptomic analyses of insect genes expressed in symbiotic and non-symbiotic regions of the midgut dissected from Burkholderia-infected and uninfected R. pedestris. Expression sequence tag analysis of cDNA libraries and quantitative reverse transcription PCR identified a number of insect genes expressed in symbiosis- or aposymbiosis-associated patterns. For example, genes up-regulated in symbiotic relative to aposymbiotic individuals, including many cysteine-rich secreted protein genes and many cathepsin protease genes, are likely to play a role in regulating the symbiosis. Conversely, genes up-regulated in aposymbiotic relative to symbiotic individuals, including a chicken-type lysozyme gene and a defensin-like protein gene, are possibly involved in regulation of non-symbiotic bacterial infections. Our study presents the first transcriptomic data on gut symbiotic organ of a stinkbug, which provides initial clues to understanding of molecular mechanisms underlying the insect-bacterium gut symbiosis and sheds light on several intriguing commonalities between endocellular and extracellular symbiotic associations.

  8. Earthworm symbiont Verminephrobacter eiseniae mediates natural transformation within the host egg capsules using type IV pili

    Directory of Open Access Journals (Sweden)

    SEANA Kelyn DAVIDSON

    2014-10-01

    Full Text Available The dense microbial communities commonly associated with plants and animals should offer many opportunities for horizontal gene transfer (HGT through described mechanisms of DNA exchange including natural transformation. However, studies of the significance of natural transformation have focused primarily on pathogens. The study presented here demonstrates highly efficient DNA exchange by natural transformation in a common symbiont of earthworms. The obligate bacterial symbiont Verminephrobacter eiseniae is a member of a microbial consortium of the earthworm Eisenia fetida that is transmitted into the egg capsules to colonize the embryonic worms. In the study presented here, by testing for transformants under different conditions in culture, we demonstrate that V. eiseniae can incorporate free DNA from the environment, that competency is regulated by environmental factors, and that it is sequence specific. Mutations in the type IV pili of V. eiseniae resulted in loss of DNA uptake, implicating the type IV pilus (TFP apparatus in DNA uptake. Furthermore, injection of DNA carrying antibiotic-resistance genes into egg capsules resulted in transformants within the capsule, demonstrating the relevance of DNA uptake within the earthworm system. The ability to take up species-specific DNA from the environment may explain the maintenance of the relatively large, intact genome of this long-associated obligate symbiont, and provides a mechanism for acquisition of foreign genes within the earthworm system.

  9. Identification of a putative triacylglycerol lipase from papaya latex by functional proteomics.

    Science.gov (United States)

    Dhouib, R; Laroche-Traineau, J; Shaha, R; Lapaillerie, D; Solier, E; Rualès, J; Pina, M; Villeneuve, P; Carrière, F; Bonneu, M; Arondel, V

    2011-01-01

    Latex from Caricaceae has been known since 1925 to contain strong lipase activity. However, attempts to purify and identify the enzyme were not successful, mainly because of the lack of solubility of the enzyme. Here, we describe the characterization of lipase activity of the latex of Vasconcellea heilbornii and the identification of a putative homologous lipase from Carica papaya. Triacylglycerol lipase activity was enriched 74-fold from crude latex of Vasconcellea heilbornii to a specific activity (SA) of 57 μmol·min(-1)·mg(-1) on long-chain triacylglycerol (olive oil). The extract was also active on trioctanoin (SA = 655 μmol·min(-1)·mg(-1) ), tributyrin (SA = 1107 μmol·min(-1)·mg(-1) ) and phosphatidylcholine (SA = 923 μmol·min(-1)·mg(-1) ). The optimum pH ranged from 8.0 to 9.0. The protein content of the insoluble fraction of latex was analyzed by electrophoresis followed by mass spectrometry, and 28 different proteins were identified. The protein fraction was incubated with the lipase inhibitor [(14) C]tetrahydrolipstatin, and a 45 kDa protein radiolabeled by the inhibitor was identified as being a putative lipase. A C. papaya cDNA encoding a 55 kDa protein was further cloned, and its deduced sequence had 83.7% similarity with peptides from the 45 kDa protein, with a coverage of 25.6%. The protein encoded by this cDNA had 35% sequence identity and 51% similarity to castor bean acid lipase, suggesting that it is the lipase responsible for the important lipolytic activities detected in papaya latex. © 2010 The Authors Journal compilation © 2010 FEBS.

  10. Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Joshi NV

    2009-01-01

    Full Text Available Abstract Background Regulation of gene expression in Plasmodium falciparum (Pf remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS; this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

  11. Key Microbiota Identification Using Functional Gene Analysis during Pepper (Piper nigrum L. Peeling.

    Directory of Open Access Journals (Sweden)

    Jiachao Zhang

    Full Text Available Pepper pericarp microbiota plays an important role in the pepper peeling process for the production of white pepper. We collected pepper samples at different peeling time points from Hainan Province, China, and used a metagenomic approach to identify changes in the pericarp microbiota based on functional gene analysis. UniFrac distance-based principal coordinates analysis revealed significant changes in the pericarp microbiota structure during peeling, which were attributed to increases in bacteria from the genera Selenomonas and Prevotella. We identified 28 core operational taxonomic units at each time point, mainly belonging to Selenomonas, Prevotella, Megasphaera, Anaerovibrio, and Clostridium genera. The results were confirmed by quantitative polymerase chain reaction. At the functional level, we observed significant increases in microbial features related to acetyl xylan esterase and pectinesterase for pericarp degradation during peeling. These findings offer a new insight into biodegradation for pepper peeling and will promote the development of the white pepper industry.

  12. Anomalies and specific functions in the clinical identification of defense mechanisms.

    Science.gov (United States)

    Perry, J Christopher

    2014-05-01

    Standard teaching about defense mechanisms generally focuses on definitions, which do not readily aid the clinician in identifying defenses whenever individuals use them. This report demonstrates a process by which the clinician can identify when a defense is used, which ones are likely being used, and with what aim. Clinicians first notice that a defense may be operating whenever the other individual presents with anomalies in the expression of affect, behavior, speech, or its content. Some of these anomalies are described. Next, to identify the specific defense or general level of defensive functioning used, the clinician must identify the specific function of the defense in context using a process of guided clinical inference. This report examines 2 verbatim examples from recorded interviews of one case to demonstrate this process. The examples present a microcosm of clinical concerns that have a surprising relationship to the individual's course and prognosis. © 2014 Wiley Periodicals, Inc.

  13. Key Microbiota Identification Using Functional Gene Analysis during Pepper (Piper nigrum L.) Peeling.

    Science.gov (United States)

    Zhang, Jiachao; Hu, Qisong; Xu, Chuanbiao; Liu, Sixin; Li, Congfa

    2016-01-01

    Pepper pericarp microbiota plays an important role in the pepper peeling process for the production of white pepper. We collected pepper samples at different peeling time points from Hainan Province, China, and used a metagenomic approach to identify changes in the pericarp microbiota based on functional gene analysis. UniFrac distance-based principal coordinates analysis revealed significant changes in the pericarp microbiota structure during peeling, which were attributed to increases in bacteria from the genera Selenomonas and Prevotella. We identified 28 core operational taxonomic units at each time point, mainly belonging to Selenomonas, Prevotella, Megasphaera, Anaerovibrio, and Clostridium genera. The results were confirmed by quantitative polymerase chain reaction. At the functional level, we observed significant increases in microbial features related to acetyl xylan esterase and pectinesterase for pericarp degradation during peeling. These findings offer a new insight into biodegradation for pepper peeling and will promote the development of the white pepper industry.

  14. Fast reproducible identification and large-scale databasing of individual functional cognitive networks

    Directory of Open Access Journals (Sweden)

    Jobert Antoinette

    2007-10-01

    Full Text Available Abstract Background Although cognitive processes such as reading and calculation are associated with reproducible cerebral networks, inter-individual variability is considerable. Understanding the origins of this variability will require the elaboration of large multimodal databases compiling behavioral, anatomical, genetic and functional neuroimaging data over hundreds of subjects. With this goal in mind, we designed a simple and fast acquisition procedure based on a 5-minute functional magnetic resonance imaging (fMRI sequence that can be run as easily and as systematically as an anatomical scan, and is therefore used in every subject undergoing fMRI in our laboratory. This protocol captures the cerebral bases of auditory and visual perception, motor actions, reading, language comprehension and mental calculation at an individual level. Results 81 subjects were successfully scanned. Before describing inter-individual variability, we demonstrated in the present study the reliability of individual functional data obtained with this short protocol. Considering the anatomical variability, we then needed to correctly describe individual functional networks in a voxel-free space. We applied then non-voxel based methods that automatically extract main features of individual patterns of activation: group analyses performed on these individual data not only converge to those reported with a more conventional voxel-based random effect analysis, but also keep information concerning variance in location and degrees of activation across subjects. Conclusion This collection of individual fMRI data will help to describe the cerebral inter-subject variability of the correlates of some language, calculation and sensorimotor tasks. In association with demographic, anatomical, behavioral and genetic data, this protocol will serve as the cornerstone to establish a hybrid database of hundreds of subjects suitable to study the range and causes of variation in the

  15. The Identification and the Functional Validation of Eye Development and Regeneration Genes in Schmidtea Mediterranea

    OpenAIRE

    Calvo Lozano, Beatriz

    2015-01-01

    Discovering the master genes necessary to build the eye in an invertebrate model such as S. mediterranea could help us to understand numerous retinopathies and age-related degeneration of the human eye. The aim of this study was to select and determine the functional activity of genes involved in the regeneration and development of the S. mediterranea eye. Gene ontology was the tool used to select the genes; while RNA interference and RNA hybridization provided the first approach towards esta...

  16. Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Sandra Goetze

    2009-11-01

    Full Text Available Protein modifications play a major role for most biological processes in living organisms. Amino-terminal acetylation of proteins is a common modification found throughout the tree of life: the N-terminus of a nascent polypeptide chain becomes co-translationally acetylated, often after the removal of the initiating methionine residue. While the enzymes and protein complexes involved in these processes have been extensively studied, only little is known about the biological function of such N-terminal modification events. To identify common principles of N-terminal acetylation, we analyzed the amino-terminal peptides from proteins extracted from Drosophila Kc167 cells. We detected more than 1,200 mature protein N-termini and could show that N-terminal acetylation occurs in insects with a similar frequency as in humans. As the sole true determinant for N-terminal acetylation we could extract the (XPX rule that indicates the prevention of acetylation under all circumstances. We could show that this rule can be used to genetically engineer a protein to study the biological relevance of the presence or absence of an acetyl group, thereby generating a generic assay to probe the functional importance of N-terminal acetylation. We applied the assay by expressing mutated proteins as transgenes in cell lines and in flies. Here, we present a straightforward strategy to systematically study the functional relevance of N-terminal acetylations in cells and whole organisms. Since the (XPX rule seems to be of general validity in lower as well as higher eukaryotes, we propose that it can be used to study the function of N-terminal acetylation in all species.

  17. Identification of a minimal functional linker in human topoisomerase I by domain swapping with Cre recombinase

    DEFF Research Database (Denmark)

    Hougaard, Rikke Frøhlich; Juul, Sissel; Vinther, Maria

    2008-01-01

    . In this study we replace 86 amino acids including the linker domain of the cellular type IB topoisomerase, human topoisomerase I, with four, six, or eight amino acids from the corresponding short loop region in Cre recombinase. In vitro characterization of the resulting chimeras, denoted Cropos, reveals...... that six amino acids from the Cre linker loop constitute the minimal length of a functional linker in human topoisomerase I....

  18. Identification of factors that function in Drosophila salivary gland cell death during development using proteomics

    Science.gov (United States)

    McPhee, C K; Balgley, B M; Nelson, C; Hill, J H; Batlevi, Y; Fang, X; Lee, C S; Baehrecke, E H

    2013-01-01

    Proteasome inhibitors induce cell death and are used in cancer therapy, but little is known about the relationship between proteasome impairment and cell death under normal physiological conditions. Here, we investigate the relationship between proteasome function and larval salivary gland cell death during development in Drosophila. Drosophila larval salivary gland cells undergo synchronized programmed cell death requiring both caspases and autophagy (Atg) genes during development. Here, we show that ubiquitin proteasome system (UPS) function is reduced during normal salivary gland cell death, and that ectopic proteasome impairment in salivary gland cells leads to early DNA fragmentation and salivary gland condensation in vivo. Shotgun proteomic analyses of purified dying salivary glands identified the UPS as the top category of proteins enriched, suggesting a possible compensatory induction of these factors to maintain proteolysis during cell death. We compared the proteome following ectopic proteasome impairment to the proteome during developmental cell death in salivary gland cells. Proteins that were enriched in both populations of cells were screened for their function in salivary gland degradation using RNAi knockdown. We identified several factors, including trol, a novel gene CG11880, and the cop9 signalsome component cop9 signalsome 6, as required for Drosophila larval salivary gland degradation. PMID:22935612

  19. Identification and diversity of functional centromere satellites in the wild rice species Oryza brachyantha.

    Science.gov (United States)

    Yi, Chuandeng; Zhang, Wenli; Dai, Xibin; Li, Xing; Gong, Zhiyun; Zhou, Yong; Liang, Guohua; Gu, Minghong

    2013-12-01

    The centromere is a key chromosomal component for sister chromatid cohesion and is the site for kinetochore assembly and spindle fiber attachment, allowing each sister chromatid to faithfully segregate to each daughter cell during cell division. It is not clear what types of sequences act as functional centromeres and how centromere sequences are organized in Oryza brachyantha, an FF genome species. In this study, we found that the three classes of centromere-specific CentO-F satellites (CentO-F1, CentO-F2, and CentOF3) in O. brachyantha share no homology with the CentO satellites in Oryza sativa. The three classes of CentO-F satellites are all located within the chromosomal regions to which the spindle fibers attach and are characterized by megabase tandem arrays that are flanked by centromere-specific retrotransposons, CRR-F, in the O. brachyantha centromeres. Although these CentO-F satellites are quantitatively variable among 12 O. brachyantha centromeres, immunostaining with an antibody specific to CENH3 indicates that they are colocated with CENH3 in functional centromere regions. Our results demonstrate that the three classes of CentO-F satellites may be the major components of functional centromeres in O. brachyantha.

  20. Identification of factors that function in Drosophila salivary gland cell death during development using proteomics.

    Science.gov (United States)

    McPhee, C K; Balgley, B M; Nelson, C; Hill, J H; Batlevi, Y; Fang, X; Lee, C S; Baehrecke, E H

    2013-02-01

    Proteasome inhibitors induce cell death and are used in cancer therapy, but little is known about the relationship between proteasome impairment and cell death under normal physiological conditions. Here, we investigate the relationship between proteasome function and larval salivary gland cell death during development in Drosophila. Drosophila larval salivary gland cells undergo synchronized programmed cell death requiring both caspases and autophagy (Atg) genes during development. Here, we show that ubiquitin proteasome system (UPS) function is reduced during normal salivary gland cell death, and that ectopic proteasome impairment in salivary gland cells leads to early DNA fragmentation and salivary gland condensation in vivo. Shotgun proteomic analyses of purified dying salivary glands identified the UPS as the top category of proteins enriched, suggesting a possible compensatory induction of these factors to maintain proteolysis during cell death. We compared the proteome following ectopic proteasome impairment to the proteome during developmental cell death in salivary gland cells. Proteins that were enriched in both populations of cells were screened for their function in salivary gland degradation using RNAi knockdown. We identified several factors, including trol, a novel gene CG11880, and the cop9 signalsome component cop9 signalsome 6, as required for Drosophila larval salivary gland degradation.

  1. Identification of Functional and Expression Polymorphisms Associated With Risk for Antineutrophil Cytoplasmic Autoantibody–Associated Vasculitis

    Science.gov (United States)

    Merkel, Peter A.; Xie, Gang; Monach, Paul A.; Ji, Xuemei; Ciavatta, Dominic J.; Byun, Jinyoung; Pinder, Benjamin D.; Zhao, Ai; Zhang, Jinyi; Tadesse, Yohannes; Qian, David; Weirauch, Matthew; Nair, Rajan; Tsoi, Alex; Pagnoux, Christian; Carette, Simon; Chung, Sharon; Cuthbertson, David; Davis, John C.; Dellaripa, Paul F.; Forbess, Lindsy; Gewurz‐Singer, Ora; Hoffman, Gary S.; Khalidi, Nader; Koening, Curry; Langford, Carol A.; Mahr, Alfred D.; McAlear, Carol; Moreland, Larry; Seo, E. Philip; Specks, Ulrich; Spiera, Robert F.; Sreih, Antoine; St.Clair, E. William; Stone, John H.; Ytterberg, Steven R.; Elder, James T.; Qu, Jia; Ochi, Toshiki; Hirano, Naoto; Edberg, Jeffrey C.; Falk, Ronald J.; Amos, Christopher I.

    2017-01-01

    Objective To identify risk alleles relevant to the causal and biologic mechanisms of antineutrophil cytoplasmic antibody (ANCA)–associated vasculitis (AAV). Methods A genome‐wide association study and subsequent replication study were conducted in a total cohort of 1,986 cases of AAV (patients with granulomatosis with polyangiitis [Wegener's] [GPA] or microscopic polyangiitis [MPA]) and 4,723 healthy controls. Meta‐analysis of these data sets and functional annotation of identified risk loci were performed, and candidate disease variants with unknown functional effects were investigated for their impact on gene expression and/or protein function. Results Among the genome‐wide significant associations identified, the largest effect on risk of AAV came from the single‐nucleotide polymorphism variants rs141530233 and rs1042169 at the HLA–DPB1 locus (odds ratio [OR] 2.99 and OR 2.82, respectively) which, together with a third variant, rs386699872, constitute a triallelic risk haplotype associated with reduced expression of the HLA–DPB1 gene and HLA–DP protein in B cells and monocytes and with increased frequency of complementary proteinase 3 (PR3)–reactive T cells relative to that in carriers of the protective haplotype. Significant associations were also observed at the SERPINA1 and PTPN22 loci, the peak signals arising from functionally relevant missense variants, and at PRTN3, in which the top‐scoring variant correlated with increased PRTN3 expression in neutrophils. Effects of individual loci on AAV risk differed between patients with GPA and those with MPA or between patients with PR3‐ANCAs and those with myeloperoxidase‐ANCAs, but the collective population attributable fraction for these variants was substantive, at 77%. Conclusion This study reveals the association of susceptibility to GPA and MPA with functional gene variants that explain much of the genetic etiology of AAV, could influence and possibly be predictors of the clinical

  2. Are aphid parasitoids locally adapted to the prevalence of defensive symbionts in their hosts?

    Science.gov (United States)

    Vorburger, Christoph; Rouchet, Romain

    2016-12-12

    Insect parasitoids are under strong selection to overcome their hosts' defences. In aphids, resistance to parasitoids is largely determined by the presence or absence of protective endosymbionts such as Hamiltonella defensa. Hence, parasitoids may become locally adapted to the prevalence of this endosymbiont in their host populations. To address this, we collected isofemale lines of the aphid parasitoid Lysiphlebus fabarum from 17 sites in Switzerland and France, at which we also estimated the frequency of infection with H. defensa as well as other bacterial endosymbionts in five important aphid host species. The parasitoids' ability to overcome H. defensa-mediated resistance was then quantified by estimating their parasitism success on a single aphid clone (Aphis fabae fabae) that was either uninfected or experimentally infected with one of three different isolates of H. defensa. The five aphid species (Aphis fabae fabae, A. f. cirsiiacanthoides, A. hederae, A. ruborum, A. urticata) differed strongly in the relative frequencies of infection with different bacterial endosymbionts, but there was also geographic variation in symbiont prevalence. Specifically, the frequency of infection with H. defensa ranged from 22 to 47 % when averaged across species. Parasitoids from sites with a high prevalence of H. defensa tended to be more infective on aphids possessing H. defensa, but this relationship was not significant, thus providing no conclusive evidence that L. fabarum is locally adapted to the occurrence of H. defensa. On the other hand, we observed a strong interaction between parasitoid line and H. defensa isolate on parasitism success, indicative of a high specificity of symbiont-conferred resistance. This study is the first, to our knowledge, to test for local adaptation of parasitoids to the frequency of defensive symbionts in their hosts. While it yielded useful information on the occurrence of facultative endosymbionts in several important host species of L

  3. Comparative Profiling of coral symbiont communities from the Caribbean, Indo-Pacific, and Arabian Seas

    KAUST Repository

    Arif, Chatchanit

    2014-12-01

    Coral reef ecosystems are in rapid decline due to global and local anthropogenic factors. Being among the most diverse ecosystems on Earth, a loss will decrease species diversity, and remove food source for people along the coast. The coral together with its symbionts (i.e. Symbiodinium, bacteria, and other microorganisms) is called the ‘coral holobiont’. The coral host offers its associated symbionts suitable habitats and nutrients, while Symbiodinium and coral-associated bacteria provide the host with photosynthates and vital nutrients. Association of corals with certain types of Symbiodinium and bacteria confer coral stress tolerance, and lack or loss of these symbionts coincides with diseased or bleached corals. However, a detailed understanding of the coral holobiont diversity and structure in regard to diseases and health states or across global scales is missing. This dissertation addressed coral-associated symbiont diversity, specifically of Symbiodinium and bacteria, in various coral species from different geographic locations and different health states. The main aims were (1) to expand the scope of existing technologies, (2) to establish a standardized framework to facilitate comparison of symbiont assemblages over coral species and sites, (3) to assess Symbiodinium diversity in the Arabian Seas, and (4) to elucidate whether coral health states have conserved bacterial footprints. In summary, a next generation sequencing pipeline for Symbiodinium diversity typing of the ITS2 marker is developed and applied to describe Symbiodinium diversity in corals around the Arabian Peninsula. The data show that corals in the Arabian Seas are dominated by a single Symbiodinium type, but harbor a rich variety of types in low abundant. Further, association with different Symbiodinium types is structured according to geographic locations. In addition, the application of 16S rRNA gene microarrays to investigate how differences in microbiome structure relate to

  4. Identification of Plasmodium falciparum DNA Repair Protein Mre11 with an Evolutionarily Conserved Nuclease Function.

    Directory of Open Access Journals (Sweden)

    Sugith Babu Badugu

    Full Text Available The eukaryotic Meiotic Recombination protein 11 (Mre11 plays pivotal roles in the DNA damage response (DDR. Specifically, Mre11 senses and signals DNA double strand breaks (DSB and facilitates their repair through effector proteins belonging to either homologous recombination (HR or non-homologous end joining (NHEJ repair mechanisms. In the human malaria parasite Plasmodium falciparum, HR and alternative-NHEJ have been identified; however, little is known about the upstream factors involved in the DDR of this organism. In this report, we identify a putative ortholog of Mre11 in P. falciparum (PfalMre11 that shares 22% sequence similarity to human Mre11. Homology modeling reveals striking structural resemblance of the predicted PfalMre11 nuclease domain to the nuclease domain of Saccharomyces cerevisiae Mre11 (ScMre11. Complementation analyses reveal functional conservation of PfalMre11 nuclease activity as demonstrated by the ability of the PfalMre11 nuclease domain, in conjunction with the C-terminal domain of ScMre11, to functionally complement an mre11 deficient yeast strain. Functional complementation was virtually abrogated by an amino acid substitution in the PfalMre11 nuclease domain (D398N. PfalMre11 is abundant in the mitotically active trophozoite and schizont stages of P. falciparum and is up-regulated in response to DNA damage, suggesting a role in the DDR. PfalMre11 exhibits physical interaction with PfalRad50. In addition, yeast 2-hybrid studies show that PfalMre11 interacts with ScRad50 and ScXrs2, two important components of the well characterized Mre11-Rad50-Xrs2 complex which is involved in DDR signaling and repair in S. cerevisiae, further supporting a role for PfalMre11 in the DDR. Taken together, these findings provide evidence that PfalMre11 is an evolutionarily conserved component of the DDR in Plasmodium.

  5. Children's Learning in Scientific Thinking: Instructional Approaches and Roles of Variable Identification and Executive Function

    Science.gov (United States)

    Blums, Angela

    The present study examines instructional approaches and cognitive factors involved in elementary school children's thinking and learning the Control of Variables Strategy (CVS), a critical aspect of scientific reasoning. Previous research has identified several features related to effective instruction of CVS, including using a guided learning approach, the use of self-reflective questions, and learning in individual and group contexts. The current study examined the roles of procedural and conceptual instruction in learning CVS and investigated the role of executive function in the learning process. Additionally, this study examined how learning to identify variables is a part of the CVS process. In two studies (individual and classroom experiments), 139 third, fourth, and fifth grade students participated in hands-on and paper and pencil CVS learning activities and, in each study, were assigned to either a procedural instruction, conceptual instruction, or control (no instruction) group. Participants also completed a series of executive function tasks. The study was carried out with two parts--Study 1 used an individual context and Study 2 was carried out in a group setting. Results indicated that procedural and conceptual instruction were more effective than no instruction, and the ability to identify variables was identified as a key piece to the CVS process. Executive function predicted ability to identify variables and predicted success on CVS tasks. Developmental differences were present, in that older children outperformed younger children on CVS tasks, and that conceptual instruction was slightly more effective for older children. Some differences between individual and group instruction were found, with those in the individual context showing some advantage over the those in the group setting in learning CVS concepts. Conceptual implications about scientific thinking and practical implications in science education are discussed.

  6. Identification of Residues in the Lipopolysaccharide ABC Transporter That Coordinate ATPase Activity with Extractor Function.

    Science.gov (United States)

    Simpson, Brent W; Owens, Tristan W; Orabella, Matthew J; Davis, Rebecca M; May, Janine M; Trauger, Sunia A; Kahne, Daniel; Ruiz, Natividad

    2016-10-18

    The surface of most Gram-negative bacteria is covered with lipopolysaccharide (LPS), creating a permeability barrier against toxic molecules, including many antimicrobials. To assemble LPS on their surface, Gram-negative bacteria must extract newly synthesized LPS from the inner membrane, transport it across the aqueous periplasm, and translocate it across the outer membrane. The LptA to -G proteins assemble into a transenvelope complex that transports LPS from the inner membrane to the cell surface. The Lpt system powers LPS transport from the inner membrane by using a poorly characterized ATP-binding cassette system composed of the ATPase LptB and the transmembrane domains LptFG. Here, we characterize a cluster of residues in the groove region of LptB that is important for controlling LPS transport. We also provide the first functional characterization of LptFG and identify their coupling helices that interact with the LptB groove. Substitutions at conserved residues in these coupling helices compromise both the assembly and function of the LptB 2 FG complex. Defects in LPS transport conferred by alterations in the LptFG coupling helices can be rescued by changing a residue in LptB that is adjacent to functionally important residues in the groove region. This suppression is achieved by increasing the ATPase activity of the LptB 2 FG complex. Taken together, these data identify a specific binding site in LptB for the coupling helices of LptFG that is responsible for coupling of ATP hydrolysis by LptB with LptFG function to achieve LPS extraction. Lipopolysaccharide (LPS) is synthesized at the cytoplasmic membrane of Gram-negative bacteria and transported across several compartments to the cell surface, where it forms a barrier that protects these organisms from antibiotics. The LptB 2 FG proteins form an ATP-binding cassette (ABC) transporter that uses energy from ATP hydrolysis in the cytoplasm to facilitate extraction of LPS from the outer face of the

  7. Identification of Functional Clusters in the Striatum Using Infinite Relational Modeling

    DEFF Research Database (Denmark)

    Andersen, Kasper Winther; Madsen, Kristoffer Hougaard; Siebner, Hartwig

    2011-01-01

    In this paper we investigate how the Infinite Relational Model can be used to infer functional groupings of the human striatum using resting state fMRI data from 30 healthy subjects. The Infinite Relational Model is a non-parametric Bayesian method for infering community structure in complex...... are involved in the same neural computations. The reproducibility of the groupings found are assessed by calculating mutual information between half splits of the subject sample for various hyperparameter values. Finally, the model's ability to predict unobserved links is assessed by randomly treating links...

  8. Identification and Structure-Function Study of Positive Allosteric Modulators of Kainate Receptors

    DEFF Research Database (Denmark)

    Larsen, Anja Probst; Fièvre, Sabine; Frydenvang, Karla

    2017-01-01

    as the AMPA receptor subunit GluA1i (5-fold). X-ray structures of the three modulators in the GluK1 ligand-binding domain were determined, locating two modulator-binding sites at the GluK1 dimer interface. In conclusion, this study may enable the design of new positive allosteric modulators selective for KARs......Kainate receptors (KARs) consist of a class of ionotropic glutamate receptors, which exert diverse pre- and postsynaptic functions through complex signaling regulating the activity of neural circuits. Whereas numerous small-molecule positive allosteric modulators of the ligand-binding domain of (S...

  9. [Measures to prevent patient identification errors in blood collection/physiological function testing utilizing a laboratory information system].

    Science.gov (United States)

    Shimazu, Chisato; Hoshino, Satoshi; Furukawa, Taiji

    2013-08-01

    We constructed an integrated personal identification workflow chart using both bar code reading and an all in-one laboratory information system. The information system not only handles test data but also the information needed for patient guidance in the laboratory department. The reception terminals at the entrance, displays for patient guidance and patient identification tools at blood-sampling booths are all controlled by the information system. The number of patient identification errors was greatly reduced by the system. However, identification errors have not been abolished in the ultrasound department. After re-evaluation of the patient identification process in this department, we recognized that the major reason for the errors came from excessive identification workflow. Ordinarily, an ultrasound test requires patient identification 3 times, because 3 different systems are required during the entire test process, i.e. ultrasound modality system, laboratory information system and a system for producing reports. We are trying to connect the 3 different systems to develop a one-time identification workflow, but it is not a simple task and has not been completed yet. Utilization of the laboratory information system is effective, but is not yet perfect for patient identification. The most fundamental procedure for patient identification is to ask a person's name even today. Everyday checks in the ordinary workflow and everyone's participation in safety-management activity are important for the prevention of patient identification errors.

  10. Subcuticular bacteria from the brittle star Ophiactis balli (Echinodermata: Ophiuroidea) represent a new lineage of extracellular marine symbionts in the alpha subdivision of the class Proteobacteria.

    Science.gov (United States)

    Burnett, W J; McKenzie, J D

    1997-01-01

    Many species of echinoderms, in all five extant classes, contain subcuticular bacterial symbionts (SCB). The role of these extracellular symbionts and the nature of the relationship remain unclear. We have sequenced 16S rRNA genes from symbionts to determine their phylogenetic affinities. Symbionts of an ophiuroid, Ophiactis balli, appear closely related to bacteria within the alpha group of the class Proteobacteria, including intracellular endosymbionts and pathogens. SCB are clearly of separate origin from other documented major groups of marine symbiotic bacteria. PMID:9143108

  11. In-silico identification of miRNAs and their regulating target functions in Ocimum basilicum.

    Science.gov (United States)

    Singh, Noopur; Sharma, Ashok

    2014-12-01

    microRNA is known to play an important role in growth and development of the plants and also in environmental stress. Ocimum basilicum (Basil) is a well known herb for its medicinal properties. In this study, we used in-silico approaches to identify miRNAs and their targets regulating different functions in O. basilicum using EST approach. Additionally, functional annotation, gene ontology and pathway analysis of identified target transcripts were also done. Seven miRNA families were identified. Meaningful regulations of target transcript by identified miRNAs were computationally evaluated. Four miRNA families have been reported by us for the first time from the Lamiaceae. Our results further confirmed that uracil was the predominant base in the first positions of identified mature miRNA sequence, while adenine and uracil were predominant in pre-miRNA sequences. Phylogenetic analysis was carried out to determine the relation between O. basilicum and other plant pre-miRNAs. Thirteen potential targets were evaluated for 4 miRNA families. Majority of the identified target transcripts regulated by miRNAs showed response to stress. miRNA 5021 was also indicated for playing an important role in the amino acid metabolism and co-factor metabolism in this plant. To the best of our knowledge this is the first in silico study describing miRNAs and their regulation in different metabolic pathways of O. basilicum. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Identification of two functional PCNA-binding domains in human DNA polymerase κ.

    Science.gov (United States)

    Yoon, Jung-Hoon; Acharya, Narottam; Park, Jeseong; Basu, Debashree; Prakash, Satya; Prakash, Louise

    2014-07-01

    Previously, we have shown that human DNA polymerase (Pol) η has two functional PCNA-binding motifs, PIP1 and PIP2, and that a C-terminal deletion of Polη that lacks the ubiquitin-binding UBZ domain and the PIP2 domain but retains the PIP1 domain promotes normal levels of translesion synthesis (TLS) opposite a cis-syn TT dimer in human cells. Here, we identify two PIP domains in Polκ and show that TLS occurs normally in human fibroblast cells in which the pip1 or pip2 mutant Polκ is expressed, but mutational inactivation of both PIP domains renders Polκ nonfunctional in TLS opposite the thymine glycol lesion. Thus, the two PIP domains of Polκ function redundantly in TLS opposite this DNA lesion in human cells. However, and surprisingly, whereas mutational inactivation of the PIP1 domain completely inhibits the stimulation of DNA synthesis by Polκ in the presence of proliferating cell nuclear antigen (PCNA), replication factor C, and replication protein A, mutations in PIP2 have no adverse effect on PCNA-dependent DNA synthesis. This raises the possibility that activation of Polκ PIP2 as a PCNA-binding domain occurs during TLS in human cells and that protein-protein interactions and post-transcriptional modifications are involved in such activation. © 2014 The Authors Genes to Cells © 2014 by the Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

  13. Identification and Functional Characterization of the Glycogen Synthesis Related Gene Glycogenin in Pacific Oysters (Crassostrea gigas).

    Science.gov (United States)

    Li, Busu; Meng, Jie; Li, Li; Liu, Sheng; Wang, Ting; Zhang, Guofan

    2017-09-06

    High glycogen levels in the Pacific oyster (Crassostrea gigas) contribute to its flavor, quality, and hardiness. Glycogenin (CgGN) is the priming glucosyltransferase that initiates glycogen biosynthesis. We characterized the full sequence and function of C. gigas CgGN. Three CgGN isoforms (CgGN-α, β, and γ) containing alternative exon regions were isolated. CgGN expression varied seasonally in the adductor muscle and gonadal area and was the highest in the adductor muscle. Autoglycosylation of CgGN can interact with glycogen synthase (CgGS) to complete glycogen synthesis. Subcellular localization analysis showed that CgGN isoforms and CgGS were located in the cytoplasm. Additionally, a site-directed mutagenesis experiment revealed that the Tyr200Phe and Tyr202Phe mutations could affect CgGN autoglycosylation. This is the first study of glycogenin function in marine bivalves. These findings will improve our understanding of glycogen synthesis and accumulation mechanisms in mollusks. The data are potentially useful for breeding high-glycogen oysters.

  14. Identification and assessment of functional performance in mild cognitive impairment: a survey of occupational therapy practices.

    Science.gov (United States)

    Belchior, Patrícia; Korner-Bitensky, Nicol; Holmes, Melanie; Robert, Alexandra

    2015-06-01

    Despite the amount of research evidence pointing to functional changes experienced by individuals with mild cognitive impairment (MCI), we still do not understand how occupational therapists are currently addressing these concerns. Thus, we designed a national study to investigate Canadian occupational therapists practices with this clientele. We conducted a Canada-wide online survey to investigate occupational therapists' practices with clients with potential MCI. Clinicians were prompted by a case vignette that described two clients: one vignette included cues associated with amnestic MCI (aMCI), the other non-amnestic MCI (naMCI). Specifically, clinicians were asked to identify potential concerns and to indicate the screening and assessment tools they would use in clinical practice. Two hundred and eighty-five participants met the inclusion criteria and were included in the final analysis. The average clinician age was 38.6 (SD = 10.3), 92% were female and 71.2% worked full-time. Almost all clinicians identified a concern in both vignettes, with cognitive concerns being identified more frequently than functional concerns [i.e. Instrumental Activities of Daily Living (IADL) concerns]. In terms of assessment practices, 18 standardised IADL assessments and 10 standardised cognitive assessments have been reported. Encouragingly, almost all clinicians identified a concern. However, some are still missing the IADL cues. Moreover, the lack of consensus in terms of which assessment practices to employ indicates that clinicians might benefit from guidelines in this area of practice. © 2015 Occupational Therapy Australia.

  15. Identification of two frataxin isoforms in Zea mays: Structural and functional studies.

    Science.gov (United States)

    Buchensky, Celeste; Sánchez, Manuel; Carrillo, Martin; Palacios, Oscar; Capdevila, Mercè; Domínguez-Vera, Jose M; Busi, Maria V; Atrian, Sílvia; Pagani, Maria A; Gomez-Casati, Diego F

    2017-09-01

    Frataxin is a ubiquitous protein that plays a role in Fe-S cluster biosynthesis and iron and heme metabolism, although its molecular functions are not entirely clear. In non-photosynthetic eukaryotes, frataxin is encoded by a single gene, and the protein localizes to mitochondria. Here we report the presence of two functional frataxin isoforms in Zea mays, ZmFH-1 and ZmFH-2. We confirmed our previous findings regarding plant frataxins: both proteins have dual localization in mitochondria and chloroplasts. Physiological, biochemical and biophysical studies show some differences in the expression pattern, protection against oxidants and in the aggregation state of both isoforms, suggesting that the two frataxin homologs would play similar but not identical roles in plant cell metabolism. In addition, two specific features of plant frataxins were evidenced: their ability to form dimers and their tendency to undergo conformational change under oxygen exposure. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  16. Genetic Analysis of the Lambda Spanins Rz and Rz1: Identification of Functional Domains

    Directory of Open Access Journals (Sweden)

    Jesse Cahill

    2017-02-01

    Full Text Available Coliphage lambda proteins Rz and Rz1 are the inner membrane and outer membrane subunits of the spanin complex—a heterotetramer that bridges the periplasm and is essential for the disruption of the outer membrane during phage lysis. Recent evidence suggests the spanin complex functions by fusing the inner and outer membrane. Here, we use a genetics approach to investigate and characterize determinants of spanin function. Because Rz1 is entirely embedded in the +1 reading frame of Rz, the genes were disembedded before using random mutagenesis to construct a library of lysis-defective alleles for both genes. Surprisingly, most of the lysis-defective missense mutants exhibited normal accumulation or localization in vivo, and also were found to be normal for complex formation in vitro. Analysis of the distribution and nature of single missense mutations revealed subdomains that resemble key motifs in established membrane-fusion systems, i.e., two coiled-coil domains in Rz, a proline-rich region of Rz1, and flexible linkers in both proteins. When coding sequences are aligned respective to the embedded genetic architecture of Rz1 within Rz, genetically silent domains of Rz1 correspond to mutationally sensitive domains in Rz, and vice versa, suggesting that the modular structure of the two subunits facilitated the evolutionary compression that resulted in the unique embedded gene architecture.

  17. Identification of the best DFT functionals for a reliable prediction of lignin vibrational properties

    DEFF Research Database (Denmark)

    Barsberg, Soren

    2015-01-01

    Lignin is the most abundant aromatic plant polymer on earth. Useful information on its structure and interactions is gained by vibrational spectroscopy and relies on the quality of band assignments. B3LYP predictions were recently shown to support band assignments. Further progress calls for a co......Lignin is the most abundant aromatic plant polymer on earth. Useful information on its structure and interactions is gained by vibrational spectroscopy and relies on the quality of band assignments. B3LYP predictions were recently shown to support band assignments. Further progress calls...... for a comprehensive study of the quality of available theoretical methods in relation to the task of predicting lignin vibrational properties. The present study examined more than 50 functionals for prediction of IR vibrations of an appropriate lignin model. Based on a basis set incompleteness study, the pc-2 basis...... functional stands out. These results provide a needed basis for further theoretical developments in relation to vibrational assignments of Infrared and Raman spectra of lignin....

  18. KB-Rank: efficient protein structure and functional annotation identification via text query.

    Science.gov (United States)

    Julfayev, Elchin S; McLaughlin, Ryan J; Tao, Yi-Ping; McLaughlin, William A

    2012-06-01

    The KB-Rank tool was developed to help determine the functions of proteins. A user provides text query and protein structures are retrieved together with their functional annotation categories. Structures and annotation categories are ranked according to their estimated relevance to the queried text. The algorithm for ranking first retrieves matches between the query text and the text fields associated with the structures. The structures are next ordered by their relative content of annotations that are found to be prevalent across all the structures retrieved. An interactive web interface was implemented to navigate and interpret the relevance of the structures and annotation categories retrieved by a given search. The aim of the KB-Rank tool is to provide a means to quickly identify protein structures of interest and the annotations most relevant to the queries posed by a user. Informational and navigational searches regarding disease topics are described to illustrate the tool's utilities. The tool is available at the URL http://protein.tcmedc.org/KB-Rank.

  19. Identification and functional analysis of SOX10 missense mutations in different subtypes of Waardenburg syndrome.

    Science.gov (United States)

    Chaoui, Asma; Watanabe, Yuli; Touraine, Renaud; Baral, Viviane; Goossens, Michel; Pingault, Veronique; Bondurand, Nadege

    2011-12-01

    Waardenburg syndrome (WS) is a rare disorder characterized by pigmentation defects and sensorineural deafness, classified into four clinical subtypes, WS1-S4. Whereas the absence of additional features characterizes WS2, association with Hirschsprung disease defines WS4. WS is genetically heterogeneous, with six genes already identified, including SOX10. About 50 heterozygous SOX10 mutations have been described in patients presenting with WS2 or WS4, with or without myelination defects of the peripheral and central nervous system (PCWH, Peripheral demyelinating neuropathy-Central dysmyelinating leukodystrophy-Waardenburg syndrome-Hirschsprung disease, or PCW, PCWH without HD). The majority are truncating mutations that most often remove the main functional domains of the protein. Only three missense mutations have been thus far reported. In the present study, novel SOX10 missense mutations were found in 11 patients and were examined for effects on SOX10 characteristics and functions. The mutations were associated with various phenotypes, ranging from WS2 to PCWH. All tested mutations were found to be deleterious. Some mutants presented with partial cytoplasmic redistribution, some lost their DNA-binding and/or transactivation capabilities on various tissue-specific target genes. Intriguingly, several mutants were redistributed in nuclear foci. Whether this phenomenon is a cause or a consequence of mutation-associated pathogenicity remains to be determined, but this observation could help to identify new SOX10 modes of action. © 2011 Wiley-Liss, Inc.

  20. Genetic identification of a network of factors that functionally interact with the nucleosome remodeling ATPase ISWI.

    Directory of Open Access Journals (Sweden)

    Giosalba Burgio

    2008-06-01

    Full Text Available Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network of factors that escaped detection in previous biochemical analyses, including the Sin3A gene. The Sin3A protein and the histone deacetylase Rpd3 are part of a conserved histone deacetylase complex involved in transcriptional repression. ISWI and the Sin3A/Rpd3 complex co-localize at specific chromosome domains. Loss of ISWI activity causes a reduction in the binding of the Sin3A/Rpd3 complex to chromatin. Biochemical analysis showed that the ISWI physically interacts with the histone deacetylase activity of the Sin3A/Rpd3 complex. Consistent with these findings, the acetylation of histone H4 is altered when ISWI activity is perturbed in vivo. These findings suggest that ISWI associates with the Sin3A/Rpd3 complex to support its function in vivo.

  1. Functional identification of glutamate cysteine ligase and glutathione synthetase in the marine yeast Rhodosporidium diobovatum

    Science.gov (United States)

    Kong, Min; Wang, Fengjuan; Tian, Liuying; Tang, Hui; Zhang, Liping

    2018-02-01

    Glutathione (GSH) fulfills a variety of metabolic functions, participates in oxidative stress response, and defends against toxic actions of heavy metals and xenobiotics. In this study, GSH was detected in Rhodosporidium diobovatum by high-performance liquid chromatography (HPLC). Then, two novel enzymes from R. diobovatum were characterized that convert glutamate, cysteine, and glycine into GSH. Based on reverse transcription PCR, we obtained the glutathione synthetase gene ( GSH2), 1866 bp, coding for a 56.6-kDa protein, and the glutamate cysteine ligase gene ( GSH1), 2469 bp, coding for a 90.5-kDa protein. The role of GSH1 and GSH2 for the biosynthesis of GSH in the marine yeast R. diobovatum was determined by deletions using the CRISPR-Cas9 nuclease system and enzymatic activity. These results also showed that GSH1 and GSH2 were involved in the production of GSH and are thus being potentially useful to engineer GSH pathways. Alternatively, pET- GSH constructed using vitro recombination could be used to detect the function of genes related to GSH biosynthesis. Finally, the fermentation parameters determined in the present study provide a reference for industrial GSH production in R. diobovatum.

  2. Differentially categorized structural brain hubs are involved in different microstructural, functional, and cognitive characteristics and contribute to individual identification.

    Science.gov (United States)

    Wang, Xindi; Lin, Qixiang; Xia, Mingrui; He, Yong

    2018-04-01

    Very little is known regarding whether structural hubs of human brain networks that enable efficient information communication may be classified into different categories. Using three multimodal neuroimaging data sets, we construct individual structural brain networks and further identify hub regions based on eight widely used graph-nodal metrics, followed by comprehensive characteristics and reproducibility analyses. We show the three categories of structural hubs in the brain network, namely, aggregated, distributed, and connector hubs. Spatially, these distinct categories of hubs are primarily located in the default-mode system and additionally in the visual and limbic systems for aggregated hubs, in the frontoparietal system for distributed hubs, and in the sensorimotor and ventral attention systems for connector hubs. These categorized hubs exhibit various distinct characteristics to support their differentiated roles, involving microstructural organization, wiring costs, topological vulnerability, functional modular integration, and cognitive flexibility; moreover, these characteristics are better in the hubs than nonhubs. Finally, all three categories of hubs display high across-session spatial similarities and act as structural fingerprints with high predictive rates (100%, 100%, and 84.2%) for individual identification. Collectively, we highlight three categories of brain hubs with differential microstructural, functional and, cognitive associations, which shed light on topological mechanisms of the human connectome. © 2018 Wiley Periodicals, Inc.

  3. Reliability of the Identification of Functional Ankle Instability (IdFAI) Scale Across Different Age Groups in Adults.

    Science.gov (United States)

    Gurav, Reshma S; Ganu, Sneha S; Panhale, Vrushali P

    2014-10-01

    Functional ankle instability (FAI) is the tendency of the foot to 'give way'. Identification of Functional Ankle Instability questionnaire (IdFAI) is a newly developed questionnaire to detect whether individuals meet the minimum criteria necessary for inclusion in an FAI population. However, the reliability of the questionnaire was studied only in a restricted age group. The purpose of this investigation was to examine the reliability of IdFAI across different age groups in adults. One hundred and twenty participants in the age group of 20-60 years consisting of 30 individuals in each age group were asked to complete the IdFAI on two occasions. Test-retest reliability was evaluated by intraclass correlation coefficient (ICC2,1). The study revealed that IdFAI has excellent test-retest reliability when studied across different age groups. The ICC2,1 in the age groups 20-30 years, 30-40 years, 40-50 years and 50-60 years was 0.978, 0.975, 0.961 and 0.922, respectively with Cronbach's alpha >0.9 in all the age groups. The IdFAI can accurately predict if an individual meets the minimum criterion for FAI across different age groups in adults. Thus, the questionnaire can be applied over different age groups in clinical and research set-ups.

  4. Infectious speciation revisited: impact of symbiont-depletion on female fitness and mating behavior of Drosophila paulistorum.

    Directory of Open Access Journals (Sweden)

    Wolfgang J Miller

    2010-12-01

    Full Text Available The neotropical Drosophila paulistorum superspecies, consisting of at least six geographically overlapping but reproductively isolated semispecies, has been the object of extensive research since at least 1955, when it was initially trapped mid-evolution in flagrant statu nascendi. In this classic system females express strong premating isolation patterns against mates belonging to any other semispecies, and yet uncharacterized microbial reproductive tract symbionts were described triggering hybrid inviability and male sterility. Based on theoretical models and limited experimental data, prime candidates fostering symbiont-driven speciation in arthropods are intracellular bacteria belonging to the genus Wolbachia. They are maternally inherited symbionts of many arthropods capable of manipulating host reproductive biology for their own benefits. However, it is an ongoing debate as to whether or not reproductive symbionts are capable of driving host speciation in nature and if so, to what extent. Here we have reevaluated this classic case of infectious speciation by means of present day molecular approaches and artificial symbiont depletion experiments. We have isolated the α-proteobacteria Wolbachia as the maternally transmitted core endosymbionts of all D. paulistorum semispecies that have coevolved towards obligate mutualism with their respective native hosts. In hybrids, however, these mutualists transform into pathogens by overreplication causing embryonic inviability and male sterility. We show that experimental reduction in native Wolbachia titer causes alterations in sex ratio, fecundity, and mate discrimination. Our results indicate that formerly designated Mycoplasma-like organisms are most likely Wolbachia that have evolved by becoming essential mutualistic symbionts in their respective natural hosts; they have the potential to trigger pre- and postmating isolation. Furthermore, in light of our new findings, we revisit the concept of

  5. The importance of methane and thiosulfate in the metabolism of the bacterial symbionts of two deep-sea mussels

    Science.gov (United States)

    Fisher, C.R.; Childress, J.J.; Oremland, R.S.; Bidigare, R.R.

    1987-01-01

    Undescribed hydrocarbon-seep mussels were collected from the Louisiana Slope, Gulf of Mexico, during March 1986, and the ultrastructure of their gills was examined and compared to Bathymodiolus thermophilus, a mussel collected from the deep-sea hydrothermal vents on the Gala??pagos Rift in March 1985. These closely related mytilids both contain abundant symbiotic bacteria in their gills. However, the bacteria from the two species are distinctly different in both morphology and biochemistry, and are housed differently within the gills of the two mussels. The symbionts from the seep mussel are larger than the symbionts from B. thermophilus and, unlike the latter, contain stacked intracytoplasmic membranes. In the seep mussel three or fewer symbionts appear to be contained in each host-cell vacuole, while in B. thermophilus there are often more than twenty bacteria visible in a single section through a vacuole. The methanotrophic nature of the seep-mussel symbionts was confirmed in 14C-methane uptake experiments by the appearance of label in both CO2 and acid-stable, non-volatile, organic compounds after a 3 h incubation of isolated gill tissue. Furthermore, methane consumption was correlated with methanol dehydrogenase activity in isolated gill tissue. Activity of ribulose-1,5-biphosphate (RuBP) carboxylase and 14CO2 assimilation studies indicate the presence of either a second type of symbiont or contaminating bacteria on the gills of freshly captured seep mussels. A reevaluation of the nutrition of the symbionts in B. thermophilus indicates that while the major symbiont is not a methanotroph, its status as a sulfur-oxidizing chemoautotroph, as has been suggested previously, is far from proven. ?? 1987 Springer-Verlag.

  6. [The spectral analysis as an instrument for the investigation of the functional-dynamic complexes of oral speech skills for the medical criminalistic identification of the speaker].

    Science.gov (United States)

    Kir'yanov, P A; Kaganov, A Sh

    The objective of the present work was the search for the theoretical foundations and the approaches to the assessment of the methodological basis for the application of the spectral analysis to the investigation of the functional-dynamic complexes (FDC) of oral speech skills for the medical criminalistic identification of the speaker. The study included the analysis of the relevant literature publications, methodological proposals of the authors of the present article, and the results of their medical criminalistics investigations and laboratory experiments. The results of the study give evidence that the spectral analysis provides an acceptable tool for distinguishing the stable identification signs of a given acoustic group that characterize the functional-dynamic complexes of oral speech skills skills for the medical criminalistic identification of the speaker.

  7. Identification and Function of a Novel Candidate Gene for Asthma:ADAM 33

    Directory of Open Access Journals (Sweden)

    John W. Holloway

    2005-01-01

    Full Text Available Asthma is a complex disorder of inflammation and remodelling largely restricted to the conducting airways. It is a disorder where there are major genetics and environmental factors that interact together to initiate and propagate the disease into a chronic relapsing disorder. Until recently the genetic factors involved in disease pathogenesis have been restricted to variants in known molecules involved in the inflammatory or remodelling pathways. In this review evidence is presented for a new susceptibility gene for asthma, ADAM 33, that was identified by positional cloning. It is suggested that ADAM 33 plays a key role in predisposing to reduced lung function and bronchial hyperresponsiveness characteristic of asthma. Through an understanding of the disease-related SNPs(in ADAM 33it may be possible, not only to identify a gene based diagnostic test, but also to focus attention on developing a new treatment that reverses remodelling changes.

  8. Identification of trombospondin-1 as a novel amelogenin interactor by functional proteomics.

    Science.gov (United States)

    Capolupo, Angela; Cassiano, Chiara; Casapullo, Agostino; Andreotti, Giuseppina; Cubellis, Maria V.; Riccio, Andrea; Riccio, Raffaele; Monti, Maria C.

    2017-10-01

    Amelogenins are a set of low molecular-weight enamel proteins belonging to a group of extracellular matrix (ECM) proteins with a key role in tooth enamel development and in other regeneration processes, such as wound healing and angiogenesis. Since only few data are actually available to unravel amelogenin mechanism of action in chronic skin healing restoration, we moved to the full characterization of the human amelogenin isoform 2 interactome in the secretome and lysate of Human Umbilical Vein Endothelial cells (HUVEC), using a functional proteomic approach. Trombospondin-1 has been identified as a novel and interesting partner of human amelogenin isoform 2 and their direct binding has been validated thought biophysical orthogonal approaches.

  9. Identification of a unique TGF-β-dependent molecular and functional signature in microglia.

    Science.gov (United States)

    Butovsky, Oleg; Jedrychowski, Mark P; Moore, Craig S; Cialic, Ron; Lanser, Amanda J; Gabriely, Galina; Koeglsperger, Thomas; Dake, Ben; Wu, Pauline M; Doykan, Camille E; Fanek, Zain; Liu, Liping; Chen, Zhuoxun; Rothstein, Jeffrey D; Ransohoff, Richard M; Gygi, Steven P; Antel, Jack P; Weiner, Howard L

    2014-01-01

    Microglia are myeloid cells of the CNS that participate both in normal CNS function and in disease. We investigated the molecular signature of microglia and identified 239 genes and 8 microRNAs that were uniquely or highly expressed in microglia versus myeloid and other immune cells. Of the 239 genes, 106 were enriched in microglia as compared with astrocytes, oligodendrocytes and neurons. This microglia signature was not observed in microglial lines or in monocytes recruited to the CNS, and was also observed in human microglia. We found that TGF-β was required for the in vitro development of microglia that express the microglial molecular signature characteristic of adult microglia and that microglia were absent in the CNS of TGF-β1-deficient mice. Our results identify a unique microglial signature that is dependent on TGF-β signaling and provide insights into microglial biology and the possibility of targeting microglia for the treatment of CNS disease.

  10. Identification of a functional type VI secretion system in Campylobacter jejuni conferring capsule polysaccharide sensitive cytotoxicity.

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    Nancy M C Bleumink-Pluym

    Full Text Available The pathogen Campylobacter jejuni is the principal cause of bacterial food-borne infections. The mechanism(s that contribute to bacterial survival and disease are still poorly understood. In other bacterial species, type VI secretion systems (T6SS are increasingly recognized to contribute to bacterial pathogenesis by toxic effects on host cells or competing bacterial species. Here we report the presence of a functional Type VI secretion system in C. jejuni. Proteome and genetic analyses revealed that C. jejuni strain 108 contains a 17-kb T6SS gene cluster consisting of 13 T6SS-conserved genes, including the T6SS hallmark genes hcp and vgrG. The cluster lacks an ortholog of the ClpV ATPase considered important for T6SS function. The sequence and organization of the C. jejuni T6SS genes resemble those of the T6SS located on the HHGI1 pathogenicity island of Helicobacter hepaticus. The C. jejuni T6SS is integrated into the earlier acquired Campylobacter integrated element CJIE3 and is present in about 10% of C. jejuni isolates including several isolates derived from patients with the rare clinical feature of C. jejuni bacteremia. Targeted mutagenesis of C. jejuni T6SS genes revealed T6SS-dependent secretion of the Hcp needle protein into the culture supernatant. Infection assays provided evidence that the C. jejuni T6SS confers contact-dependent cytotoxicity towards red blood cells but not macrophages. This trait was observed only in a capsule-deficient bacterial phenotype. The unique C. jejuni T6SS phenotype of capsule-sensitive contact-mediated hemolysis represents a novel evolutionary pathway of T6SS in bacteria and expands the repertoire of virulence properties associated with T6SS.

  11. Identification of a functional type VI secretion system in Campylobacter jejuni conferring capsule polysaccharide sensitive cytotoxicity.

    Science.gov (United States)

    Bleumink-Pluym, Nancy M C; van Alphen, Lieke B; Bouwman, Lieneke I; Wösten, Marc M S M; van Putten, Jos P M

    2013-01-01

    The pathogen Campylobacter jejuni is the principal cause of bacterial food-borne infections. The mechanism(s) that contribute to bacterial survival and disease are still poorly understood. In other bacterial species, type VI secretion systems (T6SS) are increasingly recognized to contribute to bacterial pathogenesis by toxic effects on host cells or competing bacterial species. Here we report the presence of a functional Type VI secretion system in C. jejuni. Proteome and genetic analyses revealed that C. jejuni strain 108 contains a 17-kb T6SS gene cluster consisting of 13 T6SS-conserved genes, including the T6SS hallmark genes hcp and vgrG. The cluster lacks an ortholog of the ClpV ATPase considered important for T6SS function. The sequence and organization of the C. jejuni T6SS genes resemble those of the T6SS located on the HHGI1 pathogenicity island of Helicobacter hepaticus. The C. jejuni T6SS is integrated into the earlier acquired Campylobacter integrated element CJIE3 and is present in about 10% of C. jejuni isolates including several isolates derived from patients with the rare clinical feature of C. jejuni bacteremia. Targeted mutagenesis of C. jejuni T6SS genes revealed T6SS-dependent secretion of the Hcp needle protein into the culture supernatant. Infection assays provided evidence that the C. jejuni T6SS confers contact-dependent cytotoxicity towards red blood cells but not macrophages. This trait was observed only in a capsule-deficient bacterial phenotype. The unique C. jejuni T6SS phenotype of capsule-sensitive contact-mediated hemolysis represents a novel evolutionary pathway of T6SS in bacteria and expands the repertoire of virulence properties associated with T6SS.

  12. Identification of functional mutations in GATA4 in patients with congenital heart disease.

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    Erli Wang

    Full Text Available Congenital heart disease (CHD is one of the most prevalent developmental anomalies and the leading cause of noninfectious morbidity and mortality in newborns. Despite its prevalence and clinical significance, the etiology of CHD remains largely unknown. GATA4 is a highly conserved transcription factor that regulates a variety of physiological processes and has been extensively studied, particularly on its role in heart development. With the combination of TBX5 and MEF2C, GATA4 can reprogram postnatal fibroblasts into functional cardiomyocytes directly. In the past decade, a variety of GATA4 mutations were identified and these findings originally came from familial CHD pedigree studies. Given that familial and sporadic CHD cases allegedly share a basic genetic basis, we explore the GATA4 mutations in different types of CHD. In this study, via direct sequencing of the GATA4 coding region and exon-intron boundaries in 384 sporadic Chinese CHD patients, we identified 12 heterozygous non-synonymous mutations, among which 8 mutations were only found in CHD patients when compared with 957 controls. Six of these non-synonymous mutations have not been previously reported. Subsequent functional analyses revealed that the transcriptional activity, subcellular localization and DNA binding affinity of some mutant GATA4 proteins were significantly altered. Our results expand the spectrum of GATA4 mutations linked to cardiac defects. Together with the newly reported mutations, approximately 110 non-synonymous mutations have currently been identified in GATA4. Our future analysis will explore why the evolutionarily conserved GATA4 appears to be hypermutable.

  13. Identification and functional characterization of sex pheromone receptors in the common cutworm (Spodoptera litura).

    Science.gov (United States)

    Zhang, Jin; Yan, Shuwei; Liu, Yang; Jacquin-Joly, Emmanuelle; Dong, Shuanglin; Wang, Guirong

    2015-01-01

    Male moths can finely discriminate the sex pheromone emitted by conspecific females from similar compounds. Pheromone receptors, expressed on the dendritic membrane of sensory neurons housed in the long trichoid sensilla of antennae, are thought to be associated with the pheromone reception. In this study, we identified and functionally characterized 4 pheromone receptors from the antennae of Spodoptera litura (Lepidoptera: Noctuidae). A tissue distribution analysis showed that the expression of the 4 SlituPRs was restricted to antennae. In addition, SlituOR6 and SlituOR13 were specifically expressed in male antennae whereas SlituOR11 and SlituOR16 were male-biased. Functional investigation by heterologous expression in Xenopus oocytes revealed that SlituOR6 was specifically tuned to the second major pheromone component, Z9,E12-14:OAc, SlituOR13 was equally tuned to Z9,E12-14:OAc and Z9-14:OAc, with a small response to the major pheromone component Z9,E11-14:OAc, SlituOR16 significantly responded to the behavioral antagonist Z9-14:OH, whereas SlituOR11 did not show response to any of the pheromone compounds tested in this study. Our results provide molecular data to better understand the mechanisms of sex pheromone detection in the moth S. litura and bring clues to investigate the evolution of the sexual communication channel in closely related species through comparison with previously reported pheromone receptors in other Spodoptera species. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Functional identification of the prnABCD operon and its regulation in Serratia plymuthica.

    Science.gov (United States)

    Liu, Xiaoguang; Yu, Xiaoli; Yang, Yang; Heeb, Stephan; Gao, Shao; Chan, Kok Gan; Cámara, Miguel; Gao, Kexiang

    2018-04-01

    The antibiotic pyrrolnitrin (PRN) is a tryptophan-derived secondary metabolite that plays an important role in the biocontrol of plant diseases due to its broad-spectrum of antimicrobial activities. The PRN biosynthetic gene cluster remains to be characterised in Serratia plymuthica, though it is highly conserved in PRN-producing bacteria. To better understand PRN biosynthesis and its regulation in Serratia, the prnABCD operon from S. plymuthica G3 was cloned, sequenced and expressed in Escherichia coli DH5α. Furthermore, an engineered strain prnind which is a conditional mutant of G3 prnABCD under the control of the Ptac promoter was constructed. This mutant was able to overproduce PRN with isopropylthiogalactoside (IPTG) induction by overexpressing prnABCD, whilst behaving as a conditional mutant of G3 prnABCD in the absence of IPTG. These results confirmed that prnABCD is responsible for PRN biosynthesis in strain G3. Further experiments involving lux-/dsRed-based promoter fusions, combined with site-directed mutagenesis of the putative σ S extended -10 region in the prnA promoter, and liquid chromatography-mass spectrometry (LC-MS) analysis extended our previous knowledge about G3, revealing that quorum sensing (QS) regulates PRN biosynthesis through cross talk with RpoS, which may directly activated prnABCD transcription. These findings suggest that PRN in S. plymuthica G3 is produced in a tightly controlled manner, and has diverse functions, such as modulation of cell motility, in addition to antimicrobial activities. Meanwhile, the construction of inducible mutants could be a powerful tool to improve PRN production, beyond its potential use for the investigation of the biological function of PRN.

  15. PROFSS: a screening tool for early identification of functional somatic symptoms.

    Science.gov (United States)

    Gol, Janna M; Burger, Huibert; Janssens, Karin A M; Slaets, Joris P J; Gans, Rijk O B; Rosmalen, Judith G M

    2014-12-01

    To develop and validate a brief screening tool for predicting functional somatic symptoms (FSS) based on clinical and non-clinical information from the general practitioner referral letter, and to assess its inter-rater reliability. The derivation sample consisted of 357 consecutive patients referred to an internal outpatient clinic by their general practitioner. Referral letters were scored for candidate predictors for the main outcome measure, which was a final diagnosis of FSS made by the internist. Logistic regression identified the following independent predictors: type of symptoms, somatic and psychiatric comorbidity, absence of abnormal physical findings by the general practitioner, previous specialist consultation, and the use of illness terminology. Temporal validation was performed in a cohort of 94 consecutive patients in whom predictors were scored by two independent raters. In both the derivation and validation sample, the discriminatory power of the model was good with areas under the receiver operating characteristic curves of 0.84 (95%confidence interval: 0.80-0.88) after bootstrapping and 0.82 (95%confidence interval: 0.73-0.91), respectively. Calibration of the models was excellent in both samples and the interobserver agreement in the validation sample was very good (intraclass coefficient: 0.82 (95%confidence interval: 0.75-0.88)). Based on this model, we constructed the brief screening tool PROFSS (Predicted Risk Of Functional Somatic Symptoms). PROFSS identified patient groups with risks of FSS ranging from 17% (95%CI: 10-26%) to 92% (95%CI:86-96%). The presence of FSS can be predicted with the brief screening tool PROFSS, based on a limited set of items present in the general practitioner referral letter. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae

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    Zhang Jie-Qiong

    2011-01-01

    Full Text Available Abstract Background Small non-coding RNAs (sRNAs are regarded as important regulators in prokaryotes and play essential roles in diverse cellular processes. Xanthomonas oryzae pathovar oryzae (Xoo is an important plant pathogenic bacterium which causes serious bacterial blight of rice. However, little is known about the number, genomic distribution and biological functions of sRNAs in Xoo. Results Here, we performed a systematic screen to identify sRNAs in the Xoo strain PXO99. A total of 850 putative non-coding RNA sequences originated from intergenic and gene antisense regions were identified by cloning, of which 63 were also identified as sRNA candidates by computational prediction, thus were considered as Xoo sRNA candidates. Northern blot hybridization confirmed the size and expression of 6 sRNA candidates and other 2 cloned small RNA sequences, which were then added to the sRNA candidate list. We further examined the expression profiles of the eight sRNAs in an hfq deletion mutant and found that two of them showed drastically decreased expression levels, and another exhibited an Hfq-dependent transcript processing pattern. Deletion mutants were obtained for seven of the Northern confirmed sRNAs, but none of them exhibited obvious phenotypes. Comparison of the proteomic differences between three of the ΔsRNA mutants and the wild-type strain by two-dimensional gel electrophoresis (2-DE analysis showed that these sRNAs are involved in multiple physiological and biochemical processes. Conclusions We experimentally verified eight sRNAs in a genome-wide screen and uncovered three Hfq-dependent sRNAs in Xoo. Proteomics analysis revealed Xoo sRNAs may take part in various metabolic processes. Taken together, this work represents the first comprehensive screen and functional analysis of sRNAs in rice pathogenic bacteria and facilitates future studies on sRNA-mediated regulatory networks in this important phytopathogen.

  17. Identification of novel monocistronic HTLV-1 mRNAs encoding functional Rex isoforms.

    Science.gov (United States)

    Rende, Francesca; Cavallari, Ilaria; Andresen, Vibeke; Valeri, Valerio W; D'Agostino, Donna M; Franchini, Genoveffa; Ciminale, Vincenzo

    2015-07-02

    Human T cell leukemia virus type 1 (HTLV-1) gene expression is controlled by the key regulatory proteins Tax and Rex. The concerted action of these proteins results in a two-phase kinetics of viral expression that depends on a time delay between their action. However, it is difficult to explain this delay, as Tax and Rex are produced from the same mRNA. In the present study we investigated whether HTLV-1 may produce novel mRNA species capable of expressing Rex and Tax independently. Results revealed the expression of three alternatively spliced transcripts coding for novel Rex isoforms in infected cell lines and in primary samples from infected patients. One mRNA coded for a Tax isoform and a Rex isoform, and two mRNAs coded for Rex isoforms but not Tax. Functional assays showed that these Rex isoforms exhibit activity comparable to canonic Rex. An analysis of the temporal expression of these transcripts upon ex vivo culture of cells from infected patients and cell lines transfected with a molecular clone of HTLV-1 revealed early expression of the dicistronic tax/rex mRNAs followed by the monocistronic mRNAs coding for Rex isoforms. The production of monocistronic HTLV-1 mRNAs encoding Rex isoforms with comparable activity to canonical Rex, but with distinct timing, would support a prolonged duration of Rex function with gradual loss of Tax, and is consistent with the two-phase expression kinetics. A thorough understanding of these regulatory circuits will shed light on the basis of viral latency and provide groundwork to develop strategies for eradicating persistent infections.

  18. Identification of Pleiotropic Cancer Susceptibility Variants from Genome-Wide Association Studies Reveals Functional Characteristics.

    Science.gov (United States)

    Wu, Yi-Hsuan; Graff, Rebecca E; Passarelli, Michael N; Hoffman, Joshua D; Ziv, Elad; Hoffmann, Thomas J; Witte, John S

    2018-01-01

    Background: There exists compelling evidence that some genetic variants are associated with the risk of multiple cancer sites (i.e., pleiotropy). However, the biological mechanisms through which the pleiotropic variants operate are unclear. Methods: We obtained all cancer risk associations from the National Human Genome Research Institute-European Bioinformatics Institute GWAS Catalog, and correlated cancer risk variants were clustered into groups. Pleiotropic variant groups and genes were functionally annotated. Associations of pleiotropic cancer risk variants with noncancer traits were also obtained. Results: We identified 1,431 associations between variants and cancer risk, comprised of 989 unique variants associated with 27 unique cancer sites. We found 20 pleiotropic variant groups (2.1%) composed of 33 variants (3.3%), including novel pleiotropic variants rs3777204 and rs56219066 located in the ELL2 gene. Relative to single-cancer risk variants, pleiotropic variants were more likely to be in genes (89.0% vs. 65.3%, P = 2.2 × 10 -16 ), and to have somewhat larger risk allele frequencies (median RAF = 0.49 versus 0.39, P = 0.046). The 27 genes to which the pleiotropic variants mapped were suggestive for enrichment in response to radiation and hypoxia, alpha-linolenic acid metabolism, cell cycle, and extension of telomeres. In addition, we observed that 8 of 33 pleiotropic cancer risk variants were associated with 16 traits other than cancer. Conclusions: This study identified and functionally characterized genetic variants showing pleiotropy for cancer risk. Impact: Our findings suggest biological pathways common to different cancers and other diseases, and provide a basis for the study of genetic testing for multiple cancers and repurposing cancer treatments. Cancer Epidemiol Biomarkers Prev; 27(1); 75-85. ©2017 AACR . ©2017 American Association for Cancer Research.

  19. Identification of a disulfide bridge important for transport function of SNAT4 neutral amino acid transporter.

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    Rugmani Padmanabhan Iyer

    Full Text Available SNAT4 is a member of system N/A amino acid transport family that primarily expresses in liver and muscles and mediates the transport of L-alanine. However, little is known about the structure and function of the SNAT family of transporters. In this study, we showed a dose-dependent inhibition in transporter activity of SNAT4 with the treatment of reducing agents, dithiothreitol (DTT and Tris(2-carboxyethylphosphine (TCEP, indicating the possible involvement of disulfide bridge(s. Mutation of residue Cys-232, and the two highly conserved residues Cys-249 and Cys-321, compromised the transport function of SNAT4. However, this reduction was not caused by the decrease of SNAT4 on the cell surface since the cysteine-null mutant generated by replacing all five cysteines with alanine was equally capable of being expressed on the cell surface as wild-type SNAT4. Interestingly, by retaining two cysteine residues, 249 and 321, a significant level of L-alanine uptake was restored, indicating the possible formation of disulfide bond between these two conserved residues. Biotinylation crosslinking of free thiol groups with MTSEA-biotin provided direct evidence for the existence of a disulfide bridge between Cys-249 and Cys-321. Moreover, in the presence of DTT or TCEP, transport activity of the mutant retaining Cys-249 and Cys-321 was reduced in a dose-dependent manner and this reduction is gradually recovered with increased concentration of H2O2. Disruption of the disulfide bridge also decreased the transport of L-arginine, but to a lesser degree than that of L-alanine. Together, these results suggest that cysteine residues 249 and 321 form a disulfide bridge, which plays an important role in substrate transport but has no effect on trafficking of SNAT4 to the cell surface.

  20. Identification of a transitional fibroblast function in very early rheumatoid arthritis.

    Science.gov (United States)

    Filer, Andrew; Ward, Lewis S C; Kemble, Samuel; Davies, Christopher S; Munir, Hafsa; Rogers, Rebekah; Raza, Karim; Buckley, Christopher Dominic; Nash, Gerard B; McGettrick, Helen M

    2017-12-01

    Synovial fibroblasts actively regulate the inflammatory infiltrate by communicating with neighbouring endothelial cells (EC). Surprisingly, little is known about how the development of rheumatoid arthritis (RA) alters these immunomodulatory properties. We examined the effects of phase of RA and disease outcome (resolving vs persistence) on fibroblast crosstalk with EC and regulation of lymphocyte recruitment. Fibroblasts were isolated from patients without synovitis, with resolving arthritis, very early RA (VeRA; symptom ≤12 weeks) and established RA undergoing joint replacement (JRep) surgery. Endothelial-fibroblast cocultures were formed on opposite sides of porous filters. Lymphocyte adhesion from flow, secretion of soluble mediators and interleukin 6 (IL-6) signalling were assessed. Fibroblasts from non-inflamed and resolving arthritis were immunosuppressive, inhibiting lymphocyte recruitment to cytokine-treated endothelium. This effect was lost very early in the development of RA, such that fibroblasts no longer suppressed recruitment. Changes in IL-6 and transforming growth factor beta 1 (TGF-β 1 ) signalling appeared critical for the loss of the immunosuppressive phenotype. In the absence of exogenous cytokines, JRep, but not VeRA, fibroblasts activated endothelium to support lymphocyte. In RA, fibroblasts undergo two distinct changes in function: first a loss of immunosuppressive responses early in disease development, followed by the later acquisition of a stimulatory phenotype. Fibroblasts exhibit a transitional functional phenotype during the first 3 months of symptoms that contributes to the accumulation of persistent infiltrates. Finally, the role of IL-6 and TGF-β 1 changes from immunosuppressive in resolving arthritis to stimulatory very early in the development of RA. Early interventions targeting 'pathogenic' fibroblasts may be required in order to restore protective regulatory processes. © Article author(s) (or their employer(s) unless

  1. Interaction between workers during a short time window is required for bacterial symbiont transmission in Acromyrmex leaf-cutting ants.

    Science.gov (United States)

    Marsh, Sarah E; Poulsen, Michael; Pinto-Tomás, Adrián; Currie, Cameron R

    2014-01-01

    Stable associations between partners over time are critical for the evolution of mutualism. Hosts employ a variety of mechanisms to maintain specificity with bacterial associates. Acromyrmex leaf-cutting ants farm a fungal cultivar as their primary nutrient source. These ants also carry a Pseudonocardia Actinobacteria exosymbiont on their bodies that produces antifungal compounds that help inhibit specialized parasites of the ants' fungal garden. Major workers emerge from their pupal cases (eclose) symbiont-free, but exhibit visible Actinobacterial coverage within 14 days post-eclosion. Using subcolony experiments, we investigate exosymbiont transmission within Acromyrmex colonies. We found successful transmission to newly eclosed major workers fostered by major workers with visible Actinobacteria in all cases (100% acquiring, n = 19). In contrast, newly eclosed major workers reared without exosymbiont-carrying major workers did not acquire visible Actinobacteria (0% acquiring, n = 73). We further show that the majority of ants exposed to major workers with exosymbionts within 2 hours of eclosion acquired bacteria (60.7% acquiring, n = 28), while normal acquisition did not occur when exposure occurred later than 2 hours post-eclosion (0% acquiring, n = 18). Our findings show that transmission of exosymbionts to newly eclosed major workers occurs through interactions with exosymbiont-covered workers within a narrow time window after eclosion. This mode of transmission likely helps ensure the defensive function within colonies, as well as specificity and partner fidelity in the ant-bacterium association.

  2. Functional Characterization of CYP94-Genes and Identification of a Novel Jasmonate Catabolite in Flowers.

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    Viktoria Bruckhoff

    Full Text Available Over the past decades much research focused on the biosynthesis of the plant hormone jasmonyl-isoleucine (JA-Ile. While many details about its biosynthetic pathway as well about its physiological function are established nowadays, knowledge about its catabolic fate is still scarce. Only recently, the hormonal inactivation mechanisms became a stronger research focus. Two major pathways have been proposed to inactivate JA-Ile: i The cleavage of the jasmonyl-residue from the isoleucine moiety, a reaction that is catalyzed by specific amido-hydrolases, or ii, the sequential oxidation of the ω-end of the pentenyl side-chain. This reaction is catalyzed by specific members of the cytochrome P450 (CYP subfamily CYP94: CYP94B1, CYP94B3 and CYP94C1. In the present study, we further investigated the oxidative fate of JA-Ile by expanding the analysis on Arabidopsis thaliana mutants, lacking only one (cyp94b1, cyp94b2, cyp94b3, cyp94c1, two (cyp94b1xcyp94b2, cyp94b1xcyp94b3, cyp94b2xcyp94b3, three (cyp94b1xcyp94b2xcyp94b3 or even four (cyp94b1xcyp94b2xcyp94b3xcyp94c1 CYP94 functionalities. The results obtained in the present study show that CYP94B1, CYP94B2, CYP94B3 and CYP94C1 are responsible for catalyzing the sequential ω-oxidation of JA-Ile in a semi-redundant manner. While CYP94B-enzymes preferentially hydroxylate JA-Ile to 12-hydroxy-JA-Ile, CYP94C1 catalyzes primarily the subsequent oxidation, yielding 12-carboxy-JA-Ile. In addition, data obtained from investigating the triple and quadruple mutants let us hypothesize that a direct oxidation of unconjugated JA to 12-hydroxy-JA is possible in planta. Using a non-targeted metabolite fingerprinting analysis, we identified unconjugated 12-carboxy-JA as novel jasmonate derivative in floral tissues. Using the same approach, we could show that deletion of CYP94-genes might not only affect JA-homeostasis but also other signaling pathways. Deletion of CYP94B1, for example, led to accumulation of metabolites

  3. Identification, Characterization, and Functional Validation of Drought-responsive MicroRNAs in Subtropical Maize Inbreds

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    Jayaraman Aravind

    2017-06-01

    Full Text Available MicroRNA-mediated gene regulation plays a crucial role in controlling drought tolerance. In the present investigation, 13 drought-associated miRNA families consisting of 65 members and regulating 42 unique target mRNAs were identified from drought-associated microarray expression data in maize and were subjected to structural and functional characterization. The largest number of members (14 was found in the zma-miR166 and zma-miR395 families, with several targets. However, zma-miR160, zma-miR390, zma-miR393, and zma-miR2275 each showed a single target. Twenty-three major drought-responsive cis-regulatory elements were found in the upstream regions of miRNAs. Many drought-related transcription factors, such as GAMYB, HD-Zip III, and NAC, were associated with the target mRNAs. Furthermore, two contrasting subtropical maize genotypes (tolerant: HKI-1532 and sensitive: V-372 were used to understand the miRNA-assisted regulation of target mRNA under drought stress. Approximately 35 and 31% of miRNAs were up-regulated in HKI-1532 and V-372, respectively. The up-regulation of target mRNAs was as high as 14.2% in HKI-1532 but was only 2.38% in V-372. The expression patterns of miRNA-target mRNA pairs were classified into four different types: Type I- up-regulation, Type II- down-regulation, Type III- neutral regulation, and Type IV- opposite regulation. HKI-1532 displayed 46 Type I, 13 Type II, and 23 Type III patterns, whereas V-372 had mostly Type IV interactions (151. A low level of negative regulations of miRNA associated with a higher level of mRNA activity in the tolerant genotype helped to maintain crucial biological functions such as ABA signaling, the auxin response pathway, the light-responsive pathway and endosperm expression under stress conditions, thereby leading to drought tolerance. Our study identified candidate miRNAs and mRNAs operating in important pathways under drought stress conditions, and these candidates will be useful in the

  4. Identification of Functionally Distinct Na-HCO3 Co-Transporters in Colon

    Science.gov (United States)

    Barmeyer, Christian; Ye, Jeff Huaqing; Soroka, Carol; Geibel, Peter; Hingsammer, Lukas M.; Weitgasser, Laurence; Atway, Danny; Geibel, John P.; Binder, Henry J.; Rajendran, Vazhaikkurichi M.

    2013-01-01

    Na-HCO3 cotransport (NBC) regulates intracellular pH (pHi) and HCO3 secretion in rat colon. NBC has been characterized as a 5,5′-diisothiocyanato-2-2′-stilbene (DIDS)-sensitive transporter in several tissues, while the colonic NBC is sensitive to both amiloride and DIDS. In addition, the colonic NBC has been identified as critical for pHi regulation as it is activated by intravesicular acid pH. Molecular studies have identified several characteristically distinct NBC isoforms [i.e. electrogenic (NBCe) and electroneutral (NBCn)] that exhibit tissue specific expression. This study was initiated to establish the molecular identity and specific function of NBC isoforms in rat colon. Northern blot and reverse transcriptase PCR (RT-PCR) analyses revealed that electrogenic NBCe1B or NBCe1C (NBCe1B/C) isoform is predominantly expressed in proximal colon, while electroneutral NBCn1C or NBCn1D (NBCn1C/D) is expressed in both proximal and distal colon. Functional analyses revealed that amiloride-insensitive, electrogenic, pH gradient-dependent NBC activity is present only in basolateral membranes of proximal colon. In contrast, amiloride-sensitive, electroneutral, [H+]-dependent NBC activity is present in both proximal and distal colon. Both electrogenic and electroneutral NBC activities are saturable processes with an apparent Km for Na of 7.3 and 4.3 mM, respectively; and are DIDS-sensitive with apparent Ki of 8.9 and 263.8 µM, respectively. In addition to Na-H exchanger isoform-1 (NHE1), pHi acidification is regulated by a HCO3-dependent mechanism that is HOE694-insensitive in colonic crypt glands. We conclude from these data that electroneutral, amiloride-sensitive NBC is encoded by NBCn1C/D and is present in both proximal and distal colon, while NBCe1B/C encodes electrogenic, amiloride-insensitive Na-HCO3 cotransport in proximal colon. We also conclude that NBCn1C/D regulates HCO3-dependent HOE694-insensitive Na-HCO3 cotransport and plays a critical role in p

  5. CXCR4 Antagonists: A Screening Strategy for Identification of Functionally Selective Ligands.

    Science.gov (United States)

    Castaldo, C; Benicchi, T; Otrocka, M; Mori, E; Pilli, E; Ferruzzi, P; Valensin, S; Diamanti, D; Fecke, W; Varrone, M; Porcari, V

    2014-07-01

    The CXC chemokine receptor 4 (CXCR4) is a widely expressed G protein-coupled receptor implicated in several diseases. In cancer, an increased number of surface CXCR4 receptors, in parallel with aberrant signaling, have been reported to influence several aspects of malignancy progression. CXCR4 activation by the specific ligand C-X-C motif chemokine 12 (CXCL12) induces several intracellular signaling pathways that have been selectively related to malignancy depending on the tissue or cell type. We developed a panel of CXCR4 screening assays investigating Gα(i)-mediated cyclic adenosine monophosphate modulation, β-arrestin recruitment, and receptor internalization. All of the assays were set up in recombinant cells and were used to test four reported CXCR4 antagonists. Consequently, a set of hit compounds, deriving from a screening campaign of a 30,000-small-molecule internal library, was profiled with the different assays. We identified several compounds showing a pathway-selective activity: antagonists on a Gα(i)-dependent pathway; antagonists on both the β-arrestin and Gα(i)-dependent pathways, some of which induce receptor internalization; and compounds with an antagonist behavior in all of the readouts. The identified biased antagonists induce different functional states on CXCR4 and preferentially affect specific downstream responses from the activated receptor, thus providing an improved therapeutic profile for correction of CXCR4 abnormal signaling. © 2014 Society for Laboratory Automation and Screening.

  6. Identification of partial resetting using De as a function of illumination time

    International Nuclear Information System (INIS)

    Bailey, R.M.; Singarayer, J.S.; Ward, S.; Stokes, S.

    2003-01-01

    Modern age samples from various depositional environments were examined for signal resetting. For 19 modern aeolian/beach samples all D e values obtained were e e values were e as a function of illumination (OSL measurement) time (D e (t)) plots were examined for all samples. Based on previous laboratory experiments, increases in D e (t) were expected for partially reset samples, and constant D e (t) for fully reset samples. All aeolian samples, both modern age and additional 'young' samples ( e (t) while all modern, non-zero D e , fluvial/colluvial samples showed increasing D e (t). 'Replacement plots', where a regenerated signal is substituted for the natural, yielded constant (flat) D e (t). These findings support strongly the use of D e (t) as a method of identifying incomplete resetting in fluvial samples. Potential complicating factors, such as illumination (bleaching) spectrum, thermal instability and component composition are discussed and a series of internal checks on the applicability of the D e (t) for each individual aliquot/grain level are outlined

  7. Identification of lactaldehyde dehydrogenase and glycolaldehyde dehydrogenase as functions of the same protein in Escherichia coli.

    Science.gov (United States)

    Caballero, E; Baldomá, L; Ros, J; Boronat, A; Aguilar, J

    1983-06-25

    Lactaldehyde dehydrogenase is an enzyme involved in the aerobic metabolism of fucose in wild type Escherichia coli, and glycolaldehyde dehydrogenase is an enzyme involved in the metabolism of ethylene glycol in mutant cells able to utilize this glycol. Both enzyme sources display oxidative activity on either substrate with a constant ratio between these activities. We have found that both enzymatic activities present the same electrophoretic mobility when crude extracts were electrophoresed in polyacrylamide gels and the gels stained for enzyme activities. Furthermore, both enzymatic activities co-chromatograph in a DEAE-Sephadex column. If lactaldehyde dehydrogenase of wild type cells is purified near homogeneity and the purification procedure is screened for both aldehydes as substrates, only one enzyme is apparent, giving again a constant ratio between lactaldehyde and glycolaldehyde dehydrogenase activities. Genetic evidence of the fact that both activities are functions of the same protein is provided by the observation that mutation to thermosensitivity for the production of lactaldehyde dehydrogenase affected in the same way the production of glycolaldehyde dehydrogenase. Glycolaldehyde dehydrogenase from mutant cells is purified in a procedure coincident with the lactaldehyde dehydrogenase purification, yielding a single enzyme electrophoretically indistinguishable from the purified lactaldehyde dehydrogenase. Peptide mapping of the purified preparation after digestion with chymotrypsin or Staphylococcus aureus protease V8 gives an indistinguishable band pattern between both enzymes.

  8. Identification and characterisation of a novel acylpeptide hydrolase from Sulfolobus solfataricus: structural and functional insights.

    Directory of Open Access Journals (Sweden)

    Marta Gogliettino

    Full Text Available A novel acylpeptide hydrolase, named APEH-3(Ss, was isolated from the hypertermophilic archaeon Sulfolobus solfataricus. APEH is a member of the prolyl oligopeptidase family which catalyzes the removal of acetylated amino acid residues from the N terminus of oligopeptides. The purified enzyme shows a homotrimeric structure, unique among the associate partners of the APEH cluster and, in contrast to the archaeal APEHs which show both exo/endo peptidase activities, it appears to be a "true" aminopeptidase as exemplified by its mammalian counterparts, with which it shares a similar substrate specificity. Furthermore, a comparative study on the regulation of apeh gene expression, revealed a significant but divergent alteration in the expression pattern of apeh-3(Ss and apeh(Ss (the gene encoding the previously identified APEH(Ss from S. solfataricus, which is induced in response to various stressful growth conditions. Hence, both APEH enzymes can be defined as stress-regulated proteins which play a complementary role in enabling the survival of S. solfataricus cells under different conditions. These results provide new structural and functional insights into S. solfataricus APEH, offering a possible explanation for the multiplicity of this enzyme in Archaea.

  9. How the choice of safety performance function affects the identification of important crash prediction variables.

    Science.gov (United States)

    Wang, Ketong; Simandl, Jenna K; Porter, Michael D; Graettinger, Andrew J; Smith, Randy K

    2016-03-01

    Across the nation, researchers and transportation engineers are developing safety performance functions (SPFs) to predict crash rates and develop crash modification factors to improve traffic safety at roadway segments and intersections. Generalized linear models (GLMs), such as Poisson or negative binomial regression, are most commonly used to develop SPFs with annual average daily traffic as the primary roadway characteristic to predict crashes. However, while more complex to interpret, data mining models such as boosted regression trees have improved upon GLMs crash prediction performance due to their ability to handle more data characteristics, accommodate non-linearities, and include interaction effects between the characteristics. An intersection data inventory of 36 safety relevant parameters for three- and four-legged non-signalized intersections along state routes in Alabama was used to study the importance of intersection characteristics on crash rate and the interaction effects between key characteristics. Four different SPFs were investigated and compared: Poisson regression, negative binomial regression, regularized generalized linear model, and boosted regression trees. The models did not agree on which intersection characteristics were most related to the crash rate. The boosted regression tree model significantly outperformed the other models and identified several intersection characteristics as having strong interaction effects. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Identification of a novel function of CX-4945 as a splicing regulator.

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    Hyeongki Kim

    Full Text Available Alternative splicing is a nearly ubiquitous versatile process that controls gene expression and creates numerous protein isoforms with different functions from a single gene. The significance of alternative splicing has been confirmed by the increasing number of human diseases that are caused by misregulation of splicing events. Very few compounds, however, have been reported to act as inhibitors of alternative splicing, and their potential clinical use needs to be evaluated. Here, we report that CX-4945, a previously well-characterized inhibitor of casein kinase 2 (CK2 and a molecule currently in clinical trials (Phase II for cancer treatment, regulates splicing in mammalian cells in a CK2-independent manner. Transcriptome-wide analysis using exon array also showed a widespread alteration in alternative splicing of numerous genes. We found that CX-4945 potently inhibits the Cdc2-like kinases (Clks in vitro and in turn, leads to suppression of the phosphorylation of serine/arginine-rich (SR proteins in mammalian cells. Surprisingly, the overall efficacy of CX-4945 on Clks (IC50 = 3-90 nM was stronger than that of TG-003, the strongest inhibitor reported to date. Of the Clks, Clk2 was most strongly inhibited by CX-4945 in an ATP-competitive manner. Our research revealed an unexpected activity of the drug candidate CX-4945 as a potent splicing modulator and also suggested a potential application for therapy of diseases caused by abnormal splicing.

  11. Identification and functionality prediction of pathogenesis-related protein 1 from legume family.

    Science.gov (United States)

    Tellis, Meenakshi; Mathur, Monika; Gurjar, Gayatri; Kadoo, Narendra; Gupta, Vidya

    2017-11-01

    The production and accumulation of pathogenesis-related (PR) proteins in plants is one of the important responses to biotic and abiotic stress. Large number of identified PR proteins has been categorized into 17 functional families based on their structure, phylogenetics, and biological activities. However, they are not widely studied in legume crops. Using 29 PR1 proteins from Arabidopsis thaliana, as query, here we have predicted 92 candidate PR1 proteins through the PSI-BLAST and HMMER programs. These candidate proteins were comprehensively analyzed with, multiple sequence alignment, domain architecture studies, signal peptide, and motif extraction followed by phylogenetic analysis. Further, response of two candidate PR1 proteins from chickpea against Fusarium oxysporum f.sp.ciceri attack was validated using qRT-PCR followed by their 3D structure prediction. To decipher mode of action for PR1s, docking of pathogen extracellular matrix components along with fungal elicitors was performed with two chickpea PR1 proteins. Based on these findings, we propose carbohydrate to be the unique pathogen-recognition feature for PR1 proteins and β-glucanase activity via β-glucan binding or modification. © 2017 Wiley Periodicals, Inc.

  12. Identification of the first functional toxin-antitoxin system in Streptomyces.

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    Laura Sevillano

    Full Text Available Toxin-antitoxin (TA systems are widespread among the plasmids and genomes of bacteria and archaea. This work reports the first description of a functional TA system in Streptomyces that is identical in two species routinely used in the laboratory: Streptomyces lividans and S. coelicolor. The described system belongs to the YefM/YoeB family and has a considerable similarity to Escherichia coli YefM/YoeB (about 53% identity and 73% similarity. Lethal effect of the S. lividans putative toxin (YoeBsl was observed when expressed alone in E. coli SC36 (MG1655 ΔyefM-yoeB. However, no toxicity was obtained when co-expression of the antitoxin and toxin (YefM/YoeBsl was carried out. The toxic effect was also observed when the yoeBsl was cloned in multicopy in the wild-type S. lividans or in a single copy in a S. lividans mutant, in which this TA system had been deleted. The S. lividans YefM/YoeBsl complex, purified from E. coli, binds with high affinity to its own promoter region but not to other three random selected promoters from Streptomyces. In vivo experiments demonstrated that the expression of yoeBsl in E. coli blocks translation initiation processing mRNA at three bases downstream of the initiation codon after 2 minutes of induction. These results indicate that the mechanism of action is identical to that of YoeB from E. coli.

  13. Identification of Hydrochemical Function and Behavior of the Houzhai Karst Basin, Guizhou Province, Southwestern China

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    Xian Li

    2018-01-01

    Full Text Available Due to the difference of geomorphology and the development of fractures, the hydrochemical function and behavior appear to be complex. Variations of karst water conductivity can reflect the contribution of different runoff sources and thus indirectly reflect the development characteristics of conduits and fractures. Taking Houzhai karst system (southwestern China as a case study, the frequency distribution curves of karst water conductivity were decomposed by Gaussian Mixture Analysis to identify the runoff components of different karst landform. The dominant runoff types had been distinguished, and the relative contribution of the different water types had been investigated. The results showed that the karst flow types were slope flow, rapid fracture flow, and slow fracture flow. Rapid fracture flow was the major recharge type of Houzhai karst water system. Slow fracture flow in the downstream area accounted for a larger proportion than that of the upstream area. The relative contribution of the different runoff components showed that the upstream area was a rapid flow area of conduit structure with low storage capacity, the downstream area was an aquifer spatial structure of netted fissure conduit with high storage capacity, and the midstream area was a transitional zone between the upstream and downstream area.

  14. Identification of functionally important acidic residues in transducin by group-specific labeling

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    ANA KOSOY

    2003-01-01

    Full Text Available Transducin (T, a GTP-binding protein involved in phototransduction of rod photoreceptor cells, is a heterotrimer arranged as two units, the a-subunit (Ta and the bg-complex (Tbg. The role of the carboxyl groups in T was evaluated by labeling with N, N'-dicyclohexylcarbodiimide (DCCD and 1-ethyl 3-(3-dimethylaminopropyl carbodiimide (EDC. Only a minor effect on the binding of b, g-imido guanosine 5'-triphosphate (GMPpNp to T was observed in the presence of the hydrophobic carbodiimide, DCCD. Similarly, the GMPpNp binding activity of the reconstituted holoenzyme was not significantly affected when Ta was combined with DCCD-treated Tbg. However, the binding of guanine nucleotides to the reconstituted T was ~50% inhibited when DCCD-labeled Ta was incubated with Tbg. In contrast, treatment of T with the hydrophilic carbodiimide, EDC, completely impaired its GMPpNp-binding ability. EDC-modified T was incapable of interacting with illuminated rhodopsin, as determined by sedimentation experiments. However, rhodopsin only partially protected against the inactivation of T. Additionally, analyses of trypsin digestion patterns showed that fluoroaluminate was not capable of activating the EDC-labeled T sample. The function of the reconstituted holoenzyme was also disrupted when EDC-modified Ta was combined with Tbg, and when EDC-treated Tbg was incubated with Ta

  15. PKA regulates calcineurin function through the phosphorylation of RCAN1: Identification of a novel phosphorylation site

    International Nuclear Information System (INIS)

    Kim, Seon Sook; Lee, Eun Hye; Lee, Kooyeon; Jo, Su-Hyun; Seo, Su Ryeon

    2015-01-01

    Calcineurin is a calcium/calmodulin-dependent phosphatase that has been implicated in T cell activation through the induction of nuclear factors of activated T cells (NFAT). We have previously suggested that endogenous regulator of calcineurin (RCAN1, also known as DSCR1) is targeted by protein kinase A (PKA) for the control of calcineurin activity. In the present study, we characterized the PKA-mediated phosphorylation site in RCAN1 by mass spectrometric analysis and revealed that PKA directly phosphorylated RCAN1 at the Ser 93. PKA-induced phosphorylation and the increase in the half-life of the RCAN1 protein were prevented by the substitution of Ser 93 with Ala (S93A). Furthermore, the PKA-mediated phosphorylation of RCAN1 at Ser 93 potentiated the inhibition of calcineurin-dependent pro-inflammatory cytokine gene expression by RCAN1. Our results suggest the presence of a novel phosphorylation site in RCAN1 and that its phosphorylation influences calcineurin-dependent inflammatory target gene expression. - Highlights: • We identify novel phosphorylation sites in RCAN1 by LC-MS/MS analysis. • PKA-dependent phosphorylation of RCAN1 at Ser 93 inhibits calcineurin-mediated intracellular signaling. • We show the immunosuppressive function of RCAN1 phosphorylation at Ser 93 in suppressing cytokine expression

  16. Identification of a functional connectome for long-term fear memory in mice.

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    Anne L Wheeler

    Full Text Available Long-term memories are thought to depend upon the coordinated activation of a broad network of cortical and subcortical brain regions. However, the distributed nature of this representation has made it challenging to define the neural elements of the memory trace, and lesion and electrophysiological approaches provide only a narrow window into what is appreciated a much more global network. Here we used a global mapping approach to identify networks of brain regions activated following recall of long-term fear memories in mice. Analysis of Fos expression across 84 brain regions allowed us to identify regions that were co-active following memory recall. These analyses revealed that the functional organization of long-term fear memories depends on memory age and is altered in mutant mice that exhibit premature forgetting. Most importantly, these analyses indicate that long-term memory recall engages a network that has a distinct thalamic-hippocampal-cortical signature. This network is concurrently integrated and segregated and therefore has small-world properties, and contains hub-like regions in the prefrontal cortex and thalamus that may play privileged roles in memory expression.

  17. Surrogate-assisted identification of influences of network construction on evolving weighted functional networks

    Science.gov (United States)

    Stahn, Kirsten; Lehnertz, Klaus

    2017-12-01

    We aim at identifying factors that may affect the characteristics of evolving weighted networks derived from empirical observations. To this end, we employ various chains of analysis that are often used in field studies for a data-driven derivation and characterization of such networks. As an example, we consider fully connected, weighted functional brain networks before, during, and after epileptic seizures that we derive from multichannel electroencephalographic data recorded from epilepsy patients. For these evolving networks, we estimate clustering coefficient and average shortest path length in a time-resolved manner. Lastly, we make use of surrogate concepts that we apply at various levels of the chain of analysis to assess to what extent network characteristics are dominated by properties of the electroencephalographic recordings and/or the evolving weighted networks, which may be accessible more easily. We observe that characteristics are differently affected by the unavoidable referencing of the electroencephalographic recording, by the time-series-analysis technique used to derive the properties of network links, and whether or not networks were normalized. Importantly, for the majority of analysis settings, we observe temporal evolutions of network characteristics to merely reflect the temporal evolutions of mean interaction strengths. Such a property of the data may be accessible more easily, which would render the weighted network approach—as used here—as an overly complicated description of simple aspects of the data.

  18. Identification of a KCNE2 gain-of-function mutation in patients with familial atrial fibrillation

    DEFF Research Database (Denmark)

    Yang, Yiqing; Xia, Min; Jin, Qingfeng

    2004-01-01

    Atrial fibrillation (AF) is the most common cardiac arrhythmia encountered in clinical practice. We first reported an S140G mutation of KCNQ1, an alpha subunit of potassium channels, in one Chinese kindred with AF. However, the molecular defects and cellular mechanisms in most patients with AF...... remain to be identified. We evaluated 28 unrelated Chinese kindreds with AF and sequenced eight genes of potassium channels (KCNQ1, HERG, KCNE1, KCNE2, KCNE3, KCNE4, KCNE5, and KCNJ2). An arginine-to-cysteine mutation at position 27 (R27C) of KCNE2, the beta subunit of the KCNQ1-KCNE2 channel responsible...... for a background potassium current, was found in 2 of the 28 probands. The mutation was present in all affected members in the two kindreds and was absent in 462 healthy unrelated Chinese subjects. Similar to KCNQ1 S140G, the mutation had a gain-of-function effect on the KCNQ1-KCNE2 channel; unlike long QT...

  19. [HYGIENIC AND FUNCTIONAL AND PHYSIOLOGICAL APPROACHES IN THE IDENTIFICATION OF PRENOSOLOGICAL STATES IN STUDENTS].

    Science.gov (United States)

    Galeeva, M Yu

    2015-01-01

    The study of the risk for adverse changes assumes and is considered in the study in terms of the revealing of exertion of systems, particularly due to lengthiness of the process of formation of the "state" of health in young people. sanitatary--hygienic practice, medical statistical with in-depth study of individual health. There were obtained results in the field of physiology and hygiene. There were established with assigning the class working conditions actually affecting the levels of sanitation and hygiene, factors reflecting the factor load in educational institutions. There was revealed the general direction of the functional changes according to nosological forms, including in the comparison on different training profiles. The study of the morbidity rate, including the dynamics of individual health was supplemented with features of mechanisms of adaptation in students at different stages of the education. For students of radio engineering profile of training adaptation mechanisms were established at the level of exertion. The data of the paper are aimed at the improvement of the correction of the health status of students.

  20. Identification, Expression Patterns, and Functional Characterization of Chemosensory Proteins in Dendroctonus armandi (Coleoptera: Curculionidae: Scolytinae).

    Science.gov (United States)

    Li, Zhumei; Dai, Lulu; Chu, Honglong; Fu, Danyang; Sun, Yaya; Chen, Hui

    2018-01-01

    The Chinese white pine beetle, Dendroctonus armandi Tsai and Li (Coleoptera: Curculionidae: Scolytinae), is a serious pest of coniferous forests in China. Thus, there is considerable interest in developing eco-friendly pest-control methods, with the use of semiochemicals as a distinct possibility. Olfaction is extremely important for fitness of D. armandi because it is the primary mechanism through which the insect locates hosts and mates. Thus, here we characterized nine full-length genes encoding chemosensory proteins (CSPs) from D. armandi . The genes were ubiquitously and multiply expressed across different developmental stages and adult tissues, indicating various roles in developmental metamorphosis, olfaction, and gustation. Ligand-binding assays implied that DarmCSP2 may be the carrier of D. armandi pheromones and various plant host volatiles. These volatiles were identified through RNA interference of DarmCSP2 as: (+)-α-pinene, (+)-β-pinene, (-)-β-pinene, (+)-camphene, (+)-3-carene, and myrcene. The systematic chemosensory functional analysis of DarmCSP2 in this study clarified the molecular mechanisms underlying D. armandi olfaction and provided a theoretical foundation for eco-friendly pest control.

  1. Non-Gaussian Distributions Affect Identification of Expression Patterns, Functional Annotation, and Prospective Classification in Human Cancer Genomes

    Science.gov (United States)

    Marko, Nicholas F.; Weil, Robert J.

    2012-01-01

    Introduction Gene expression data is often assumed to be normally-distributed, but this assumption has not been tested rigorously. We investigate the distribution of expression data in human cancer genomes and study the implications of deviations from the normal distribution for translational molecular oncology research. Methods We conducted a central moments analysis of five cancer genomes and performed empiric distribution fitting to examine the true distribution of expression data both on the complete-experiment and on the individual-gene levels. We used a variety of parametric and nonparametric methods to test the effects of deviations from normality on gene calling, functional annotation, and prospective molecular classification using a sixth cancer genome. Results Central moments analyses reveal statistically-significant deviations from normality in all of the analyzed cancer genomes. We observe as much as 37% variability in gene calling, 39% variability in functional annotation, and 30% variability in prospective, molecular tumor subclassification associated with this effect. Conclusions Cancer gene expression profiles are not normally-distributed, either on the complete-experiment or on the individual-gene level. Instead, they exhibit complex, heavy-tailed distributions characterized by statistically-significant skewness and kurtosis. The non-Gaussian distribution of this data affects identification of differentially-expressed genes, functional annotation, and prospective molecular classification. These effects may be reduced in some circumstances, although not completely eliminated, by using nonparametric analytics. This analysis highlights two unreliable assumptions of translational cancer gene expression analysis: that “small” departures from normality in the expression data distributions are analytically-insignificant and that “robust” gene-calling algorithms can fully compensate for these effects. PMID:23118863

  2. Characterization and Functional Analysis of Five MADS-Box B Class Genes Related to Floral Organ Identification in Tagetes erecta.

    Directory of Open Access Journals (Sweden)

    Ye Ai

    Full Text Available According to the floral organ development ABC model, B class genes specify petal and stamen identification. In order to study the function of B class genes in flower development of Tagetes erecta, five MADS-box B class genes were identified and their expression and putative functions were studied. Sequence comparisons and phylogenetic analyses indicated that there were one PI-like gene-TePI, two euAP3-like genes-TeAP3-1 and TeAP3-2, and two TM6-like genes-TeTM6-1 and TeTM6-2 in T. erecta. Strong expression levels of these genes were detected in stamens of the disk florets, but little or no expression was detected in bracts, receptacles or vegetative organs. Yeast hybrid experiments of the B class proteins showed that TePI protein could form a homodimer and heterodimers with all the other four B class proteins TeAP3-1, TeAP3-2, TeTM6-1 and TeTM6-2. No homodimer or interaction was observed between the euAP3 and TM6 clade members. Over-expression of five B class genes of T. erecta in Nicotiana rotundifolia showed that only the transgenic plants of 35S::TePI showed altered floral morphology compared with the non-transgenic line. This study could contribute to the understanding of the function of B class genes in flower development of T. erecta, and provide a theoretical basis for further research to change floral organ structures and create new materials for plant breeding.

  3. AUTOMATION OF OPTIMAL IDENTIFICATION OF DYNAMIC ELEMENT TRANSFER FUNCTIONS IN COMPLEX TECHNICAL OBJECTS BASED ON ACCELERATION CURVES

    Directory of Open Access Journals (Sweden)

    A. Yu. Alikov

    2017-01-01

    Full Text Available Objectives. The aim of present paper is to minimise the errors in the approximation of experimentally obtained acceleration curves.Methods. Based on the features and disadvantages of the well-known Simoyu method for calculating transfer functions on the basis of acceleration curves, a modified version of the method is developed using the MathLab and MathCad software. This is based on minimising the sum of the squares of the experimental point deviations from the solution of the differential equation at the same points.Results. Methods for the implementation of parametric identification are analysed and the Simoyu method is chosen as the most effective. On the basis of the analysis of its advantages and disadvantages, a modified method is proposed that allows the structure and parameters of the transfer function to be identified according to the experimental acceleration curve, as well as the choice of optimal numerical values of those parameters obtained for minimising errors in the approximation of the experimentally obtained acceleration curves.Conclusion. The problem of optimal control over a complex technical facility was solved. On the basis of the modified Simoyu method, an algorithm for the automated selection of the optimal shape and calculation of transfer function parameters of dynamic elements of complex technical objects according to the acceleration curves in the impact channels was developed. This has allowed the calculation efficiency of the dynamic characteristics of control objects to be increased by minimising the approximation errors. The efficiency of the proposed calculation method is shown. Its simplicity makes it possible to apply to practical calculations, especially for use in the design of complex technical objects within the framework of the computer aided design system. The proposed method makes it possible to increase the accuracy of the approximation by at least 20%, which is an important advantage for its practical

  4. Equine cytochrome P450 2B6 — Genomic identification, expression and functional characterization with ketamine

    Energy Technology Data Exchange (ETDEWEB)

    Peters, L.M.; Demmel, S. [Division Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University Bern, Laenggassstr. 124, 3012 Bern (Switzerland); Pusch, G.; Buters, J.T.M. [ZAUM — Center of Allergy and Environment, Helmholtz Zentrum München/Technische Universität München, Biedersteiner Str. 29, 80802 München (Germany); Thormann, W. [Clinical Pharmacology Laboratory, Institute for Infectious Diseases, University of Bern, Murtenstrasse 35, 3010 Bern (Switzerland); Zielinski, J. [Division Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University Bern, Laenggassstr. 124, 3012 Bern (Switzerland); Leeb, T. [Institute of Genetics, Vetsuisse Faculty, University Bern, Bremgartenstr. 109, 3012 Bern (Switzerland); Mevissen, M. [Division Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University Bern, Laenggassstr. 124, 3012 Bern (Switzerland); Schmitz, A., E-mail: andrea.schmitz@vetsuisse.unibe.ch [Division Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University Bern, Laenggassstr. 124, 3012 Bern (Switzerland)

    2013-01-01

    Ketamine is an anesthetic and analgesic regularly used in veterinary patients. As ketamine is almost always administered in combination with other drugs, interactions between ketamine and other drugs bear the risk of either adverse effects or diminished efficacy. Since cytochrome P450 enzymes (CYPs) play a pivotal role in the phase I metabolism of the majority of all marketed drugs, drug–drug interactions often occur at the active site of these enzymes. CYPs have been thoroughly examined in humans and laboratory animals, but little is known about equine CYPs. The characterization of equine CYPs is essential for a better understanding of drug metabolism in horses. We report annotation, cloning and heterologous expression of the equine CYP2B6 in V79 Chinese hamster fibroblasts. After computational annotation of all CYP2B genes, the coding sequence (CDS) of equine CYP2B6 was amplified by RT-PCR from horse liver total RNA and revealed an amino acid sequence identity of 77% and a similarity of 93.7% to its human ortholog. A non-synonymous variant c.226G>A in exon 2 of the equine CYP2B6 was detected in 97 horses. The mutant A-allele showed an allele frequency of 82%. Two further variants in exon 3 were detected in one and two horses of this group, respectively. Transfected V79 cells were incubated with racemic ketamine and norketamine as probe substrates to determine metabolic activity. The recombinant equine CYP2B6 N-demethylated ketamine to norketamine and produced metabolites of norketamine, such as hydroxylated norketamines and 5,6-dehydronorketamine. V{sub max} for S-/and R-norketamine formation was 0.49 and 0.45 nmol/h/mg cellular protein and K{sub m} was 3.41 and 2.66 μM, respectively. The N-demethylation of S-/R-ketamine was inhibited concentration-dependently with clopidogrel showing an IC{sub 50} of 5.63 and 6.26 μM, respectively. The functional importance of the recorded genetic variants remains to be explored. Equine CYP2B6 was determined to be a CYP

  5. Identification of Histone Deacetylase 2 as a Functional Gene for Skeletal Muscle Development in Chickens

    Directory of Open Access Journals (Sweden)

    Md. Shahjahan

    2016-04-01

    Full Text Available A previous genome-wide association study (GWAS exposed histone deacetylase 2 (HDAC2 as a possible candidate gene for breast muscle weight in chickens. The present research has examined the possible role of HDAC2 in skeletal muscle development in chickens. Gene expression was measured by quantitative polymerase chain reaction in breast and thigh muscles during both embryonic (four ages and post-hatch (five ages development and in cultures of primary myoblasts during both proliferation and differentiation. The expression of HDAC2 increased significantly across embryonic days (ED in breast (ED 14, 16, 18, and 21 and thigh (ED 14 and 18, and ED 14 and 21 muscles suggesting that it possibly plays a role in myoblast hyperplasia in both breast and thigh muscles. Transcript abundance of HDAC2 identified significantly higher in fast growing muscle than slow growing in chickens at d 90 of age. Expression of HDAC2 during myoblast proliferation in vitro declined between 24 h and 48 h when expression of the marker gene paired box 7 (PAX7 increased and cell numbers increased throughout 72 h of culture. During induced differentiation of myoblasts to myotubes, the abundance of HDAC2 and the marker gene myogenic differentiation 1 (MYOD1, both increased significantly. Taken together, it is suggested that HDAC2 is most likely involved in a suppressive fashion in myoblast proliferation and may play a positive role in myoblast differentiation. The present results confirm the suggestion that HDAC2 is a functional gene for pre-hatch and post-hatch (fast growing muscle development of chicken skeletal muscle.

  6. Identification of a functional, CRM-1-dependent nuclear export signal in hepatitis C virus core protein.

    Science.gov (United States)

    Cerutti, Andrea; Maillard, Patrick; Minisini, Rosalba; Vidalain, Pierre-Olivier; Roohvand, Farzin; Pecheur, Eve-Isabelle; Pirisi, Mario; Budkowska, Agata

    2011-01-01

    Hepatitis C virus (HCV) infection is a major cause of chronic liver disease worldwide. HCV core protein is involved in nucleocapsid formation, but it also interacts with multiple cytoplasmic and nuclear molecules and plays a crucial role in the development of liver disease and hepatocarcinogenesis. The core protein is found mostly in the cytoplasm during HCV infection, but also in the nucleus in patients with hepatocarcinoma and in core-transgenic mice. HCV core contains nuclear localization signals (NLS), but no nuclear export signal (NES) has yet been identified.We show here that the aa(109-133) region directs the translocation of core from the nucleus to the cytoplasm by the CRM-1-mediated nuclear export pathway. Mutagenesis of the three hydrophobic residues (L119, I123 and L126) in the identified NES or in the sequence encoding the mature core aa(1-173) significantly enhanced the nuclear localisation of the corresponding proteins in transfected Huh7 cells. Both the NES and the adjacent hydrophobic sequence in domain II of core were required to maintain the core protein or its fragments in the cytoplasmic compartment. Electron microscopy studies of the JFH1 replication model demonstrated that core was translocated into the nucleus a few minutes after the virus entered the cell. The blockade of nucleocytoplasmic export by leptomycin B treatment early in infection led to the detection of core protein in the nucleus by confocal microscopy and coincided with a decrease in virus replication.Our data suggest that the functional NLS and NES direct HCV core protein shuttling between the cytoplasmic and nuclear compartments, with at least some core protein transported to the nucleus. These new properties of HCV core may be essential for virus multiplication and interaction with nuclear molecules, influence cell signaling and the pathogenesis of HCV infection.

  7. Remodeling Pearson's Correlation for Functional Brain Network Estimation and Autism Spectrum Disorder Identification

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    Weikai Li

    2017-08-01

    Full Text Available Functional brain network (FBN has been becoming an increasingly important way to model the statistical dependence among neural time courses of brain, and provides effective imaging biomarkers for diagnosis of some neurological or psychological disorders. Currently, Pearson's Correlation (PC is the simplest and most widely-used method in constructing FBNs. Despite its advantages in statistical meaning and calculated performance, the PC tends to result in a FBN with dense connections. Therefore, in practice, the PC-based FBN needs to be sparsified by removing weak (potential noisy connections. However, such a scheme depends on a hard-threshold without enough flexibility. Different from this traditional strategy, in this paper, we propose a new approach for estimating FBNs by remodeling PC as an optimization problem, which provides a way to incorporate biological/physical priors into the FBNs. In particular, we introduce an L1-norm regularizer into the optimization model for obtaining a sparse solution. Compared with the hard-threshold scheme, the proposed framework gives an elegant mathematical formulation for sparsifying PC-based networks. More importantly, it provides a platform to encode other biological/physical priors into the PC-based FBNs. To further illustrate the flexibility of the proposed method, we extend the model to a weighted counterpart for learning both sparse and scale-free networks, and then conduct experiments to identify autism spectrum disorders (ASD from normal controls (NC based on the constructed FBNs. Consequently, we achieved an 81.52% classification accuracy which outperforms the baseline and state-of-the-art methods.

  8. Identification and functional activity of a staphylocoagulase type XI variant originating from staphylococcal food poisoning isolates.

    Science.gov (United States)

    Suzuki, Y; Matsushita, S; Kubota, H; Kobayashi, M; Murauchi, K; Higuchi, Y; Kato, R; Hirai, A; Sadamasu, K

    2016-09-01

    Staphylocoagulase, an extracellular protein secreted by Staphylococcus aureus, has been used as an epidemiological marker. At least 12 serotypes and 24 genotypes subdivided on the basis of nucleotide sequence have been reported to date. In this study, we identified a novel staphylocoagulase nucleotide sequence, coa310, from staphylococcal food poisoning isolates that had the ability to coagulate plasma, but could not be typed using the conventional method. The protein encoded by coa310 contained the six fundamental conserved domains of staphylocoagulase. The full-length nucleotide sequence of coa310 shared the highest similarity (77·5%) with that of staphylocoagulase-type (SCT) XIa. The sequence of the D1 region, which would be responsible for the determination of SCT, shared the highest similarity (91·8%) with that of SCT XIa. These results suggest that coa310 is a novel variant of SCT XI. Moreover, we demonstrated that coa310 encodes a functioning coagulase, by confirming the coagulating activity of the recombinant protein expressed from coa310. This is the first study to directly demonstrate that Coa310, a putative SCT XI, has coagulating activity. These findings may be useful for the improvement of the staphylocoagulase-typing method, including serotyping and genotyping. This is the first study to identify a novel variant of staphylocoagulase type XI based on its nucleotide sequence and to demonstrate coagulating activity in the variant using a recombinant protein. Elucidation of the variety of staphylocoagulases will provide suggestions for further improvement of the staphylocoagulase-typing method and contribute to our understanding of the epidemiologic characterization of Staphylococcus aureus. © 2016 The Society for Applied Microbiology.

  9. Functional Identification and Characterization of Genes Cloned from Halophyte Seashore Paspalum Conferring Salinity and Cadmium Tolerance

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    Yu eChen

    2016-02-01

    Full Text Available Salinity-affected and heavy metal-contaminated soils limit the growth of glycophytic plants. Identifying genes responsible for superior tolerance to salinity and heavy metals in halophytes has great potential for use in developing salinity- and Cd-tolerant glycophytes. The objective of this study was to identify salinity- and Cd-tolerance related genes in seashore paspalum (Paspalum vaginatum, a halophytic perennial grass species, using the yeast cDNA expression library screening method. Based on the Gateway-compatible vector system, a high quality entry library was constructed, which contained 9.9×106 clones with an average inserted fragments length of 1.48 kb representing a 100% full-length rate. The yeast expression libraries were screened in a salinity-sensitive and a Cd-sensitive yeast mutant. The screening yielded 32 salinity-tolerant clones harboring 18 salinity-tolerance genes and 20 Cd-tolerant clones, including 5 Cd-tolerance genes. qPCR analysis confirmed that most of the 18 salinity-tolerance and 5 Cd-tolerance genes were up-regulated at the transcript level in response to salinity or Cd stress in seashore paspalum. Functional analysis indicated that salinity-tolerance genes from seashore paspalum could be mainly involved in photosynthetic metabolism, antioxidant systems, protein modification, iron transport, vesicle traffic, and phospholipid biosynthesis. Cd-tolerance genes from seashore paspalum could be associated with regulating pathways involved in phytochelatin synthesis, HSFA4-relsted stress protection, CYP450 complex and sugar metabolism. The 18 salinity-tolerance genes and 5 Cd-tolerance genes could be potentially used as candidate genes for genetic modification of glycophytic grass species to improve salinity and Cd tolerance and for further analysis of molecular mechanisms regulating salinity and Cd tolerance.

  10. Functional Identification and Characterization of Genes Cloned from Halophyte Seashore Paspalum Conferring Salinity and Cadmium Tolerance.

    Science.gov (United States)

    Chen, Yu; Chen, Chuanming; Tan, Zhiqun; Liu, Jun; Zhuang, Lili; Yang, Zhimin; Huang, Bingru

    2016-01-01

    Salinity-affected and heavy metal-contaminated soils limit the growth of glycophytic plants. Identifying genes responsible for superior tolerance to salinity and heavy metals in halophytes has great potential for use in developing salinity- and Cd-tolerant glycophytes. The objective of this study was to identify salinity- and Cd-tolerance related genes in seashore paspalum (Paspalum vaginatum), a halophytic perennial grass species, using yeast cDNA expression library screening method. Based on the Gateway-compatible vector system, a high-quality entry library was constructed, which contained 9.9 × 10(6) clones with an average inserted fragment length of 1.48 kb representing a 100% full-length rate. The yeast expression libraries were screened in a salinity-sensitive and a Cd-sensitive yeast mutant. The screening yielded 32 salinity-tolerant clones harboring 18 salinity-tolerance genes and 20 Cd-tolerant clones, including five Cd-tolerance genes. qPCR analysis confirmed that most of the 18 salinity-tolerance and five Cd-tolerance genes were up-regulated at the transcript level in response to salinity or Cd stress in seashore paspalum. Functional analysis indicated that salinity-tolerance genes from seashore paspalum could be involved mainly in photosynthetic metabolism, antioxidant systems, protein modification, iron transport, vesicle traffic, and phospholipid biosynthesis. Cd-tolerance genes could be associated with regulating pathways that are involved in phytochelatin synthesis, HSFA4-related stress protection, CYP450 complex, and sugar metabolism. The 18 salinity-tolerance genes and five Cd-tolerance genes could be potentially used as candidate genes for genetic modification of glycophytic grass species to improve salinity and Cd tolerance and for further analysis of molecular mechanisms regulating salinity and Cd tolerance.

  11. Identification of functional DNA variants in the constitutive promoter region of MDM2

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    Lalonde Marie-Eve

    2012-09-01

    Full Text Available Abstract Although mutations in the oncoprotein murine double minute 2 (MDM2 are rare, MDM2 gene overexpression has been observed in several human tumors. Given that even modest changes in MDM2 levels might influence the p53 tumor suppressor signaling pathway, we postulated that sequence variation in the promoter region of MDM2 could lead to disregulated expression and variation in gene dosage. Two promoters have been reported for MDM2; an internal promoter (P2, which is located near the end of intron 1 and is p53-responsive, and an upstream constitutive promoter (P1, which is p53-independent. Both promoter regions contain DNA variants that could influence the expression levels of MDM2, including the well-studied single nucleotide polymorphism (SNP SNP309, which is located in the promoter P2; i.e., upstream of exon 2. In this report, we screened the promoter P1 for DNA variants and assessed the functional impact of the corresponding SNPs. Using the dbSNP database and genotyping validation in individuals of European descent, we identified three common SNPs (−1494 G > A; indel 40 bp; and −182 C > G. Three major promoter haplotypes were inferred by using these three promoter SNPs together with rs2279744 (SNP309. Following subcloning into a gene reporter system, we found that two of the haplotypes significantly influenced MDM2 promoter activity in a haplotype-specific manner. Site-directed mutagenesis experiments indicated that the 40 bp insertion/deletion variation is causing the observed allelic promoter activity. This study suggests that part of the variability in the MDM2 expression levels could be explained by allelic p53-independent P1 promoter activity.

  12. Identification and functional characterization of an uncharacterized antimicrobial peptide from a ciliate Paramecium caudatum.

    Science.gov (United States)

    Cui, Pengfei; Dong, Yuan; Li, Zhijian; Zhang, Yubo; Zhang, Shicui

    2016-07-01

    The global ever-growing concerns about multi-drug resistant (MDR) microbes leads to urgent demands for exploration of new antibiotics including antimicrobial peptides (AMPs). Here we demonstrated that a cDNA from Ciliata Paramecium caudatum, designated Pcamp1, coded for a protein with features characteristic of AMPs, which is not homologous to any AMPs currently known. Both the C-terminal 91 amino acid residues of PcAMP1, cPcAMP1, expressed in Escherichia coli and the C-terminal 26 amino acid residues (predicted mature AMP), cPcAMP1/26, synthesized, underwent a coil-to-helix transition in the presence of TFE, SDS or DPC. Functional assays revealed that cPcAMP1 and cPcAMP1/26 were both able to kill Aeromonas hydrophila and Staphylococcus aureus. ELISA showed that cPcAMP1 and cPcAMP1/26 were able to bind to microbe-associated molecular pattern molecules LPS and LTA, which was further corroborated by the observations that cPcAMP1 could deposit onto the bacterial membranes. Importantly, both cPcAMP1 and cPcAMP1/26 were able to induce bacterial membrane permeabilization and depolarization, and to increase intracellular ROS levels. Additionally, cPcAMP1 and cPcAMP1/26 were not cytotoxic to mammalian cells. Taken together, our results show that PcAMP1 is a potential AMP with a membrane selectivity towards bacterial cells, which renders it a promising template for the design of novel peptide antibiotics against MDR microbes. It also shows that use of signal conserved sequence of AMPs can be an effective tool to identify potential AMPs across different animal classes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Multiple functions of CREB-binding protein during postembryonic development: identification of target genes.

    Science.gov (United States)

    Roy, Amit; George, Smitha; Palli, Subba Reddy

    2017-12-29

    Juvenile hormones (JH) and ecdysteroids control postembryonic development in insects. They serve as valuable targets for pest management. Hence, understanding the molecular mechanisms of their action is of crucial importance. CREB-binding protein (CBP) is a universal transcriptional co-regulator. It controls the expression of several genes including those from hormone signaling pathways through co-activation of many transcription factors. However, the role of CBP during postembryonic development in insects is not well understood. Therefore, we have studied the role of CBP in postembryonic development in Tribolium, a model coleopteran insect. CBP is ubiquitously expressed in the red flour beetle, Tribolium castaneum. RNA interference (RNAi) mediated knockdown of CBP resulted in a decrease in JH induction of Kr-h1 gene expression in Tribolium larvae and led to a block in their development. Moreover, the injection of CBP double-stranded RNA (dsRNA) showed lethal phenotypes within 8 days of injection. RNA-seq and subsequent differential gene expression analysis identified CBP target genes in Tribolium. Knockdown of CBP caused a decrease in the expression of 1306 genes coding for transcription factors and other proteins associated with growth and development. Depletion of CBP impaired the expression of several JH response genes (e.g., Kr-h1, Hairy, early trypsin) and ecdysone response genes (EcR, E74, E75, and broad complex). Further, GO enrichment analyses of the downregulated genes showed enrichment in different functions including developmental processes, pigmentation, anatomical structure development, regulation of biological and cellular processes, etc. These data suggest diverse but crucial roles for CBP during postembryonic development in the coleopteran model insect, Tribolium. It can serve as a target for RNAi mediated pest management of this stored product pest.

  14. Molecular cloning, functional identification and expressional analyses of FasL in Tilapia, Oreochromis niloticus.

    Science.gov (United States)

    Ma, Tai-yang; Wu, Jin-ying; Gao, Xiao-ke; Wang, Jing-yuan; Zhan, Xu-liang; Li, Wen-sheng

    2014-10-01

    FasL is the most extensively studied apoptosis ligand. In 2000, tilapia FasL was identified using anti-human FasL monoclonal antibody by Evans's research group. Recently, a tilapia FasL-like protein of smaller molecule weight was predicted in Genbank (XM_003445156.2). Based on several clues drawn from previous studies, we cast doubt on the authenticity of the formerly identified tilapia FasL. Conversely, using reverse transcription polymerase chain reaction (RT-PCR), the existence of the predicted FasL-like was verified at the mRNA level (The Genbank accession number of the FasL mRNA sequence we cloned is KM008610). Through multiple alignments, this FasL-like protein was found to be highly similar to the FasL of the Japanese flounder. Moreover, we artificially expressed the functional region of the predicted protein and later confirmed its apoptosis-inducing activity using a methyl thiazolyl tetrazolium (MTT) assay, Annexin-V/Propidium iodide (PI) double staining, and DNA fragment detection. Supported by these evidences, we suggest that the predicted protein is the authentic tilapia FasL. To advance this research further, tilapia FasL mRNA and its protein across different tissues were quantified. High expression levels were identified in the tilapia immune system and sites where active cell turnover conservatively occurs. In this regard, FasL may assume an active role in the immune system and cell homeostasis maintenance in tilapia, similar to that shown in other species. In addition, because the distribution pattern of FasL mRNA did not synchronize with that of the protein, post-transcriptional expression regulation is suggested. Such regulation may be dominated by potential adenylate- and uridylate-rich elements (AREs) featuring AUUUA repeats found in the 3' untranslated region (UTR) of tilapia FasL mRNA. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Functional identification of the input-output transforms of mammalian motoneurones.

    Science.gov (United States)

    Binder, M D; Poliakov, A V; Powers, R K

    1999-01-01

    transform could be predicted from the mean firing rate and the linear impulse response, yielding a relatively simple, general description of the motoneurone's input-output function.

  16. Identification of a functional, CRM-1-dependent nuclear export signal in hepatitis C virus core protein.

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    Andrea Cerutti

    Full Text Available Hepatitis C virus (HCV infection is a major cause of chronic liver disease worldwide. HCV core protein is involved in nucleocapsid formation, but it also interacts with multiple cytoplasmic and nuclear molecules and plays a crucial role in the development of liver disease and hepatocarcinogenesis. The core protein is found mostly in the cytoplasm during HCV infection, but also in the nucleus in patients with hepatocarcinoma and in core-transgenic mice. HCV core contains nuclear localization signals (NLS, but no nuclear export signal (NES has yet been identified.We show here that the aa(109-133 region directs the translocation of core from the nucleus to the cytoplasm by the CRM-1-mediated nuclear export pathway. Mutagenesis of the three hydrophobic residues (L119, I123 and L126 in the identified NES or in the sequence encoding the mature core aa(1-173 significantly enhanced the nuclear localisation of the corresponding proteins in transfected Huh7 cells. Both the NES and the adjacent hydrophobic sequence in domain II of core were required to maintain the core protein or its fragments in the cytoplasmic compartment. Electron microscopy studies of the JFH1 replication model demonstrated that core was translocated into the nucleus a few minutes after the virus entered the cell. The blockade of nucleocytoplasmic export by leptomycin B treatment early in infection led to the detection of core protein in the nucleus by confocal microscopy and coincided with a decrease in virus replication.Our data suggest that the functional NLS and NES direct HCV core protein shuttling between the cytoplasmic and nuclear compartments, with at least some core protein transported to the nucleus. These new properties of HCV core may be essential for virus multiplication and interaction with nuclear molecules, influence cell signaling and the pathogenesis of HCV infection.

  17. Identification of functional peptides from natural and synthetic products on their anticancer activities by tumor targeting.

    Science.gov (United States)

    Ko, Joshua K; Auyeung, Kathy K

    2014-01-01

    Cancer cells can express specific membrane proteins, which act as biomarkers for chemotherapeutic targeting. Functional peptides possess unique properties that will ensure efficacy, selectivity, specificity and low toxicity when used as therapeutic agents. Therapeutic peptides have been derived in treatment of cancers through improvement of cellular uptake, drug targeting and vaccine development. Peptides from natural source have been used for chemoprevention and therapy of various cancers. These include peptides derived from food, marine products, venom components and other animal constituents. Besides, chemically- and recombinantly-synthesized peptides have also been produced and extensively studied in contemporary applications. Improvement of tumor targeting is essential for chemotherapeutic development. This can be achieved through enhancement of intracellular delivery and/or increased specific binding affinity to cancer cells by pore-forming and cytotoxic peptides. Cytotoxic peptides such as the Bcl-2 family members can induce receptor-specific binding to tumor cells and promote apoptosis by targeting lipid membranes. This approach has some limitations in targeting, penetration and localization within tumors. Cell-penetrating peptides (CPPs) belong to a new class of tumor-targeting peptides that can facilitate internalization of tumor markers and/or chemotherapeutic drugs. In order to overcome the problem of serum instability in classical CPPs (e.g. Tat), newer classes of CPPs has been recently introduced. Nevertheless, some cyclized CPPs can further enhance cellular uptake and binding selectivity when compared to activities of their linear counterpart, especially when treating chemoresistant tumors. This review compiles the use of effective tumor-targeting peptides including novel CPPs that represents new therapeutic strategies for the treatment of cancers.

  18. Functional identification of HugZ, a heme oxygenase from Helicobacter pylori

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    Xiao Bin

    2008-12-01

    Full Text Available Abstract Background Iron is recognized as an important trace element, essential for most organisms including pathogenic bacteria. HugZ, a protein related to heme iron utilization, is involved in bacterial acquisition of iron from the host. We previously observed that a hugZ homologue is correlated with the adaptive colonization of Helicobacter pylori (H. pylori, a major gastro-enteric pathogen. However, its exact physiological role remains unclear. Results A gene homologous to hugZ, designated hp0318, identified in H. pylori ATCC 26695, exhibits 66% similarity to cj1613c of Campylobacter jejuni NCTC 11168. Soluble 6 × His fused-HugZ protein was expressed in vitro. Hemin-agrose affinity analysis indicated that the recombinant HugZ protein can bind to hemin. Absorption spectroscopy at 411 nm further revealed a heme:HugZ binding ratio of 1:1. Enzymatic assays showed that purified recombinant HugZ protein can degrade hemin into biliverdin and carbon monoxide in the presence of either ascorbic acid or NADPH and cytochrome P450 reductase. The biochemical and enzymatic characteristics agreed closely with those of Campylobacter jejuni Cj1613c protein, implying that hp0318 is a functional member of the HugZ family. A hugZ deletion mutant was obtained by homologous recombination. This mutant strain showed poor growth when hemoglobin was provided as the source of iron, partly because of its failure to utilize hemoglobin efficiently. Real-time quantitative PCR also confirmed that the expression of hugZ was regulated by iron levels. Conclusion These findings provide biochemical and genetic evidence that hugZ (hp0318 encodes a heme oxygenase involved in iron release/uptake in H. pylori.

  19. Functionalization of nanotextured substrates for enhanced identification of metastatic breast cancer cells

    Science.gov (United States)

    Mansur, Nuzhat; Raziul Hasan, Mohammad; Kim, Young-tae; Iqbal, Samir M.

    2017-09-01

    Metastasis is the major cause of low survival rates among cancer patients. Once cancer cells metastasize, it is extremely difficult to contain the disease. We report on a nanotextured platform for enhanced detection of metastatic cells. We captured metastatic (MDA-MDB-231) and non-metastatic (MCF-7) breast cancer cells on anti-EGFR aptamer modified plane and nanotextured substrates. Metastatic cells were seen to change their morphology at higher rates when captured on nanotextured substrates than on plane substrates. Analysis showed statistically different morphological behaviors of metastatic cells that were very pronounced on the nanotextured substrates. Several distance matrices were calculated to quantify the dissimilarity of cell shape change. Nanotexturing increased the dissimilarity of the metastatic cells and as a result the contrast between metastatic and non-metastatic cells increased. Jaccard distance measurements found that the shape change ratio of the non-metastatic and metastatic cells was enhanced from 1:1.01 to 1:1.81, going from plane to nanotextured substrates. The shape change ratio of the non-metastatic to metastatic cells improved from 1:1.48 to 1:2.19 for the Hausdorff distance and from 1:1.87 to 1:4.69 for the Mahalanobis distance after introducing nanotexture. Distance matrix analysis showed that nanotexture increased the shape change ratios of non-metastatic and metastatic cells. Hence, the detectability of metastatic cells increased. These calculated matrices provided clear and explicit measures to discriminate single cells for their metastatic state on functional nanotextured substrates.

  20. Fusobacterium nucleatum-associated beta-defensin inducer (FAD-I): identification, isolation, and functional evaluation.

    Science.gov (United States)

    Gupta, Sanhita; Ghosh, Santosh K; Scott, Mary E; Bainbridge, Brian; Jiang, Bin; Lamont, Richard J; McCormick, Thomas S; Weinberg, Aaron

    2010-11-19

    Human β-defensins (hBDs) are small, cationic antimicrobial peptides, secreted by mucosal epithelial cells that regulate adaptive immune functions. We previously reported that Fusobacterium nucleatum, a ubiquitous gram-negative bacterium of the human oral cavity, induces human β-defensin 2 (hBD2) upon contact with primary oral epithelial cells. We now report the isolation and characterization of an F. nucleatum (ATCC 25586)-associated defensin inducer (FAD-I). Biochemical approaches revealed a cell wall fraction containing four proteins that stimulated the production of hBD2 in human oral epithelial cells (HOECs). Cross-referencing of the N-terminal sequences of these proteins with the F. nucleatum genome revealed that the genes encoding the proteins were FadA, FN1527, FN1529, and FN1792. Quantitative PCR of HOEC monolayers challenged with Escherichia coli clones expressing the respective cell wall proteins revealed that FN1527 was most active in the induction of hBD2 and hence was termed FAD-I. We tagged FN1527 with a c-myc epitope on the C-terminal end to identify and purify it from the E. coli clone. Purified FN1527 (FAD-I) induced hBD2 mRNA and protein expression in HOEC monolayers. F. nucleatum cell wall and FAD-I induced hBD2 via TLR2. Porphorymonas gingivalis, an oral pathogen that does not induce hBD2 in HOECs, was able to significantly induce expression of hBD2 in HOECs only when transformed to express FAD-I. FAD-I or its derivates offer a potentially new paradigm in immunoregulatory therapeutics because they may one day be used to bolster the innate defenses of vulnerable mucosae.

  1. Functional Identification of Dendritic Cells in the Teleost Model, Rainbow Trout (Oncorhynchus mykiss)

    Science.gov (United States)

    Bassity, Elizabeth; Clark, Theodore G.

    2012-01-01

    Dendritic cells are specialized antigen presenting cells that bridge innate and adaptive immunity in mammals. This link between the ancient innate immune system and the more evolutionarily recent adaptive immune system is of particular interest in fish, the oldest vertebrates to have both innate and adaptive immunity. It is unknown whether dendritic cells co-evolved with the adaptive response, or if the connection between innate and adaptive immunity relied on a fundamentally different cell type early in evolution. We approached this question using the teleost model organism, rainbow trout (Oncorhynchus mykiss), with the aim of identifying dendritic cells based on their ability to stimulate naïve T cells. Adapting mammalian protocols for the generation of dendritic cells, we established a method of culturing highly motile, non-adherent cells from trout hematopoietic tissue that had irregular membrane processes and expressed surface MHCII. When side-by-side mixed leukocyte reactions were performed, these cells stimulated greater proliferation than B cells or macrophages, demonstrating their specialized ability to present antigen and therefore their functional homology to mammalian dendritic cells. Trout dendritic cells were then further analyzed to determine if they exhibited other features of mammalian dendritic cells. Trout dendritic cells were found to have many of the hallmarks of mammalian DCs including tree-like morphology, the expression of dendritic cell markers, the ability to phagocytose small particles, activation by toll-like receptor-ligands, and the ability to migrate in vivo. As in mammals, trout dendritic cells could be isolated directly from the spleen, or larger numbers could be derived from hematopoietic tissue and peripheral blood mononuclear cells in vitro. PMID:22427987

  2. Infection of Bacterial Endosymbionts in Insects: A Comparative Study of Two Techniques viz PCR and FISH for Detection and Localization of Symbionts in Whitefly, Bemisia tabaci.

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    Harpreet Singh Raina

    Full Text Available Bacterial endosymbionts have been associated with arthropods and large number of the insect species show interaction with such bacteria. Different approaches have been used to understand such symbiont- host interactions. The whitefly, Bemisia tabaci, a highly invasive agricultural pest, harbors as many as seven different bacterial endosymbionts. These bacterial endosymbionts are known to provide various nutritional, physiological, environmental and evolutionary benefits to its insect host. In this study, we have tried to compare two techniques, Polymerase chain reaction (PCR and Flourescence in situ Hybridisation (FISH commonly used for identification and localization of bacterial endosymbionts in B. tabaci as it harbors one of the highest numbers of endosymbionts which have helped it in becoming a successful global invasive agricultural pest. The amplified PCR products were observed as bands on agarose gel by electrophoresis while the FISH samples were mounted on slides and observed under confocal microscope. Analysis of results obtained by these two techniques revealed the advantages of FISH over PCR. On a short note, performing FISH, using LNA probes proved to be more sensitive and informative for identification as well as localization of bacterial endosymbionts in B. tabaci than relying on PCR. This study would help in designing more efficient experiments based on much reliable detection procedure and studying the role of endosymbionts in insects.

  3. Effects of long-term starvation on a host bivalve (Codakia orbicularis, Lucinidae) and its symbiont population.

    Science.gov (United States)

    Caro, Audrey; Got, Patrice; Bouvy, Marc; Troussellier, Marc; Gros, Olivier

    2009-05-01

    The bivalve Codakia orbicularis, hosting sulfur-oxidizing gill endosymbionts, was starved (in artificial seawater filtered through a 0.22-mum-pore-size membrane) for a long-term experiment (4 months). The effects of starvation were observed using transmission electron microscopy, fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH), and flow cytometry to monitor the anatomical and physiological modifications in the gill organization of the host and in the symbiotic population housed in bacteriocytes. The abundance of the symbiotic population decreased through starvation, with a loss of one-third of the bacterial population each month, as shown by CARD-FISH. At the same time, flow cytometry revealed significant changes in the physiology of symbiotic cells, with a decrease in cell size and modifications to the nucleic acid content, while most of the symbionts maintained a high respiratory activity (measured using the 5-cyano-2,3-ditolyl tetrazolium chloride method). Progressively, the number of symbiont subpopulations was reduced, and the subsequent multigenomic state, characteristic of this symbiont in freshly collected clams, turned into one and five equivalent genome copies for the two remaining subpopulations after 3 months. Concomitant structural modifications appeared in the gill organization. Lysosymes became visible in the bacteriocytes, while large symbionts disappeared, and bacteriocytes were gradually replaced by granule cells throughout the entire lateral zone. Those data suggested that host survival under these starvation conditions was linked to symbiont digestion as the main nutritional source.

  4. A nonnative and a native fungal plant pathogen similarly stimulate ectomycorrhizal development but are perceived differently by a fungal symbiont.

    Science.gov (United States)

    Zampieri, Elisa; Giordano, Luana; Lione, Guglielmo; Vizzini, Alfredo; Sillo, Fabiano; Balestrini, Raffaella; Gonthier, Paolo

    2017-03-01

    The effects of plant symbionts on host defence responses against pathogens have been extensively documented, but little is known about the impact of pathogens on the symbiosis and if such an impact may differ for nonnative and native pathogens. Here, this issue was addressed in a study of the model system comprising Pinus pinea, its ectomycorrhizal symbiont Tuber borchii, and the nonnative and native pathogens Heterobasidion irregulare and Heterobasidion annosum, respectively. In a 6-month inoculation experiment and using both in planta and gene expression analyses, we tested the hypothesis that H. irregulare has greater effects on the symbiosis than H. annosum. Although the two pathogens induced the same morphological reaction in the plant-symbiont complex, with mycorrhizal density increasing exponentially with pathogen colonization of the host, the number of target genes regulated in T. borchii in plants inoculated with the native pathogen (i.e. 67% of tested genes) was more than twice that in plants inoculated with the nonnative pathogen (i.e. 27% of genes). Although the two fungal pathogens did not differentially affect the amount of ectomycorrhizas, the fungal symbiont perceived their presence differently. The results may suggest that the symbiont has the ability to recognize a self/native and a nonself/nonnative pathogen, probably through host plant-mediated signal transduction. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  5. Experimental evolution of parasitoid infectivity on symbiont-protected hosts leads to the emergence of genotype specificity.

    Science.gov (United States)

    Rouchet, Romain; Vorburger, Christoph

    2014-06-01

    Host-parasitoid interactions may lead to strong reciprocal selection for traits involved in host defense and parasitoid counterdefense. In aphids, individuals harboring the facultative bacterial endosymbiont, Hamiltonella defensa, exhibit enhanced resistance to parasitoid wasps. We used an experimental evolution approach to investigate the ability of the parasitoid wasp, Lysiphlebus fabarum, to adapt to the presence of H. defensa in its aphid host Aphis fabae. Sexual populations of the parasitoid were exposed for 11 generations to a single clone of A. fabae, either free of H. defensa or harboring artificial infections with three different isolates of H. defensa. Parasitoids adapted rapidly to the presence of H. defensa in their hosts, but this adaptation was in part specific to the symbiont isolate they were evolving against and did not result in an improved infectivity on all symbiont-protected hosts. Comparisons of life-history traits among the evolved lines of parasitoids did not reveal any evidence for costs of adaptation to H. defensa in terms of correlated responses that could constrain such adaptation. These results show that parasitoids readily evolve counter-adaptations to heritable defensive symbionts of their hosts, but that different symbiont strains impose different evolutionary challenges. The symbionts thus mediate the host-parasite interaction by inducing line-by-line genetic specificity. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  6. Deep learning analysis of the myocardium in coronary CT angiography for identification of patients with functionally significant coronary artery stenosis.

    Science.gov (United States)

    Zreik, Majd; Lessmann, Nikolas; van Hamersvelt, Robbert W; Wolterink, Jelmer M; Voskuil, Michiel; Viergever, Max A; Leiner, Tim; Išgum, Ivana

    2018-02-01

    In patients with coronary artery stenoses of intermediate severity, the functional significance needs to be determined. Fractional flow reserve (FFR) measurement, performed during invasive coronary angiography (ICA), is most often used in clinical practice. To reduce the number of ICA procedures, we present a method for automatic identification of patients with functionally significant coronary artery stenoses, employing deep learning analysis of the left ventricle (LV) myocardium in rest coronary CT angiography (CCTA). The study includes consecutively acquired CCTA scans of 166 patients who underwent invasive FFR measurements. To identify patients with a functionally significant coronary artery stenosis, analysis is performed in several stages. First, the LV myocardium is segmented using a multiscale convolutional neural network (CNN). To characterize the segmented LV myocardium, it is subsequently encoded using unsupervised convolutional autoencoder (CAE). As ischemic changes are expected to appear locally, the LV myocardium is divided into a number of spatially connected clusters, and statistics of the encodings are computed as features. Thereafter, patients are classified according to the presence of functionally significant stenosis using an SVM classifier based on the extracted features. Quantitative evaluation of LV myocardium segmentation in 20 images resulted in an average Dice coefficient of 0.91 and an average mean absolute distance between the segmented and reference LV boundaries of 0.7 mm. Twenty CCTA images were used to train the LV myocardium encoder. Classification of patients was evaluated in the remaining 126 CCTA scans in 50 10-fold cross-validation experiments and resulted in an area under the receiver operating characteristic curve of 0.74 ± 0.02. At sensitivity levels 0.60, 0.70 and 0.80, the corresponding specificity was 0.77, 0.71 and 0.59, respectively. The results demonstrate that automatic analysis of the LV myocardium in a single

  7. Identification and functional characterization of multiple interleukin 12 in amberjack (Seriola dumerili).

    Science.gov (United States)

    Matsumoto, Megumi; Hayashi, Kazuma; Suetake, Hiroaki; Yamamoto, Atsushi; Araki, Kyosuke

    2016-08-01

    Interleukin (IL) -12 is a heterodimeric cytokine mainly produced by monocytes, macrophages, and dendritic cells in mammals. IL-12p70 composed of IL-12p35 and IL-12p40, is known to play a crucial role in promoting cell-mediated immunity (CMI) through Th1 differentiation and IFN-γ production. Although two types of IL-12p35 (p35a, p35b) and three types of IL-12p40 (p40a, p40b and p40c) have been identified in several fish species, the knowledge on functional characteristics of teleost IL-12 is still limited. In the present study, we cloned two types of IL-12p35 and three types of IL-12p40 genes in amberjack and yellowtail, and analyzed their expressions in response to stimulation with Nocardia seriolae in amberjack. As a result, four types of IL-12 (IL-12p35a, p35b, p40a and p40b) and IFN-γ mRNA were increased by live-N. seriolae stimulation but not by formalin-killed N. seriolae, suggesting that four types of IL-12 (p35, p35b, p40a and p40c) participate in promoting CMI. Subsequently, we produced six types of recombinant IL-12p70 (rIL12p70) protein in insect cells. Head kidney leukocytes were cultured with formalin-killed N. seriolae and six types of rIL-12p70 to elucidate the role of amberjack IL-12p70 in induction of CMI. After stimulation, IFN-γ expression was elevated whereas IL-10 expression was suppressed in Head kidney leukocytes stimulated with four types of rIL-12 (p40a/p35a, p40c/p35a, p40a/p35b, p40a/p35b). On the other hand, two types of rIL-12 (p40b/p35a, p40b/p35b) only elicited down regulation of IL-10 expression. These results indicate that all amberjack IL-12p70 isoforms are involved in Th1 -differentiation and promotion of CMI with different manners. Fish IL-12 has a potential for the promising vaccine adjuvant. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Identification, Expression, and Functional Analysis of the Fructokinase Gene Family in Cassava

    Directory of Open Access Journals (Sweden)

    Yuan Yao

    2017-11-01

    Full Text Available Fructokinase (FRK proteins play important roles in catalyzing fructose phosphorylation and participate in the carbohydrate metabolism of storage organs in plants. To investigate the roles of FRKs in cassava tuber root development, seven FRK genes (MeFRK1–7 were identified, and MeFRK1–6 were isolated. Phylogenetic analysis revealed that the MeFRK family genes can be divided into α (MeFRK 1, 2, 6, 7 and β (MeFRK 3, 4, 5 groups. All the MeFRK proteins have typical conserved regions and substrate binding residues similar to those of the FRKs. The overall predicted three-dimensional structures of MeFRK1–6 were similar, folding into a catalytic domain and a β-sheet ‘‘lid” region, forming a substrate binding cleft, which contains many residues involved in the binding to fructose. The gene and the predicted three-dimensional structures of MeFRK3 and MeFRK4 were the most similar. MeFRK1–6 displayed different expression patterns across different tissues, including leaves, stems, tuber roots, flowers, and fruits. In tuber roots, the expressions of MeFRK3 and MeFRK4 were much higher compared to those of the other genes. Notably, the expression of MeFRK3 and MeFRK4 as well as the enzymatic activity of FRK were higher at the initial and early expanding tuber stages and were lower at the later expanding and mature tuber stages. The FRK activity of MeFRK3 and MeFRK4 was identified by the functional complementation of triple mutant yeast cells that were unable to phosphorylate either glucose or fructose. The gene expression and enzymatic activity of MeFRK3 and MeFRK4 suggest that they might be the main enzymes in fructose phosphorylation for regulating the formation of tuber roots and starch accumulation at the tuber root initial and expanding stages.

  9. Functional Identification and Structure Determination of Two Novel Prolidases from cog1228 in the Amidohydrolase Superfamily

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, Dao Feng; Patskovsky, Yury; Xu, Chengfu; Fedorov, Alexander A.; Fedorov, Elena V.; Sisco, Abby A.; Sauder, J. Michael; Burley, Stephen K.; Almo, Steven C.; Raushel, Frank M. (Einstein); (TAM); (Lilly)

    2010-12-07

    Two uncharacterized enzymes from the amidohydrolase superfamily belonging to cog1228 were cloned, expressed, and purified to homogeneity. The two proteins, Sgx9260c (gi|44242006) and Sgx9260b (gi|44479596), were derived from environmental DNA samples originating from the Sargasso Sea. The catalytic function and substrate profiles for Sgx9260c and Sgx9260b were determined using a comprehensive library of dipeptides and N-acyl derivative of L-amino acids. Sgx9260c catalyzes the hydrolysis of Gly-L-Pro, L-Ala-L-Pro, and N-acyl derivatives of L-Pro. The best substrate identified to date is N-acetyl-L-Pro with a value of k{sub cat}/K{sub m} of 3 x 10{sup 5} M{sup -1} s{sup -1}. Sgx9260b catalyzes the hydrolysis of L-hydrophobic L-Pro dipeptides and N-acyl derivatives of L-Pro. The best substrate identified to date is N-propionyl-L-Pro with a value of k{sub cat}/K{sub m} of 1 x 10{sup 5} M{sup -1} s{sup -1}. Three-dimensional structures of both proteins were determined by X-ray diffraction methods (PDB codes 3MKV and 3FEQ). These proteins fold as distorted ({beta}/{alpha})8-barrels with two divalent cations in the active site. The structure of Sgx9260c was also determined as a complex with the N-methylphosphonate derivative of L-Pro (PDB code 3N2C). In this structure the phosphonate moiety bridges the binuclear metal center, and one oxygen atom interacts with His-140. The {alpha}-carboxylate of the inhibitor interacts with Tyr-231. The proline side chain occupies a small substrate binding cavity formed by residues contributed from the loop that follows {beta}-strand 7 within the ({beta}/{alpha})8-barrel. A total of 38 other proteins from cog1228 are predicted to have the same substrate profile based on conservation of the substrate binding residues. The structure of an evolutionarily related protein, Cc2672 from Caulobacter crecentus, was determined as a complex with the N-methylphosphonate derivative of L-arginine (PDB code 3MTW).

  10. Functional identification of the input-output transforms of motoneurones in the rat and cat.

    Science.gov (United States)

    Poliakov, A V; Powers, R K; Binder, M D

    1997-10-15

    associated PSTH. This linear model provided good matches to the PSTHs associated with a wide range of current transients. However, for the largest amplitude current transients, a significant improvement in the PSTH match was often achieved by expanding the model to include the convolution of the second-order Wiener kernel with the input. 4. The overall transformation of current inputs into firing rate could be approximated by a second-order Wiener model, i.e. a cascade of a dynamic, linear filter followed by a static non-linearity. At a given mean firing rate, the non-linear component of the response of the motoneurone could be described by the square of the linear component multiplied by a constant coefficient. The amplitude of the response of the linear component increased with the average firing rate, whereas the value of the multiplicative coefficient in the non-linear component decreased. As a result, the overall transform could be predicted from the mean firing rate and the linear impulse response, yielding a relatively simple, general description of the motoneurone input-output function.

  11. Identification of novel genes affecting mesoderm formation and morphogenesis through an enhanced large scale functional screen in Xenopus.

    Science.gov (United States)

    Chen, Jun-An; Voigt, Jana; Gilchrist, Mike; Papalopulu, Nancy; Amaya, Enrique

    2005-03-01

    The formation of mesoderm is an important developmental process of vertebrate embryos, which can be broken down into several steps; mesoderm induction, patterning, morphogenesis and differentiation. Although mesoderm formation in Xenopus has been intensively studied, much remains to be learned about the molecular events responsible for each of these steps. Furthermore, the interplay between mesoderm induction, patterning and morphogenesis remains obscure. Here, we describe an enhanced functional screen in Xenopus designed for large-scale identification of genes controlling mesoderm formation. In order to improve the efficiency of the screen, we used a Xenopus tropicalis unique set of cDNAs, highly enriched in full-length clones. The screening strategy incorporates two mesodermal markers, Xbra and Xmyf-5, to assay for cell fate specification and patterning, respectively. In addition we looked for phenotypes that would suggest effects in morphogenesis, such as gastrulation defects and shortened anterior-posterior axis. Out of 1728 full-length clones we isolated 82 for their ability to alter the phenotype of tadpoles and/or the expression of Xbra and Xmyf-5. Many of the clones gave rise to similar misexpression phenotypes (synphenotypes) and many of the genes within each synphenotype group appeared to be involved in similar pathways. We determined the expression pattern of the 82 genes and found that most of the genes were regionalized and expressed in mesoderm. We expect that many of the genes identified in this screen will be important in mesoderm formation.

  12. Identification of calcium-dependent protein kinase (CDPK): A multi-functional gene family in Rafflesia cantleyi

    Science.gov (United States)

    Amini, Safoora; Goh, Hoe-Han; Wan, Kiew-Lian

    2016-11-01

    Rafflesia, a parasitic plant that belongs to the Rafflesiaceae family, is notable for producing the largest flowers in the world. This study focused on identification of Calcium-dependent protein kinases (CDPKs) due to their vital roles in plant growth and development, biotic and abiotic stress responses, and hormone signaling. RNA-seq data generated from three bud stages of Rafflesia cantleyi ie BS1, BS2, and BS3 and were assembled. Based on the BLAST searches of Rafflesia unique transcripts (UTs) to Arabidopsis TAIR database, a total of 14 unique transcripts (UTs) were identified as CDPK1 to CDPK5, CDPK7 to CDPK11, CDPK16, CDPK18, CDPK19, and CDPK28. These genes are expressed at all three bud stages of R. cantleyi with up-regulation pattern at BS1 vs. BS2 and BS2 vs. BS3. This result shows that the expression of CDPK gene family increases by developmental progress in Rafflesia in order to regulate biochemical and molecular changes at the cellular level in response to exposure to environmental changes. However, CDPKs functions in plants growth and defense process still need more experimental evidence to deeply understand their biological roles in R. cantleyi.

  13. In Silico Identification for α-Amino-ε-Caprolactam Racemases by Using Information on the Structure and Function Relationship.

    Science.gov (United States)

    Payoungkiattikun, Wisarut; Okazaki, Seiji; Nakano, Shogo; Ina, Atsutoshi; H-Kittikun, Aran; Asano, Yasuhisa

    2015-07-01

    In silico identification for enzymes having desired functions is attractive because there is a possibility that numerous desirable enzymes have been deposited in databases. In this study, α-amino-ε-caprolactam (ACL) racemases were searched from the NCBI protein database. Four hundred thirteen fold-type I pyridoxal 5'-phosphate-dependent enzymes which are considered to contain sequences of ACL racemase were firstly obtained by submitting the sequence of ACL racemase from Achromobacter obae to the database. By identifying Lys241 as a key amino acid residue, 13 candidates for ACL racemase were selected. Then, putative ACL racemase genes were synthesized as codon-optimized sequences for expression in Escherichia coli. They were subcloned and expressed in E. coli BL21 and underwent His-tag purification. ACL and amino acid amide racemizing activities were detected among ten of the candidates. The locus tags Oant_4493, Smed_5339, and CSE45_2055 derived from Ochrobactrum anthropi ATCC49188, Sinorhizobium medicae WSM 419, and Citreicella sp. SE45, respectively, showed higher racemization activity against D- and L-ACLs rather than that of ACL racemase from A. obae. Our results demonstrate that the newly discovered ACL racemases were unique from ACL racemase from A. obae and might be useful for applications in dynamic kinetic resolution for D- or L-amino acid production.

  14. Identification of two aflatrem biosynthesis gene loci in Aspergillus flavus and metabolic engineering of Penicillium paxilli to elucidate their function.

    Science.gov (United States)

    Nicholson, Matthew J; Koulman, Albert; Monahan, Brendon J; Pritchard, Beth L; Payne, Gary A; Scott, Barry

    2009-12-01

    Aflatrem is a potent tremorgenic toxin produced by the soil fungus Aspergillus flavus, and a member of a structurally diverse group of fungal secondary metabolites known as indole-diterpenes. Gene clusters for indole-diterpene biosynthesis have recently been described in several species of filamentous fungi. A search of Aspergillus complete genome sequence data identified putative aflatrem gene clusters in the genomes of A. flavus and Aspergillus oryzae. In both species the genes for aflatrem biosynthesis cluster at two discrete loci; the first, ATM1, is telomere proximal on chromosome 5 and contains a cluster of three genes, atmG, atmC, and atmM, and the second, ATM2, is telomere distal on chromosome 7 and contains five genes, atmD, atmQ, atmB, atmA, and atmP. Reverse transcriptase PCR in A. flavus demonstrated that aflatrem biosynthesis transcript levels increased with the onset of aflatrem production. Transfer of atmP and atmQ into Penicillium paxilli paxP and paxQ deletion mutants, known to accumulate paxilline intermediates paspaline and 13-desoxypaxilline, respectively, showed that AtmP is a functional homolog of PaxP and that AtmQ utilizes 13-desoxypaxilline as a substrate to synthesize aflatrem pathway-specific intermediates, paspalicine and paspalinine. We propose a scheme for aflatrem biosynthesis in A. flavus based on these reconstitution experiments in P. paxilli and identification of putative intermediates in wild-type cultures of A. flavus.

  15. Identification of abnormal motor cortex activation patterns in children with cerebral palsy by functional near-infrared spectroscopy

    Science.gov (United States)

    Khan, Bilal; Tian, Fenghua; Behbehani, Khosrow; Romero, Mario I.; Delgado, Mauricio R.; Clegg, Nancy J.; Smith, Linsley; Reid, Dahlia; Liu, Hanli; Alexandrakis, George

    2010-05-01

    We demonstrate the utility of functional near-infrared spectroscopy (fNIRS) as a tool for physicians to study cortical plasticity in children with cerebral palsy (CP). Motor cortex activation patterns were studied in five healthy children and five children with CP (8.4+/-2.3 years old in both groups) performing a finger-tapping protocol. Spatial (distance from center and area difference) and temporal (duration and time-to-peak) image metrics are proposed as potential biomarkers for differentiating abnormal cortical activation in children with CP from healthy pediatric controls. In addition, a similarity image-analysis concept is presented that unveils areas that have similar activation patterns as that of the maximum activation area, but are not discernible by visual inspection of standard activation images. Metrics derived from the images presenting areas of similarity are shown to be sensitive identifiers of abnormal activation patterns in children with CP. Importantly, the proposed similarity concept and related metrics may be applicable to other studies for the identification of cortical activation patterns by fNIRS.

  16. Identification and typization of bacteria of the genus Enterococcus supposed to be used for the production of functional foods

    Directory of Open Access Journals (Sweden)

    Radka Burdychová

    2007-01-01

    Full Text Available In this study, the species identification of 12 probiotic strains of the genus Enterococcus from Culture Collection of Dairy Microorganisms Lactoflora (CCDM, Milcom, Tábor, Czech Republic were done using PCR described by DUTKA-MALEN et al. (1995. All strains were classified to be of the genus Enterococcus and species E. faecium. These strains are supposed to be used as probiotics for the production of functional foods. According to the fact that E. faecium was described to have decarboxylase activity responsible for biogenic amine production in fermented products, the presence of genes coding for microbial tyrosine and histidine decarboxylase was screened in all strains using PCR described by COTON et al. (2004. Whereas the presence of DNA sequences for histidine decarboxylase was not detected in any strain, specific DNA sequences coding for tyrosine decarboxylases were detected in all tested strains. When applying as starter probiotic cultures to fermented milk products, the production of biogenic amine tyramine have to be observed during both fermentation and storage.

  17. Identification, structure, and function of a novel type VI secretion peptidoglycan glycoside hydrolase effector-immunity pair.

    Science.gov (United States)

    Whitney, John C; Chou, Seemay; Russell, Alistair B; Biboy, Jacob; Gardiner, Taylor E; Ferrin, Michael A; Brittnacher, Mitchell; Vollmer, Waldemar; Mougous, Joseph D

    2013-09-13

    Bacteria employ type VI secretion systems (T6SSs) to facilitate interactions with prokaryotic and eukaryotic cells. Despite the widespread identification of T6SSs among Gram-negative bacteria, the number of experimentally validated substrate effector proteins mediating these interactions remains small. Here, employing an informatics approach, we define novel families of T6S peptidoglycan glycoside hydrolase effectors. Consistent with the known intercellular self-intoxication exhibited by the T6S pathway, we observe that each effector gene is located adjacent to a hypothetical open reading frame encoding a putative periplasmically localized immunity determinant. To validate our sequence-based approach, we functionally investigate a representative family member from the soil-dwelling bacterium Pseudomonas protegens. We demonstrate that this protein is secreted in a T6SS-dependent manner and that it confers a fitness advantage in growth competition assays with Pseudomonas putida. In addition, we determined the 1.4 Å x-ray crystal structure of this effector in complex with its cognate immunity protein. The structure reveals the effector shares highest overall structural similarity to a glycoside hydrolase family associated with peptidoglycan N-acetylglucosaminidase activity, suggesting that T6S peptidoglycan glycoside hydrolase effector families may comprise significant enzymatic diversity. Our structural analyses also demonstrate that self-intoxication is prevented by the immunity protein through direct occlusion of the effector active site. This work significantly expands our current understanding of T6S effector diversity.

  18. Identification, Structure, and Function of a Novel Type VI Secretion Peptidoglycan Glycoside Hydrolase Effector-Immunity Pair*

    Science.gov (United States)

    Whitney, John C.; Chou, Seemay; Russell, Alistair B.; Biboy, Jacob; Gardiner, Taylor E.; Ferrin, Michael A.; Brittnacher, Mitchell; Vollmer, Waldemar; Mougous, Joseph D.

    2013-01-01

    Bacteria employ type VI secretion systems (T6SSs) to facilitate interactions with prokaryotic and eukaryotic cells. Despite the widespread identification of T6SSs among Gram-negative bacteria, the number of experimentally validated substrate effector proteins mediating these interactions remains small. Here, employing an informatics approach, we define novel families of T6S peptidoglycan glycoside hydrolase effectors. Consistent with the known intercellular self-intoxication exhibited by the T6S pathway, we observe that each effector gene is located adjacent to a hypothetical open reading frame encoding a putative periplasmically localized immunity determinant. To validate our sequence-based approach, we functionally investigate a representative family member from the soil-dwelling bacterium Pseudomonas protegens. We demonstrate that this protein is secreted in a T6SS-dependent manner and that it confers a fitness advantage in growth competition assays with Pseudomonas putida. In addition, we determined the 1.4 Å x-ray crystal structure of this effector in complex with its cognate immunity protein. The structure reveals the effector shares highest overall structural similarity to a glycoside hydrolase family associated with peptidoglycan N-acetylglucosaminidase activity, suggesting that T6S peptidoglycan glycoside hydrolase effector families may comprise significant enzymatic diversity. Our structural analyses also demonstrate that self-intoxication is prevented by the immunity protein through direct occlusion of the effector active site. This work significantly expands our current understanding of T6S effector diversity. PMID:23878199

  19. Enhanced identification and functional protective role of carbon nanoparticles on parathyroid in thyroid cancer surgery: A retrospective Chinese population study.

    Science.gov (United States)

    Shi, Chenlei; Tian, Bo; Li, Shengze; Shi, Tiefeng; Qin, Huadong; Liu, Shaoyan

    2016-11-01

    The aim of this study was to determine the effects of nanocarbon particles in combination with meticulous capsular dissection on enhancing the identification and protecting the function of parathyroid glands in thyroid cancer surgery.The data of 97 patients with papillary thyroid tumors diagnosed and treated at the Second Affiliated Hospital, Harbin Medical University between January 2014 and February 2015 were reviewed. Data regarding the sex, age, calcium and parathyroid hormone (PTH) levels, tumor size, multifocality, T stage, and extrathyroid invasion were collected. The incidence of surgeries in which the parathyroid glands were cut mistakenly, the concentration of serum calcium and parathyroid hormone before surgery (baseline) and after surgery on days 1, 3, and 7, and 1 and 6 months in the patients of the two groups (the nanocarbon and control groups) were analyzed.Fifty-two patients underwent meticulous capsular dissection combined with nanocarbon treatment (nanocarbon group), and 45 underwent meticulous capsular dissection alone (control group). The nanocarbon group showed a significantly higher total and average number of revealed parathyroid glands (average number is the mean for different individuals have different number) and a lower incidence of the parathyroid glands being mistakenly cut, in addition to a lower level of hypoparathyroidism than control group following surgery (P parathyroid in thyroid cancer surgery, reduce the risk of mistakenly cutting the parathyroid, and reduce the incidence of postoperative hypoparathyroidism.

  20. Relative symbiont input and the lichen symbiotic outcome.

    Science.gov (United States)

    Spribille, Toby

    2018-03-09

    The term symbiosis was first used in biology to describe the 'living together' of fungi and algae in lichens. For much of the 20th century, the fungal partner was assumed to be invested with the ability to produce the lichen body plan in presence of a photosynthesizing partner. However, studies of fungal evolution have uncovered discordance between lichen symbiotic outcomes and genome evolution of the fungus. At the same time, evidence has emerged that the structurally important lichen cortex contains lichen-specific, single-celled microbes, suggesting it may function like a biofilm. Together, these observations suggest we may not have a complete overview of symbiotic interactions in lichens. Understanding phenotype development and evolution in lichens will require greater insight into fungal-fungal and fungal-bacterial interplay and the physical properties of the cortex. Copyright © 2018 Elsevier Ltd. All rights reserved.

  1. Human Gut Symbiont Roseburia hominis Promotes and Regulates Innate Immunity

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    Angela M. Patterson

    2017-09-01

    Full Text Available ObjectiveRoseburia hominis is a flagellated gut anaerobic bacterium belonging to the Lachnospiraceae family within the Firmicutes phylum. A significant decrease of R. hominis colonization in the gut of ulcerative colitis patients has recently been demonstrated. In this work, we have investigated the mechanisms of R. hominis–host cross talk using both murine and in vitro models.DesignThe complete genome sequence of R. hominis A2-183 was determined. C3H/HeN germ-free mice were mono-colonized with R. hominis, and the host–microbe interaction was studied using histology, transcriptome analyses and FACS. Further investigations were performed in vitro and using the TLR5KO and DSS-colitis murine models.ResultsIn the bacterium, R. hominis, host gut colonization upregulated genes involved in conjugation/mobilization, metabolism, motility, and chemotaxis. In the host cells, bacterial colonization upregulated genes related to antimicrobial peptides, gut barrier function, toll-like receptors (TLR signaling, and T cell biology. CD4+CD25+FoxP3+ T cell numbers increased in the lamina propria of both mono-associated and conventional mice treated with R. hominis. Treatment with the R. hominis bacterium provided protection against DSS-induced colitis. The role of flagellin in host–bacterium interaction was also investigated.ConclusionMono-association of mice with R. hominis bacteria results in specific bidirectional gene expression patterns. A set of genes thought to be important for host colonization are induced in R. hominis, while the host cells respond by strengthening gut barrier function and enhancing Treg population expansion, possibly via TLR5-flagellin signaling. Our data reveal the immunomodulatory properties of R. hominis that could be useful for the control and treatment of gut inflammation.

  2. Candidatus Dactylopiibacterium carminicum, a Nitrogen-Fixing Symbiont of Dactylopius Cochineal Insects (Hemiptera: Coccoidea: Dactylopiidae)

    Science.gov (United States)

    Vera-Ponce de León, Arturo; Ormeño-Orrillo, Ernesto; Ramírez-Puebla, Shamayim T.; Rosenblueth, Mónica; Degli Esposti, Mauro; Martínez-Romero, Julio

    2017-01-01

    Abstract The domesticated carmine cochineal Dactylopius coccus (scale insect) has commercial value and has been used for more than 500 years for natural red pigment production. Besides the domesticated cochineal, other wild Dactylopius species such as Dactylopius opuntiae are found in the Americas, all feeding on nutrient poor sap from native cacti. To compensate nutritional deficiencies, many insects harbor symbiotic bacteria which provide essential amino acids or vitamins to their hosts. Here, we characterized a symbiont from the carmine cochineal insects, Candidatus Dactylopiibacterium carminicum (betaproteobacterium, Rhodocyclaceae family) and found it in D. coccus and in D. opuntiae ovaries by fluorescent in situ hybridization, suggesting maternal inheritance. Bacterial genomes recovered from metagenomic data derived from whole insects or tissues both from D. coccus and from D. opuntiae were around 3.6 Mb in size. Phylogenomics showed that dactylopiibacteria constituted a closely related clade neighbor to nitrogen fixing bacteria from soil or from various plants including rice and other grass endophytes. Metabolic capabilities were inferred from genomic analyses, showing a complete operon for nitrogen fixation, biosynthesis of amino acids and vitamins and putative traits of anaerobic or microoxic metabolism as well as genes for plant interaction. Dactylopiibacterium nif gene expression and acetylene reduction activity detecting nitrogen fixation were evidenced in D. coccus hemolymph and ovaries, in congruence with the endosymbiont fluorescent in situ hybridization location. Dactylopiibacterium symbionts may compensate for the nitrogen deficiency in the cochineal diet. In addition, this symbiont may provide essential amino acids, recycle uric acid, and increase the cochineal life span.

  3. Rapid evolution of symbiont-mediated resistance compromises biological control of aphids by parasitoids.

    Science.gov (United States)

    Käch, Heidi; Mathé-Hubert, Hugo; Dennis, Alice B; Vorburger, Christoph

    2018-02-01

    There is growing interest in biological control as a sustainable and environmentally friendly way to control pest insects. Aphids are among the most detrimental agricultural pests worldwide, and parasitoid wasps are frequently employed for their control. The use of asexual parasitoids may improve the effectiveness of biological control because only females kill hosts and because asexual populations have a higher growth rate than sexuals. However, asexuals may have a reduced capacity to track evolutionary change in their host populations. We used a factorial experiment to compare the ability of sexual and asexual populations of the parasitoid Lysiphlebus fabarum to control caged populations of black bean aphids ( Aphis fabae ) of high and low clonal diversity. The aphids came from a natural population, and one-third of the aphid clones harbored Hamiltonella defensa , a heritable bacterial endosymbiont that increases resistance to parasitoids. We followed aphid and parasitoid population dynamics for 3 months but found no evidence that the reproductive mode of parasitoids affected their effectiveness as biocontrol agents, independent of host clonal diversity. Parasitoids failed to control aphids in most cases, because their introduction resulted in strong selection for clones protected by H. defensa . The increasingly resistant aphid populations escaped control by parasitoids, and we even observed parasitoid extinctions in many cages. The rapid evolution of symbiont-conferred resistance in turn imposed selection on parasitoids. In cages where asexual parasitoids persisted until the end of the experiment, they became dominated by a single genotype able to overcome the protection provided by H. defensa . Thus, there was evidence for parasitoid counteradaptation, but it was generally too slow for parasitoids to regain control over aphid populations. It appears that when pest aphids possess defensive symbionts, the presence of parasitoid genotypes able to overcome

  4. Phylogenetic analysis of algal symbionts associated with four North American amphibian egg masses.

    Science.gov (United States)

    Kim, Eunsoo; Lin, Yuan; Kerney, Ryan; Blumenberg, Lili; Bishop, Cory

    2014-01-01

    Egg masses of the yellow-spotted salamander Ambystoma maculatum form an association with the green alga "Oophila amblystomatis" (Lambert ex Wille), which, in addition to growing within individual egg capsules, has recently been reported to invade embryonic tissues and cells. The binomial O. amblystomatis refers to the algae that occur in A. maculatum egg capsules, but it is unknown whether this population of symbionts constitutes one or several different algal taxa. Moreover, it is unknown whether egg masses across the geographic range of A. maculatum, or other amphibians, associate with one or multiple algal taxa. To address these questions, we conducted a phylogeographic study of algae sampled from egg capsules of A. maculatum, its allopatric congener A. gracile, and two frogs: Lithobates sylvatica and L. aurora. All of these North American amphibians form associations with algae in their egg capsules. We sampled algae from egg capsules of these four amphibians from localities across North America, established representative algal cultures, and amplified and sequenced a region of 18S rDNA for phylogenetic analysis. Our combined analysis shows that symbiotic algae found in egg masses of four North American amphibians are closely related to each other, and form a well-supported clade that also contains three strains of free-living chlamydomonads. We designate this group as the 'Oophila' clade, within which the symbiotic algae are further divided into four distinct subclades. Phylogenies of the host amphibians and their algal symbionts are only partially congruent, suggesting that host-switching and co-speciation both play roles in their associations. We also established conditions for isolating and rearing algal symbionts from amphibian egg capsules, which should facilitate further study of these egg mass specialist algae.

  5. Phylogenetic analysis of algal symbionts associated with four North American amphibian egg masses.

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    Eunsoo Kim

    Full Text Available Egg masses of the yellow-spotted salamander Ambystoma maculatum form an association with the green alga "Oophila amblystomatis" (Lambert ex Wille, which, in addition to growing within individual egg capsules, has recently been reported to invade embryonic tissues and cells. The binomial O. amblystomatis refers to the algae that occur in A. maculatum egg capsules, but it is unknown whether this population of symbionts constitutes one or several different algal taxa. Moreover, it is unkno