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Sample records for means-end chain analysis

  1. A customer value analysis of Taiwan ice cream market: a means-end chain approach across consumption situations.

    PubMed

    Chen, Yan-Kwang; Tsai, Pei-Shan; Chiu, Fei-Rung

    2015-01-01

    In the highly competitive market, it is increasingly hard for ice cream stores to develop creative marketing strategies to retain existing customers and attract new ones. This study applies the means-end chain approach to identify the customer value, consequences, and attributes of ice cream and to suggest useful information for ice cream sellers to develop differential marketing strategies across various consumption situations (i.e. on a date, gathering with friends, craving for ice cream). This study conducted one-on-one in-depth interviews with participants. The interview content was subsequently analyzed and coded to produce an implication matrix and a hierarchical value map, which was further used to determine customers' value perceptions. The results indicate the terminal values of the highest strength comprised economy, pleasure, and efficiency. Pleasure was emphasized among consumers who were on a date or gathering with friends, whereas satisfaction was emphasized among consumers who craved ice cream. Based on the results, the study also provides suggestions to the industry and future researchers. PMID:26682112

  2. Measuring product meaning for prescribed medication using a means-end chain model.

    PubMed

    Doucette, W R; Wiederholt, J B

    1992-03-01

    On the basis of a means-end chain model, the product attribute and consequence levels of consumers' product meaning for prescribed medication were measured for a sample of 550 consumers. Using exploratory factor analysis on a 30-item scale, the authors identified five product attribute dimensions and three consequence dimensions. The means-end chain model can help marketers of health care learn more about how consumers categorize product meanings, which in turn can be used in the development of marketing strategies. PMID:10116755

  3. Discussing Laddering Application by the Means-End Chain Theory

    ERIC Educational Resources Information Center

    Veludo-de-Oliveira, Tania Modesto; Ikeda, Ana Akemi; Campomar, Marcos Cortez

    2006-01-01

    This article aims at analyzing laddering as a technique of qualitative research, emphasizing the procedures for data collection, analysis and interpretation, and its main limitations as well. "Laddering refers to an in-depth, one-on-one interviewing technique used to develop an understanding of how consumers translate the attributes of products…

  4. The Values of College Students in Business Simulation Game: A Means-End Chain Approach

    ERIC Educational Resources Information Center

    Lin, Yu-Ling; Tu, Yu-Zu

    2012-01-01

    Business simulation games (BSGs) enable students to practice making decisions in a virtual environment, accumulate experience in application of strategies, and train themselves in modes of decision-making. This study examines the value sought by players of BSG. In this study, a means-end chain (MEC) model was adopted as the basis, and ladder…

  5. That's why I take my ONS. Means-end chain as a novel approach to elucidate the personally relevant factors driving ONS consumption in nutritionally frail elderly users.

    PubMed

    den Uijl, Louise C; Kremer, Stefanie; Jager, Gerry; van der Stelt, Annelies J; de Graaf, Cees; Gibson, Peter; Godfrey, James; Lawlor, J Ben

    2015-06-01

    Oral nutritional supplements (ONS) are a recommended form of nutritional intervention for older malnourished persons when a 'food first' approach and/or food fortification prove ineffective. The efficacy of ONS will depend on, amongst other factors, whether persons do, or do not, consume their prescribed amount. Factors influencing ONS consumption can be product, context, or person related. Whereas product and context have received some attention, little is known about the person factors driving ONS consumption. In addition, the relative importance of the product, context, and person factors to ONS consumption is not known. Using the means-end chain (MEC) method, the current study elucidated personally relevant factors (product, context, and person factors) related to ONS consumption in two groups of older nutritionally frail ONS users: community-dwelling persons and care home residents with mainly somatic disorders. To our knowledge, the current work is the first to apply the MEC method to study older nutritionally frail ONS users. Forty ONS users (n = 20 per group) were recruited via healthcare professionals. The level of frailty was assessed using the FRAIL scale. Both groups were interviewed for 30 to 45 minutes using the soft laddering technique. The laddering data were analysed using LadderUX software™. The MEC method appeared to work well in both groups. The majority of the participants took ONS on their doctor's or dietician's prescription as they trusted their advice. The community-dwelling group took ONS to prolong their independence, whereas the care home group reported values that related more to small improvements in quality of life. In addition, care home residents perceived themselves as dependent on their caregiver for their ONS arrangements, whereas this dependence was not reported by community-dwelling persons. Key insights from this work will enable doctors and dieticians to customize their nutritional interventions to ONS users' personal

  6. Three Randomized Controlled Trials of Early Long-Chain Polyunsaturated Fatty Acid Supplementation on Means-End Problem Solving in 9-Month-Olds

    ERIC Educational Resources Information Center

    Drover, James; Hoffman, Dennis R.; Castaneda, Yolanda S.; Morale, Sarah E.; Birch, Eileen E.

    2009-01-01

    This study examines whether feeding infants formula supplemented with long-chain polyunsaturated fatty acids (LCPUFA) improves cognitive function of 9-month-olds. Participants included 229 infants from 3 randomized controlled trials. Children received either formula supplemented with docosahexaenoic acid and arachidonic acid, or a control formula…

  7. Supporting Children with Severe Disabilities to Achieve Means-End

    ERIC Educational Resources Information Center

    Bruce, Susan; Campbell, Cailen; Sullivan, Meghan

    2009-01-01

    Means-end behavior occurs when the child can carry out a sequence of steps, including the removal of a physical obstacle, to achieve a goal. The development of means-end knowledge occurs in three stages: transitional, intentional, and comprehensive. Comprehensive means-end is achieved when the child can generate solutions without demonstration of…

  8. Means-End Theory: Getting the Service Customer's Attention.

    ERIC Educational Resources Information Center

    Rosen, Deborah E.; Greenlee, Timothy B.

    2001-01-01

    Examined the usefulness of Means-End Theory in developing effective college recruitment brochures. Found evidence that brochures that emphasize attributes (e.g., cost, location) over consequences (e.g., getting a job) or values (e.g., security) will generate greater interest in an educational institution. (EV)

  9. Using Means-End Theory To Understand the Outdoor Adventure Experience.

    ERIC Educational Resources Information Center

    Goldenberg, Marni; Klenosky, David; McAvoy, Leo; Holman, Tom

    Means-end analysis was used to examine the linkages between elements of an Outward Bound course and the personal benefits and outcomes obtained or reinforced by course completion. A self-administered questionnaire was completed by 216 persons, who completed a course at the North Carolina Outward Bound School. Respondents were aged 14-66 (83…

  10. Dogs are able to solve a means-end task

    PubMed Central

    Range, Friederike; Hentrup, Marleen; Viranyi, Zsofia

    2014-01-01

    Dogs, although very skilled in social communicative tasks, have shown limited abilities in the domain of physical cognition. Consequently, several researchers hypothesized that domestication enhanced dogs’ cognitive abilities in the social realm, but relaxed selection on the physical one. For instance, dogs failed to demonstrate means-end understanding, an important form of relying on physical causal connection, when tested in a string-pulling task. Here, we tested dogs in an ‘on/off’ task using a novel approach. Thirty-two dogs were confronted with four different conditions in which they could choose between two boards one with a reward ‘on’ and another one with a reward ‘off’ (reward was placed next to the board). The dogs chose the correct board when 1) both rewards were placed at the same distance from the dog, when 2) the reward placed ‘on’ the board was closer to the dog, and 3) even when the reward placed ‘off’ the board was much closer to the dog and was food. Interestingly, in the latter case dogs did not perform above chance, if instead of a direct reward, the dogs had to retrieve an object placed on the board to get a food reward. In contrast to previous string pulling studies, our results show that dogs are able to solve a means-end task even if proximity of the unsupported reward is a confounding factor. PMID:21445577

  11. Relation chain based clustering analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Cheng-ning; Zhao, Ming-yang; Luo, Hai-bo

    2011-08-01

    Clustering analysis is currently one of well-developed branches in data mining technology which is supposed to find the hidden structures in the multidimensional space called feature or pattern space. A datum in the space usually possesses a vector form and the elements in the vector represent several specifically selected features. These features are often of efficiency to the problem oriented. Generally, clustering analysis goes into two divisions: one is based on the agglomerative clustering method, and the other one is based on divisive clustering method. The former refers to a bottom-up process which regards each datum as a singleton cluster while the latter refers to a top-down process which regards entire data as a cluster. As the collected literatures, it is noted that the divisive clustering is currently overwhelming both in application and research. Although some famous divisive clustering methods are designed and well developed, clustering problems are still far from being solved. The k - means algorithm is the original divisive clustering method which initially assigns some important index values, such as the clustering number and the initial clustering prototype positions, and that could not be reasonable in some certain occasions. More than the initial problem, the k - means algorithm may also falls into local optimum, clusters in a rigid way and is not available for non-Gaussian distribution. One can see that seeking for a good or natural clustering result, in fact, originates from the one's understanding of the concept of clustering. Thus, the confusion or misunderstanding of the definition of clustering always derives some unsatisfied clustering results. One should consider the definition deeply and seriously. This paper demonstrates the nature of clustering, gives the way of understanding clustering, discusses the methodology of designing a clustering algorithm, and proposes a new clustering method based on relation chains among 2D patterns. In

  12. Means-End Behavior in Young Infants: The Interplay of Action Perception and Action Production

    ERIC Educational Resources Information Center

    Daum, Moritz M.; Prinz, Wolfgang; Aschersleben, Gisa

    2009-01-01

    In 2 experiments, the interplay of action perception and action production was investigated in 6-month-old infants. In Experiment 1, infants received 2 versions of a means-end task in counterbalanced order. In the action perception version, a preferential looking paradigm in which infants were shown an actor performing means-end behavior with an…

  13. “Insight” in Pigeons: Absence of Means-End Processing in Displacement Tests

    PubMed Central

    Cook, Robert G.; Fowler, Catherine

    2013-01-01

    The understanding of functional relations between action and consequence is a critical component of intelligence. To examine this linkage in pigeons, we investigated their understanding of the relations of the elements tested in an extension of Köhler's box-stacking task to this species (Epstein et al. 1984). In the experiments, the pigeons had to move a spatially displaced box under an out-of-reach target. Experiment 1 successfully replicated and extended the previous finding showing that when separately trained to move a box and stand on it to peck the target, pigeons can synthesize these behaviors to solve the single-box displacement problem quickly on their first attempt. Experiment 2 tested whether pigeons, when given a simultaneous choice among two boxes with identical reinforcement histories, would selectively choose the box with the correct functional affordance (i.e., permitting standing) to solve the problem rather than a nonfunctional one. Their extensive, equivalent, and undirected behavior in moving both boxes during these tests suggests the pigeons did not possess a means-end understanding of the functional properties of the boxes. Instead, their results were consistent with an analysis of their earlier synthetic behavior as being due to the temporal and spatial relations of the physical elements in the task and their prior learned behaviors. PMID:23774955

  14. How Group Experience Affects Outcomes from NOLS Programs: A Means-End Investigation

    ERIC Educational Resources Information Center

    Goldenberg, Marni; Soule, Katherine

    2011-01-01

    Using means-end theory, this study evaluates how being part of a group influences outcomes of National Outdoor Leadership School (NOLS) participants. This study examines outcomes from NOLS courses during the summer of 2006 in the Wind River Mountain Range of Wyoming. Immediately following 2006 course completion, a convenience sample of 345…

  15. A Four-Year Follow-Up of Means-End Outcomes from Outdoor Adventure Programs

    ERIC Educational Resources Information Center

    Goldenberg, Marni; Soule, Katherine E.

    2015-01-01

    Means-end theory was used to analyze differences in outcomes from original interviews and follow-up interviews occurring four years after Outward Bound (OB) and National Outdoor Leadership School (NOLS) 2006 course participation. In 2006, a semi-structured, in-person interview was conducted after participants (N = 510) completed their course. In…

  16. Postural and Object-Oriented Experiences Advance Early Reaching, Object Exploration, and Means-End Behavior

    ERIC Educational Resources Information Center

    Lobo, Michele A.; Galloway, James C.

    2008-01-01

    The effects of 3 weeks of social (control), postural, or object-oriented experiences on 9- to 21-week-old infants' (N = 42) reaching, exploration, and means-end behaviors were assessed. Coders recorded object contacts, mouthing, fingering, attention, and affect from video. Postural and object-oriented experiences advanced reaching, haptic…

  17. Concurrent and Discriminant Validity of the Means-Ends Spirituality Questionnaire.

    ERIC Educational Resources Information Center

    Ryan, Kathleen; Fiorito, Basil A.

    This paper describes the reliability of the Means-Ends Spirituality Questionnaire to assess preferred ways and goals of spiritual expression. The means subscales assessed thinking, feeling, acting, and relating in the area of spiritual expression. A total of 405 university students participated in this investigation. Study 1 analyzed the…

  18. Bridging the Gap: Solving Spatial Means-Ends Relations in a Locomotor Task

    ERIC Educational Resources Information Center

    Berger, Sarah E.; Adolph, Karen E.; Kavookjian, Alisan E.

    2010-01-01

    Using a means-means-ends problem-solving task, this study examined whether 16-month-old walking infants (N = 28) took into account the width of a bridge as a means for crossing a precipice and the location of a handrail as a means for augmenting balance on a narrow bridge. Infants were encouraged to cross from one platform to another over narrow…

  19. An episodic specificity induction enhances means-end problem solving in young and older adults

    PubMed Central

    Madore, Kevin P.; Schacter, Daniel L.

    2014-01-01

    Episodic memory plays an important role not only in remembering past experiences, but also in constructing simulations of future experiences and solving means-end social problems. We recently found that an episodic specificity induction- brief training in recollecting details of past experiences- enhances performance of young and older adults on memory and imagination tasks. Here we tested the hypothesis that this specificity induction would also positively impact a means-end problem solving task on which age-related changes have been linked to impaired episodic memory. Young and older adults received the specificity induction or a control induction before completing a means-end problem solving task as well as memory and imagination tasks. Consistent with previous findings, older adults provided fewer relevant steps on problem solving than did young adults, and their responses also contained fewer internal (i.e., episodic) details across the three tasks. There was no difference in the number of other (e.g., irrelevant) steps on problem solving or external (i.e., semantic) details generated on the three tasks as a function of age. Critically, the specificity induction increased the number of relevant steps and internal details (but not other steps or external details) that both young and older adults generated in problem solving compared with the control induction, as well as the number of internal details (but not external details) generated for memory and imagination. Our findings support the idea that episodic retrieval processes are involved in means-end problem solving, extend the range of tasks on which a specificity induction targets these processes, and show that the problem solving performance of older adults can benefit from a specificity induction as much as that of young adults. PMID:25365688

  20. Biofuel supply chain, market, and policy analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Leilei

    Renewable fuel is receiving an increasing attention as a substitute for fossil based energy. The US Department of Energy (DOE) has employed increasing effort on promoting the advanced biofuel productions. Although the advanced biofuel remains at its early stage, it is expected to play an important role in climate policy in the future in the transportation sector. This dissertation studies the emerging biofuel supply chain and markets by analyzing the production cost, and the outcomes of the biofuel market, including blended fuel market price and quantity, biofuel contract price and quantity, profitability of each stakeholder (farmers, biofuel producers, biofuel blenders) in the market. I also address government policy impacts on the emerging biofuel market. The dissertation is composed with three parts, each in a paper format. The first part studies the supply chain of emerging biofuel industry. Two optimization-based models are built to determine the number of facilities to deploy, facility locations, facility capacities, and operational planning within facilities. Cost analyses have been conducted under a variety of biofuel demand scenarios. It is my intention that this model will shed light on biofuel supply chain design considering operational planning under uncertain demand situations. The second part of the dissertation work focuses on analyzing the interaction between the key stakeholders along the supply chain. A bottom-up equilibrium model is built for the emerging biofuel market to study the competition in the advanced biofuel market, explicitly formulating the interactions between farmers, biofuel producers, blenders, and consumers. The model simulates the profit maximization of multiple market entities by incorporating their competitive decisions in farmers' land allocation, biomass transportation, biofuel production, and biofuel blending. As such, the equilibrium model is capable of and appropriate for policy analysis, especially for those policies

  1. Domestication has not affected the understanding of means-end connections in dogs

    PubMed Central

    Range, Friederike; Möslinger, Helene; Virányi, Zs

    2015-01-01

    Recent studies have revealed that dogs often perform well in cognitive tasks in the social domain, but rather poorly in the physical domain. This dichotomy has led to the hypothesis that the domestication process might have enhanced the social cognitive skills of dogs (Hare et al. in Science 298:1634–1636, 2002; Miklósi et al. in Curr Biol 13:763–766, 2003) but at the same time had a detrimental effect on their physical cognition (Frank in Z Tierpsychol 5:389–399, 1980). Despite the recent interest in dog cognition and especially the effects of domestication, the latter hypothesis has hardly been tested and we lack detailed knowledge of the physical understanding of wolves in comparison with dogs. Here, we set out to examine whether adult wolves and dogs rely on means-end connections using the string-pulling task, to test the prediction that wolves would perform better than dogs in such a task of physical cognition. We found that at the group level, dogs were more prone to commit the proximity error, while the wolves showed a stronger side bias. Neither wolves nor dogs showed an instantaneous understanding of means-end connection, but made different mistakes. Thus, the performance of the wolves and dogs in this string-pulling task did not confirm that domestication has affected the physical cognition of dogs. PMID:22460629

  2. Evidence of means-end behavior in Asian elephants (Elephas maximus).

    PubMed

    Irie-Sugimoto, Naoko; Kobayashi, Tessei; Sato, Takao; Hasegawa, Toshikazu

    2008-04-01

    The present study explores to what extent Asian elephants show "means-end" behavior. We used captive Asian elephants (N = 2) to conduct four variations of the Piagetian "support" problem, which involves a goal object that is out of reach, but rests on a support within reach. In the first condition, elephants were simultaneously presented with two identical trays serving as the "support", with the bait on one tray and the other tray left empty. In the next two conditions, the bait was placed on one tray, while additional bait was placed beside the other tray. In the last condition, both trays contained bait, but one of the trays had a small gap which prevented the elephants from reaching the reward. Subjects were required to choose and pull either tray with their trunk and to obtain the bait (i.e. goal). Results showed that one elephant performed all of the support problems significantly above chance after several sessions, suggesting that the elephant was capable of understanding that pulling the tray was the "means" for achieving the "end" of obtaining the bait. This study showed that elephants show means-end behavior when subjected to a Piagetian "support" task, and indicates that such goal-directed behavior occurs in species other than primates. PMID:18087732

  3. The Goal Trumps the Means: Highlighting Goals is More Beneficial than Highlighting Means in Means-End Training

    ERIC Educational Resources Information Center

    Gerson, Sarah A.; Woodward, Amanda L.

    2013-01-01

    Means-end actions are an early-emerging form of problem solving. These actions require initiating initial behaviors with a goal in mind. In this study, we explored the origins of 8-month-old infants' means-end action production using a cloth-pulling training paradigm. We examined whether highlighting the goal (toy) or the means (cloth) was more…

  4. SCit: web tools for protein side chain conformation analysis.

    PubMed

    Gautier, R; Camproux, A-C; Tufféry, P

    2004-07-01

    SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit. PMID:15215438

  5. The Desired Teaching Qualities of Lecturers in Higher Education: A Means End Analysis

    ERIC Educational Resources Information Center

    Voss, Roediger; Gruber, Thorsten

    2006-01-01

    Purpose: The purpose of this research is to aim to develop a deeper understanding of the teaching qualities of effective lecturers that students desire and to uncover the constructs that underlie these desire expectations and reveal the underlying benefits for which students look. Design/methodology/approach: A semi-standardized qualitative…

  6. Means-end comprehension in four parrot species: explained by social complexity.

    PubMed

    Krasheninnikova, Anastasia; Bräger, Stefan; Wanker, Ralf

    2013-09-01

    A comparative approach is required to investigate the evolutionary origins of cognitive abilities. In this paper, we compare the performance of four parrot species, spectacled parrotlets (Forpus conspicillatus), rainbow lorikeets (Trichoglossus haematodus), green-winged macaws (Ara chloroptera) and sulphur-crested cockatoos (Cacatua galerita triton) in standardized string-pulling and string-choice paradigms. We varied the spatial relationship between the strings, the presence of a reward and the physical contact between the string and the reward to test different cognitive skills requiring means-end comprehension. The species tested showed a high individual and inter-specific variation in their ability to solve the tasks. Spectacled parrotlets performed best among the four species and solved the most complex choice tasks, namely crossed-string task and broken-string task, spontaneously. In contrast, macaws and cockatoos failed to identify the correct string in these two tasks. The rainbow lorikeets were outperformed by the parrotlets, but outperformed in turn the macaws and the cockatoos. The findings can be best explained by the variation in social complexity among species, rather than in their ecology. PMID:23397182

  7. Deubiquitinase–based analysis of ubiquitin chain architecture using Ubiquitin Chain Restriction (UbiCRest)

    PubMed Central

    Komander, David

    2016-01-01

    Protein ubiquitination is a versatile protein modification that regulates virtually all cellular processes. This versatility originates from polyubiquitin chains, which can be linked in eight distinct ways. The combinatorial complexity of eight linkage types in homotypic (one chain type per polymer) and heterotypic (multiple linkage types per polymer) chains poses significant problems for biochemical analysis. Here we describe UbiCRest, in which substrates (ubiquitinated proteins or polyubiquitin chains) are treated with a panel of linkage-specific deubiquitinating enzymes (DUBs) in parallel reactions, followed by gel-based analysis. UbiCRest can be used to show that a protein is ubiquitinated, to identify which linkage type(s) are present on polyubiquitinated proteins and to assess the architecture of heterotypic polyubiquitin chains. DUBs used in UbiCRest can be obtained commercially; however, we include details for generating a toolkit of purified DUBs and for profiling their linkage preferences in vitro. UbiCRest is a qualitative method that yields insights into ubiquitin chain linkage types and architecture within hours, and it can be performed on western blotting quantities of endogenously ubiquitinated proteins. PMID:25633630

  8. Markov Chain Analysis of Musical Dice Games

    NASA Astrophysics Data System (ADS)

    Volchenkov, D.; Dawin, J. R.

    2012-07-01

    A system for using dice to compose music randomly is known as the musical dice game. The discrete time MIDI models of 804 pieces of classical music written by 29 composers have been encoded into the transition matrices and studied by Markov chains. Contrary to human languages, entropy dominates over redundancy, in the musical dice games based on the compositions of classical music. The maximum complexity is achieved on the blocks consisting of just a few notes (8 notes, for the musical dice games generated over Bach's compositions). First passage times to notes can be used to resolve tonality and feature a composer.

  9. Fast analysis of radionuclide decay chain migration

    NASA Astrophysics Data System (ADS)

    Chen, J. S.; Liang, C. P.; Liu, C. W.; Li, L.

    2014-12-01

    A novel tool for rapidly predicting the long-term plume behavior of an arbitrary length radionuclide decay chain is presented in this study. This fast tool is achieved based on generalized analytical solutions in compact format derived for a set of two-dimensional advection-dispersion equations coupled with sequential first-order decay reactions in groundwater system. The performance of the developed tool is evaluated by a numerical model using a Laplace transform finite difference scheme. The results of performance evaluation indicate that the developed model is robust and accurate. The developed model is then used to fast understand the transport behavior of a four-member radionuclide decay chain. Results show that the plume extents and concentration levels of any target radionuclide are very sensitive to longitudinal, transverse dispersion, decay rate constant and retardation factor. The developed model are useful tools for rapidly assessing the ecological and environmental impact of the accidental radionuclide releases such as the Fukushima nuclear disaster where multiple radionuclides leaked through the reactor, subsequently contaminating the local groundwater and ocean seawater in the vicinity of the nuclear plant.

  10. Analysis of a complex shape chain plate using Transmission Photoelasticity

    NASA Astrophysics Data System (ADS)

    Dasari, N.; Ramesh, K.

    2010-06-01

    fixture was used to load the model during stress freezing in the furnace. The integrated fringe pattern of the offset chain plate is shown in Figure 2. Slices are cut in the offset zone to understand the nature of the stress distribution. A Simple photoelastic analysis of this has revealed a wealth of information to take suitable decision on the design of such plates taking into account the constraints in manufacturing.

  11. A Case Study on Engineering Failure Analysis of Link Chain

    PubMed Central

    Lee, Seong-Beom; Lee, Hong-Chul

    2010-01-01

    Objectives The objective of this study was to investigate the effect of chain installation condition on stress distribution that could eventually cause disastrous failure from sudden deformation and geometric rupture. Methods Fractographic method used for the failed chain indicates that over-stress was considered as the root cause of failure. 3D modeling and finite element analysis for the chain, used in a crane hook, were performed with a three-dimensional interactive application program, CATIA, commercial finite element analysis and computational fluid dynamic software, ANSYS. Results The results showed that the state of stress was changed depending on the initial position of the chain that was installed in the hook. Especially, the magnitude of the stress was strongly affected by the bending forces, which are 2.5 times greater (under the simulation condition currently investigated) than that from the plain tensile load. Also, it was noted that the change of load state is strongly related to the failure of parts. The chain can hold an ultimate load of about 8 tons with only the tensile load acting on it. Conclusion The conclusions of this research clearly showed that a reduction of the loss from similar incidents can be achieved when an operator properly handles the installation of the chain. PMID:22953162

  12. Space system operations and support cost analysis using Markov chains

    NASA Technical Reports Server (NTRS)

    Unal, Resit; Dean, Edwin B.; Moore, Arlene A.; Fairbairn, Robert E.

    1990-01-01

    This paper evaluates the use of Markov chain process in probabilistic life cycle cost analysis and suggests further uses of the process as a design aid tool. A methodology is developed for estimating operations and support cost and expected life for reusable space transportation systems. Application of the methodology is demonstrated for the case of a hypothetical space transportation vehicle. A sensitivity analysis is carried out to explore the effects of uncertainty in key model inputs.

  13. Food chain analysis at a mining waste-contaminated wetland

    SciTech Connect

    Pascoe, G.A.; Blanchet, R.J.; Linder, G.

    1994-12-31

    A food chain analysis was performed in support of a baseline ecological risk assessment oat the Milltown Reservoir Sediments Superfund site in Montana. The site consists of over 450 acres of primarily palustrine wetland contaminated with metals from mining-wastes transported from upstream sources. The food chain analysis focused on several species of terrestrial and aquatic animals indigenous to montane wetlands of the northern Rocky Mountains. Samples of small mammal tissues, grasses, forbs, invertebrates, soils, sediment, aquatic plants, and fish were collected and analyzed for As, Cd, Cu, Pb, and Zn. A linear multimedia food-chain model was constructed to estimate daily intakes of the metals for each receptor, with assumed values for aquatic and terrestrial food items from the site, ingestion of local surface water, incidental ingestion of soils or sediments, and estimated bioavailability of soil metals. Evaluation of health risks was performed by the quotient method, where exposures expressed as daily intakes were compared to literature toxicity values. Results from the food chain analysis suggested that the health of primary consumers and higher trophic organisms (including mice, voles, muskrats, beaver, various waterfowl species, osprey, bald eagles, and deer) is not at risk due to the presence of elevated metals in sediments or upland soils at the site.

  14. Modeling Value Chain Analysis of Distance Education using UML

    NASA Astrophysics Data System (ADS)

    Acharya, Anal; Mukherjee, Soumen

    2010-10-01

    Distance education continues to grow as a methodology for the delivery of course content in higher education in India as well as abroad. To manage this growing demand and to provide certain flexibility, there must be certain strategic planning about the use of ICT tools. Value chain analysis is a framework for breaking down the sequence of business functions into a set of activities through which utility could be added to service. Thus it can help to determine the competitive advantage that is enjoyed by an institute. To implement these business functions certain visual representation is required. UML allows for this representation by using a set of structural and behavioral diagrams. In this paper, the first section defines a framework for value chain analysis and highlights its advantages. The second section gives a brief overview of related work in this field. The third section gives a brief discussion on distance education. The fourth section very briefly introduces UML. The fifth section models value chain of distance education using UML. Finally we discuss the limitations and the problems posed in this domain.

  15. Modelling and analysis of workflow for lean supply chains

    NASA Astrophysics Data System (ADS)

    Ma, Jinping; Wang, Kanliang; Xu, Lida

    2011-11-01

    Cross-organisational workflow systems are a component of enterprise information systems which support collaborative business process among organisations in supply chain. Currently, the majority of workflow systems is developed in perspectives of information modelling without considering actual requirements of supply chain management. In this article, we focus on the modelling and analysis of the cross-organisational workflow systems in the context of lean supply chain (LSC) using Petri nets. First, the article describes the assumed conditions of cross-organisation workflow net according to the idea of LSC and then discusses the standardisation of collaborating business process between organisations in the context of LSC. Second, the concept of labelled time Petri nets (LTPNs) is defined through combining labelled Petri nets with time Petri nets, and the concept of labelled time workflow nets (LTWNs) is also defined based on LTPNs. Cross-organisational labelled time workflow nets (CLTWNs) is then defined based on LTWNs. Third, the article proposes the notion of OR-silent CLTWNS and a verifying approach to the soundness of LTWNs and CLTWNs. Finally, this article illustrates how to use the proposed method by a simple example. The purpose of this research is to establish a formal method of modelling and analysis of workflow systems for LSC. This study initiates a new perspective of research on cross-organisational workflow management and promotes operation management of LSC in real world settings.

  16. Analysis of Chains of Metric Solar Type I Bursts

    NASA Astrophysics Data System (ADS)

    Sodré, Z. A. L.; Cunha-Silva, R. D.; Fernandes, F. C. R.

    2015-01-01

    Type I radio noise storms are believed to provide a diagnostic of electron acceleration in the corona. Most type I bursts appear in chains of five or more individual bursts. An analysis of the chain properties may indicate electron density, height of emission source, and magnetic-field intensity. We studied 255 chains of solar type I solar bursts recorded by the Compact Astronomical Low-cost Low-frequency Instrument for Spectroscopy and Transportable Observatory (CALLISTO-BLEN) spectrograph from 30 July to 9 August 2011 in the frequency range 170 - 870 MHz. Based on the morphological characteristics identified in the dynamic spectra, we determined the physical parameters for the events. The source electron density was found to be in the range 0.5 - 1.6×109 cm-3, the radial velocity of the emitting plasma varied from -1600 - 1500 km s-1, the magnetic-field strength was in the range 2.2 - 3.3 G, and the height of the source ranged from 0.95 to 1.15 solar radii. The results are consistent with previously reported values.

  17. Managing Distance Education Institutions through Value Chain Analysis: the Nigerian Experience.

    ERIC Educational Resources Information Center

    Aderinto, J. A.; Akintayo, M. O.

    Value chain analysis can gauge, analyze, and predict organization effects to control cost in light of achieving strategic organization objectives of distance education. Value chain analysis enables organizations to accomplish their goal or mission through cost effectiveness or differentiation. The value chain activity structure in a distance…

  18. SATMC: Spectral energy distribution Analysis Through Markov Chains

    NASA Astrophysics Data System (ADS)

    Johnson, S. P.; Wilson, G. W.; Tang, Y.; Scott, K. S.

    2013-12-01

    We present the general purpose spectral energy distribution (SED) fitting tool SED Analysis Through Markov Chains (SATMC). Utilizing Monte Carlo Markov Chain (MCMC) algorithms, SATMC fits an observed SED to SED templates or models of the user's choice to infer intrinsic parameters, generate confidence levels and produce the posterior parameter distribution. Here, we describe the key features of SATMC from the underlying MCMC engine to specific features for handling SED fitting. We detail several test cases of SATMC, comparing results obtained from traditional least-squares methods, which highlight its accuracy, robustness and wide range of possible applications. We also present a sample of submillimetre galaxies (SMGs) that have been fitted using the SED synthesis routine GRASIL as input. In general, these SMGs are shown to occupy a large volume of parameter space, particularly in regards to their star formation rates which range from ˜30 to 3000 M⊙ yr-1 and stellar masses which range from ˜1010 to 1012 M⊙. Taking advantage of the Bayesian formalism inherent to SATMC, we also show how the fitting results may change under different parametrizations (i.e. different initial mass functions) and through additional or improved photometry, the latter being crucial to the study of high-redshift galaxies.

  19. Stability analysis of three species food chain with competition

    NASA Astrophysics Data System (ADS)

    Abadi, Savitri, D.

    2015-03-01

    We study a food chain system that consists of 1 prey and 2 predators populations. The prey population grows logistically while the predators apply different Holling functional responses. The first predator preys on the prey following Holling type II functional response and the second predator preys on both the prey and the first predator following Holling type II and III functional responses, respectively. The study starts with the stability analysis of critical points of the systems. Then, by using normal form and centre manifold method the information about other nontrivial solutions due to bifurcation including possible limit cycles appearance is obtained. The results are confirmed by numerical simulation using MatCont and biological interpretation of the results are also presented.

  20. Analysis of the gravitaxis signal transduction chain in Euglena gracilis

    NASA Astrophysics Data System (ADS)

    Nasir, Adeel

    Abstract Euglena gracilis is a photosynthetic, eukaryotic flagellate. It can adapt autotrophic and heterotrophic mode of growth and respond to different stimuli, this makes it an organism of choice for different research disciplines. It swims to reach a suitable niche by employing different stimuli such as oxygen, light, gravity and different chemicals. Among these stimuli light and gravity are the most important. Phototaxis (locomotion under light stimulus) and gravitaxis (locomotion under gravity stimulus) synergistically help cells to attain an optimal niche in the environment. However, in the complete absence of light or under scarcity of detectable light, cells can totally depend on gravity to find its swimming path. Therefore gravity has certain advantages over other stimuli.Unlike phototatic signal transduction chain of Euglena gracilis no clear primary gravity receptor has been identified in Euglena cells so far. However, there are some convincing evidence that TRP like channels act as a primary gravity receptor in Euglena gracilis.Use of different inhibitors gave rise to the involvement of protein kinase and calmodulin proteins in signal transduction chain of Euglena gracilis. Recently, specific calmodulin (Calmodulin 2) and protein kinase (PKA) have been identified as potential candidates of gravitactic signal transduction chain. Further characterization and investigation of these candidates was required. Therefore a combination of biochemical and genetic techniques was employed to localize proteins in cells and also to find interacting partners. For localization studies, specific antibodies were raised and characterized. Specificity of antibodies was validated by knockdown mutants, Invitro-translated proteins and heterologously expressed proteins. Cell fractionation studies, involving separation of the cell body and flagella for western blot analysis and confocal immunofluorescence studies were performed for subcellular localization. In order to find

  1. Rouse mode analysis of chain relaxation in homopolymer melts

    DOE PAGESBeta

    Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; Grest, Gary S.

    2014-09-15

    We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inverselymore » with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. As a result, these facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion.« less

  2. Rouse Mode Analysis of Chain Relaxation in Homopolymer Melts

    PubMed Central

    2015-01-01

    We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inversely with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. These facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion. PMID:25328247

  3. Rouse mode analysis of chain relaxation in homopolymer melts

    SciTech Connect

    Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; Grest, Gary S.

    2014-09-15

    We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inversely with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. As a result, these facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion.

  4. Identifying Innovative Interventions to Promote Healthy Eating Using Consumption-Oriented Food Supply Chain Analysis

    PubMed Central

    Hawkes, Corinna

    2009-01-01

    The mapping and analysis of supply chains is a technique increasingly used to address problems in the food system. Yet such supply chain management has not yet been applied as a means of encouraging healthier diets. Moreover, most policies recommended to promote healthy eating focus on the consumer end of the chain. This article proposes a consumption-oriented food supply chain analysis to identify the changes needed in the food supply chain to create a healthier food environment, measured in terms of food availability, prices, and marketing. Along with established forms of supply chain analysis, the method is informed by a historical overview of how food supply chains have changed over time. The method posits that the actors and actions in the chain are affected by organizational, financial, technological, and policy incentives and disincentives, which can in turn be levered for change. It presents a preliminary example of the supply of Coca-Cola beverages into school vending machines and identifies further potential applications. These include fruit and vegetable supply chains, local food chains, supply chains for health-promoting versions of food products, and identifying financial incentives in supply chains for healthier eating. PMID:23144674

  5. Identifying Innovative Interventions to Promote Healthy Eating Using Consumption-Oriented Food Supply Chain Analysis.

    PubMed

    Hawkes, Corinna

    2009-07-01

    The mapping and analysis of supply chains is a technique increasingly used to address problems in the food system. Yet such supply chain management has not yet been applied as a means of encouraging healthier diets. Moreover, most policies recommended to promote healthy eating focus on the consumer end of the chain. This article proposes a consumption-oriented food supply chain analysis to identify the changes needed in the food supply chain to create a healthier food environment, measured in terms of food availability, prices, and marketing. Along with established forms of supply chain analysis, the method is informed by a historical overview of how food supply chains have changed over time. The method posits that the actors and actions in the chain are affected by organizational, financial, technological, and policy incentives and disincentives, which can in turn be levered for change. It presents a preliminary example of the supply of Coca-Cola beverages into school vending machines and identifies further potential applications. These include fruit and vegetable supply chains, local food chains, supply chains for health-promoting versions of food products, and identifying financial incentives in supply chains for healthier eating. PMID:23144674

  6. Design and analysis of the Gemini chain system in dual clutch transmission of automobile

    NASA Astrophysics Data System (ADS)

    Cheng, Yabing; Guo, Haitao; Fu, Zhenming; Wan, Nen; Li, Lei; Wang, Yang

    2015-01-01

    Chain drive system is widely used in the conditions of high-speed, overload, variable speed and load. Many studies are focused on the meshing theory and wear characteristics of chain drive system, but system design, analysis, and noise characteristics of the chain drive system are weak. System design and noise characteristic are studied for a new type Gemini chain of dual-clutch automatic transmission. Based on the meshing theory of silent chain, the design parameters of the Gemini chain system are calculated and the mathematical models and dynamic analysis models of the Gemini chain system are established. Dynamic characteristics of the Gemini chain system is simulated and the contact force of plate and pin, plate and sprockets, the chain tension forces, the transmission error and the stress of plates and pins are analyzed. According to the simulation results of the Gemini chain system, the noise experiment about system is carried out. The noise values are tested at different speed and load and spectral characteristics are analyzed. The results of simulation and experimental show that the contact forces of plate and pin, plate and sprockets are smaller than the allowable stress values, the chain tension force is less than ultimate tension and transmission error is limited in 1.2%. The noise values can meet the requirements of industrial design, and it is proved that the design and analysis method of the Gemini chain system is scientific and feasible. The design and test system is built from analysis to test of Gemini chain system. This research presented will provide a corresponding theoretical guidance for the design and dynamic characteristics and noise characteristics of chain drive system.

  7. Markov chain analysis of succession in a rocky subtidal community.

    PubMed

    Hill, M Forrest; Witman, Jon D; Caswell, Hal

    2004-08-01

    We present a Markov chain model of succession in a rocky subtidal community based on a long-term (1986-1994) study of subtidal invertebrates (14 species) at Ammen Rock Pinnacle in the Gulf of Maine. The model describes successional processes (disturbance, colonization, species persistence, and replacement), the equilibrium (stationary) community, and the rate of convergence. We described successional dynamics by species turnover rates, recurrence times, and the entropy of the transition matrix. We used perturbation analysis to quantify the response of diversity to successional rates and species removals. The equilibrium community was dominated by an encrusting sponge (Hymedesmia) and a bryozoan (Crisia eburnea). The equilibrium structure explained 98% of the variance in observed species frequencies. Dominant species have low probabilities of disturbance and high rates of colonization and persistence. On average, species turn over every 3.4 years. Recurrence times varied among species (7-268 years); rare species had the longest recurrence times. The community converged to equilibrium quickly (9.5 years), as measured by Dobrushin's coefficient of ergodicity. The largest changes in evenness would result from removal of the dominant sponge Hymedesmia. Subdominant species appear to increase evenness by slowing the dominance of Hymedesmia. Comparison of the subtidal community with intertidal and coral reef communities revealed that disturbance rates are an order of magnitude higher in coral reef than in rocky intertidal and subtidal communities. Colonization rates and turnover times, however, are lowest and longest in coral reefs, highest and shortest in intertidal communities, and intermediate in subtidal communities. PMID:15278851

  8. Analysis of magnetosome chains in magnetotactic bacteria by magnetic measurements and automated image analysis of electron micrographs.

    PubMed

    Katzmann, E; Eibauer, M; Lin, W; Pan, Y; Plitzko, J M; Schüler, D

    2013-12-01

    Magnetotactic bacteria (MTB) align along the Earth's magnetic field by the activity of intracellular magnetosomes, which are membrane-enveloped magnetite or greigite particles that are assembled into well-ordered chains. Formation of magnetosome chains was found to be controlled by a set of specific proteins in Magnetospirillum gryphiswaldense and other MTB. However, the contribution of abiotic factors on magnetosome chain assembly has not been fully explored. Here, we first analyzed the effect of growth conditions on magnetosome chain formation in M. gryphiswaldense by electron microscopy. Whereas higher temperatures (30 to 35°C) and high oxygen concentrations caused increasingly disordered chains and smaller magnetite crystals, growth at 20°C and anoxic conditions resulted in long chains with mature cuboctahedron-shaped crystals. In order to analyze the magnetosome chain in electron microscopy data sets in a more quantitative and unbiased manner, we developed a computerized image analysis algorithm. The collected data comprised the cell dimensions and particle size and number as well as the intracellular position and extension of the magnetosome chain. The chain analysis program (CHAP) was used to evaluate the effects of the genetic and growth conditions on magnetosome chain formation. This was compared and correlated to data obtained from bulk magnetic measurements of wild-type (WT) and mutant cells displaying different chain configurations. These techniques were used to differentiate mutants due to magnetosome chain defects on a bulk scale. PMID:24096429

  9. Analysis of Magnetosome Chains in Magnetotactic Bacteria by Magnetic Measurements and Automated Image Analysis of Electron Micrographs

    PubMed Central

    Katzmann, E.; Eibauer, M.; Lin, W.; Pan, Y.; Plitzko, J. M.

    2013-01-01

    Magnetotactic bacteria (MTB) align along the Earth's magnetic field by the activity of intracellular magnetosomes, which are membrane-enveloped magnetite or greigite particles that are assembled into well-ordered chains. Formation of magnetosome chains was found to be controlled by a set of specific proteins in Magnetospirillum gryphiswaldense and other MTB. However, the contribution of abiotic factors on magnetosome chain assembly has not been fully explored. Here, we first analyzed the effect of growth conditions on magnetosome chain formation in M. gryphiswaldense by electron microscopy. Whereas higher temperatures (30 to 35°C) and high oxygen concentrations caused increasingly disordered chains and smaller magnetite crystals, growth at 20°C and anoxic conditions resulted in long chains with mature cuboctahedron-shaped crystals. In order to analyze the magnetosome chain in electron microscopy data sets in a more quantitative and unbiased manner, we developed a computerized image analysis algorithm. The collected data comprised the cell dimensions and particle size and number as well as the intracellular position and extension of the magnetosome chain. The chain analysis program (CHAP) was used to evaluate the effects of the genetic and growth conditions on magnetosome chain formation. This was compared and correlated to data obtained from bulk magnetic measurements of wild-type (WT) and mutant cells displaying different chain configurations. These techniques were used to differentiate mutants due to magnetosome chain defects on a bulk scale. PMID:24096429

  10. Rouse mode analysis of chain relaxation in polymer nanocomposites

    DOE PAGESBeta

    Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; Grest, Gary S.

    2015-04-20

    Large-scale molecular dynamics simulations are used to study the internal relaxations of chains in nanoparticle (NP)/polymer composites. We examine the Rouse modes of the chains, a quantity that is closest in spirit to the self-intermediate scattering function, typically determined in an (incoherent) inelastic neutron scattering experiment. Our simulations show that for weakly interacting mixtures of NPs and polymers, the effective monomeric relaxation rates are faster than in a neat melt when the NPs are smaller than the entanglement mesh size. In this case, the NPs serve to reduce both the monomeric friction and the entanglements in the polymer melt, asmore » in the case of a polymer–solvent system. However, for NPs larger than half the entanglement mesh size, the effective monomer relaxation is essentially unaffected for low NP concentrations. Even in this case, we observe a strong reduction in chain entanglements for larger NP loadings. Furthermore, the role of NPs is to always reduce the number of entanglements, with this effect only becoming pronounced for small NPs or for high concentrations of large NPs. Our studies of the relaxation of single chains resonate with recent neutron spin echo (NSE) experiments, which deduce a similar entanglement dilution effect.« less

  11. Rouse mode analysis of chain relaxation in polymer nanocomposites

    SciTech Connect

    Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; Grest, Gary S.

    2015-04-20

    Large-scale molecular dynamics simulations are used to study the internal relaxations of chains in nanoparticle (NP)/polymer composites. We examine the Rouse modes of the chains, a quantity that is closest in spirit to the self-intermediate scattering function, typically determined in an (incoherent) inelastic neutron scattering experiment. Our simulations show that for weakly interacting mixtures of NPs and polymers, the effective monomeric relaxation rates are faster than in a neat melt when the NPs are smaller than the entanglement mesh size. In this case, the NPs serve to reduce both the monomeric friction and the entanglements in the polymer melt, as in the case of a polymer–solvent system. However, for NPs larger than half the entanglement mesh size, the effective monomer relaxation is essentially unaffected for low NP concentrations. Even in this case, we observe a strong reduction in chain entanglements for larger NP loadings. Furthermore, the role of NPs is to always reduce the number of entanglements, with this effect only becoming pronounced for small NPs or for high concentrations of large NPs. Our studies of the relaxation of single chains resonate with recent neutron spin echo (NSE) experiments, which deduce a similar entanglement dilution effect.

  12. OTU Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis

    PubMed Central

    Mevissen, Tycho E.T.; Hospenthal, Manuela K.; Geurink, Paul P.; Elliott, Paul R.; Akutsu, Masato; Arnaudo, Nadia; Ekkebus, Reggy; Kulathu, Yogesh; Wauer, Tobias; El Oualid, Farid; Freund, Stefan M.V.; Ovaa, Huib; Komander, David

    2013-01-01

    Summary Sixteen ovarian tumor (OTU) family deubiquitinases (DUBs) exist in humans, and most members regulate cell-signaling cascades. Several OTU DUBs were reported to be ubiquitin (Ub) chain linkage specific, but comprehensive analyses are missing, and the underlying mechanisms of linkage specificity are unclear. Using Ub chains of all eight linkage types, we reveal that most human OTU enzymes are linkage specific, preferring one, two, or a defined subset of linkage types, including unstudied atypical Ub chains. Biochemical analysis and five crystal structures of OTU DUBs with or without Ub substrates reveal four mechanisms of linkage specificity. Additional Ub-binding domains, the ubiquitinated sequence in the substrate, and defined S1’ and S2 Ub-binding sites on the OTU domain enable OTU DUBs to distinguish linkage types. We introduce Ub chain restriction analysis, in which OTU DUBs are used as restriction enzymes to reveal linkage type and the relative abundance of Ub chains on substrates. PMID:23827681

  13. Analysis of ratio-dependent food chain model

    NASA Astrophysics Data System (ADS)

    Ko, Wonlyul; Ahn, Inkyung

    2007-11-01

    In this paper, a food chain model with ratio-dependent functional response is studied under homogeneous Neumann boundary conditions. The large time behavior of all non-negative equilibria in the time-dependent system is investigated, i.e., conditions for the stability at equilibria are found. Moreover, non-constant positive steady-states are studied in terms of diffusion effects, namely, Turing patterns arising from diffusion-driven instability (Turing instability) are demonstrated. The employed methods are comparison principle for parabolic problems and Leray-Schauder Theorem.

  14. Mathematical supply-chain modelling: Product analysis of cost and time

    NASA Astrophysics Data System (ADS)

    Easters, D. J.

    2014-03-01

    Establishing a mathematical supply-chain model is a proposition that has received attention due to its inherent benefits of evolving global supply-chain efficiencies. This paper discusses the prevailing relationships found within apparel supply-chain environments, and contemplates the complex issues indicated for constituting a mathematical model. Principal results identified within the data suggest, that the multifarious nature of global supply-chain activities require a degree of simplification in order to fully dilate the necessary factors which affect, each sub-section of the chain. Subsequently, the research findings allowed the division of supply-chain components into sub-sections, which amassed a coherent method of product development activity. Concurrently, the supply-chain model was found to allow systematic mathematical formulae analysis, of cost and time, within the multiple contexts of each subsection encountered. The paper indicates the supply-chain model structure, the mathematics, and considers how product analysis of cost and time can improve the comprehension of product lifecycle management.

  15. A BENCHMARKING ANALYSIS FOR FIVE RADIONUCLIDE VADOSE ZONE MODELS (CHAIN, MULTIMED_DP, FECTUZ, HYDRUS, AND CHAIN 2D) IN SOIL SCREENING LEVEL CALCULATIONS

    EPA Science Inventory

    Five radionuclide vadose zone models with different degrees of complexity (CHAIN, MULTIMED_DP, FECTUZ, HYDRUS, and CHAIN 2D) were selected for use in soil screening level (SSL) calculations. A benchmarking analysis between the models was conducted for a radionuclide (99Tc) rele...

  16. Dynamics of global supply chain and electric power networks: Models, pricing analysis, and computations

    NASA Astrophysics Data System (ADS)

    Matsypura, Dmytro

    In this dissertation, I develop a new theoretical framework for the modeling, pricing analysis, and computation of solutions to electric power supply chains with power generators, suppliers, transmission service providers, and the inclusion of consumer demands. In particular, I advocate the application of finite-dimensional variational inequality theory, projected dynamical systems theory, game theory, network theory, and other tools that have been recently proposed for the modeling and analysis of supply chain networks (cf. Nagurney (2006)) to electric power markets. This dissertation contributes to the extant literature on the modeling, analysis, and solution of supply chain networks, including global supply chains, in general, and electric power supply chains, in particular, in the following ways. It develops a theoretical framework for modeling, pricing analysis, and computation of electric power flows/transactions in electric power systems using the rationale for supply chain analysis. The models developed include both static and dynamic ones. The dissertation also adds a new dimension to the methodology of the theory of projected dynamical systems by proving that, irrespective of the speeds of adjustment, the equilibrium of the system remains the same. Finally, I include alternative fuel suppliers, along with their behavior into the supply chain modeling and analysis framework. This dissertation has strong practical implications. In an era in which technology and globalization, coupled with increasing risk and uncertainty, complicate electricity demand and supply within and between nations, the successful management of electric power systems and pricing become increasingly pressing topics with relevance not only for economic prosperity but also national security. This dissertation addresses such related topics by providing models, pricing tools, and algorithms for decentralized electric power supply chains. This dissertation is based heavily on the following

  17. Opportunities and Challenges in the Design and Analysis of Biomass Supply Chains.

    PubMed

    Lautala, Pasi T; Hilliard, Michael R; Webb, Erin; Busch, Ingrid; Richard Hess, J; Roni, Mohammad S; Hilbert, Jorge; Handler, Robert M; Bittencourt, Roger; Valente, Amir; Laitinen, Tuuli

    2015-12-01

    The biomass supply chain is one of the most critical elements of large-scale bioenergy production and in many cases a key barrier for procuring initial funding for new developments on specific energy crops. Most productions rely on complex transforming chains linked to feed and food markets. The term 'supply chain' covers various aspects from cultivation and harvesting of the biomass, to treatment, transportation, and storage. After energy conversion, the product must be delivered to final consumption, whether it is in the form of electricity, heat, or more tangible products, such as pellets and biofuels. Effective supply chains are of utmost importance for bioenergy production, as biomass tends to possess challenging seasonal production cycles and low mass, energy and bulk densities. Additionally, the demand for final products is often also dispersed, further complicating the supply chain. The goal of this paper is to introduce key components of biomass supply chains, examples of related modeling applications, and if/how they address aspects related to environmental metrics and management. The paper will introduce a concept of integrated supply systems for sustainable biomass trade and the factors influencing the bioenergy supply chain landscape, including models that can be used to investigate the factors. The paper will also cover various aspects of transportation logistics, ranging from alternative modal and multi-modal alternatives to introduction of support tools for transportation analysis. Finally gaps and challenges in supply chain research are identified and used to outline research recommendations for the future direction in this area of study. PMID:26122631

  18. Opportunities and Challenges in the Design and Analysis of Biomass Supply Chains

    SciTech Connect

    Lautala, Pasi T.; Hilliard, Michael R.; Webb, Erin; Busch, Ingrid; Richard Hess, J.; Roni, Mohammad S.; Hilbert, Jorge; Handler, Robert M.; Bittencourt, Roger; Valente, Amir; Laitinen, Tuuli

    2015-06-30

    The biomass supply chain is one of the most critical elements of large-scale bioenergy production and in many cases a key barrier for procuring initial funding for new developments on specific energy crops. Most productions rely on complex transforming chains linked to feed and food markets. The term 'supply chain' covers various aspects from cultivation and harvesting of the biomass, to treatment, transportation, and storage. After energy conversion, the product must be delivered to final consumption, whether it is in the form of electricity, heat, or more tangible products, such as pellets and biofuels. Effective supply chains are of utmost importance for bioenergy production, as biomass tends to possess challenging seasonal production cycles and low mass, energy and bulk densities. Additionally, the demand for final products is often also dispersed, further complicating the supply chain. The goal of this paper is to introduce key components of biomass supply chains, examples of related modeling applications, and if/how they address aspects related to environmental metrics and management. The paper will introduce a concept of integrated supply systems for sustainable biomass trade and the factors influencing the bioenergy supply chain landscape, including models that can be used to investigate the factors. Our paper will also cover various aspects of transportation logistics, ranging from alternative modal and multi-modal alternatives to introduction of support tools for transportation analysis. Lastly, gaps and challenges in supply chain research are identified and used to outline research recommendations for the future direction in this area of study.

  19. Opportunities and Challenges in the Design and Analysis of Biomass Supply Chains

    NASA Astrophysics Data System (ADS)

    Lautala, Pasi T.; Hilliard, Michael R.; Webb, Erin; Busch, Ingrid; Richard Hess, J.; Roni, Mohammad S.; Hilbert, Jorge; Handler, Robert M.; Bittencourt, Roger; Valente, Amir; Laitinen, Tuuli

    2015-12-01

    The biomass supply chain is one of the most critical elements of large-scale bioenergy production and in many cases a key barrier for procuring initial funding for new developments on specific energy crops. Most productions rely on complex transforming chains linked to feed and food markets. The term `supply chain' covers various aspects from cultivation and harvesting of the biomass, to treatment, transportation, and storage. After energy conversion, the product must be delivered to final consumption, whether it is in the form of electricity, heat, or more tangible products, such as pellets and biofuels. Effective supply chains are of utmost importance for bioenergy production, as biomass tends to possess challenging seasonal production cycles and low mass, energy and bulk densities. Additionally, the demand for final products is often also dispersed, further complicating the supply chain. The goal of this paper is to introduce key components of biomass supply chains, examples of related modeling applications, and if/how they address aspects related to environmental metrics and management. The paper will introduce a concept of integrated supply systems for sustainable biomass trade and the factors influencing the bioenergy supply chain landscape, including models that can be used to investigate the factors. The paper will also cover various aspects of transportation logistics, ranging from alternative modal and multi-modal alternatives to introduction of support tools for transportation analysis. Finally gaps and challenges in supply chain research are identified and used to outline research recommendations for the future direction in this area of study.

  20. Analysis of a closed-kinematic chain robot manipulator

    NASA Technical Reports Server (NTRS)

    Nguyen, Charles C.; Pooran, Farhad J.

    1988-01-01

    Presented are the research results from the research grant entitled: Active Control of Robot Manipulators, sponsored by the Goddard Space Flight Center (NASA) under grant number NAG-780. This report considers a class of robot manipulators based on the closed-kinematic chain mechanism (CKCM). This type of robot manipulators mainly consists of two platforms, one is stationary and the other moving, and they are coupled together through a number of in-parallel actuators. Using spatial geometry and homogeneous transformation, a closed-form solution is derived for the inverse kinematic problem of the six-degree-of-freedom manipulator, built to study robotic assembly in space. Iterative Newton Raphson method is employed to solve the forward kinematic problem. Finally, the equations of motion of the above manipulators are obtained by employing the Lagrangian method. Study of the manipulator dynamics is performed using computer simulation whose results show that the robot actuating forces are strongly dependent on the mass and centroid locations of the robot links.

  1. Functional Analysis of a Mosquito Short Chain Dehydrogenase Cluster

    PubMed Central

    Mayoral, Jaime G.; Leonard, Kate T.; Defelipe, Lucas A.; Turjansksi, Adrian G.; Nouzova, Marcela; Noriegal, Fernando G.

    2013-01-01

    The short chain dehydrogenases (SDR) constitute one the oldest and largest families of enzymes with over 46,000 members in sequence databases. About 25% of all known dehydrogenases belong to the SDR family. SDR enzymes have critical roles in lipid, amino acid, carbohydrate, hormone and xenobiotic metabolism as well as in redox sensor mechanisms. This family is present in archaea, bacteria, and eukaryota, emphasizing their versatility and fundamental importance for metabolic processes. We identified a cluster of eight SDRs in the mosquito Aedes aegypti (AaSDRs). Members of the cluster differ in tissue specificity and developmental expression. Heterologous expression produced recombinant proteins that had diverse substrate specificities, but distinct from the conventional insect alcohol (ethanol) dehydrogenases. They are all NADP+-dependent and they have S-enantioselectivity and preference for secondary alcohols with 8–15 carbons. Homology modeling was used to build the structure of AaSDR1 and two additional cluster members. The computational study helped explain the selectivity towards the (10S)-isomers as well as the reduced activity of AaSDR4 and AaSDR9 for longer isoprenoid substrates. Similar clusters of SDRs are present in other species of insects, suggesting similar selection mechanisms causing duplication and diversification of this family of enzymes. PMID:23238893

  2. Kinematic and dynamic modeling and approximate analysis of a roller chain drive

    NASA Astrophysics Data System (ADS)

    Fuglede, Niels; Thomsen, Jon Juel

    2016-03-01

    A simple roller chain drive consisting of two sprockets connected by tight chain spans is investigated. First, a kinematic model is presented which include both spans and sprockets. An approach for calculating the chain wrapping length is presented, which also allows for the exact calculation of sprocket center positions for a given chain length. The kinematic analysis demonstrates that the total length of the chain wrapped around the sprockets generally varies during one tooth period. Analytical predictions for the wrapping length are compared to multibody simulation results and show very good agreement. It is thereby demonstrated that chain drives with tight chain spans must include compliant components to function. Second, a dynamic model is presented which includes the two spans and the driven sprocket. Assuming the presence of a stationary operating state, the presented dynamic model allows for analytical studies of the coupled motion of the chain spans and driven sprocket. Parametric excitation of the spans come from sprocket angular displacements, and the driven sprocket acts as a boundary which can be compliant in the axial direction. External transverse excitation of the spans comes from polygonal action, and is treated through kinematic forcing at the moving string boundaries. Perturbation analysis of the model is carried out using the method of multiple scales. Results show a multitude of internal and external resonance conditions, and some examples are presented of both decoupled and coupled motion. Together, the kinematic and dynamic model are aimed toward providing a framework for conducting and understanding both numerical, and experimental investigations of roller chain drive dynamics.

  3. Sequence Analysis and Domain Motifs in the Porcine Skin Decorin Glycosaminoglycan Chain*

    PubMed Central

    Zhao, Xue; Yang, Bo; Solakylidirim, Kemal; Joo, Eun Ji; Toida, Toshihiko; Higashi, Kyohei; Linhardt, Robert J.; Li, Lingyun

    2013-01-01

    Decorin proteoglycan is comprised of a core protein containing a single O-linked dermatan sulfate/chondroitin sulfate glycosaminoglycan (GAG) chain. Although the sequence of the decorin core protein is determined by the gene encoding its structure, the structure of its GAG chain is determined in the Golgi. The recent application of modern MS to bikunin, a far simpler chondroitin sulfate proteoglycans, suggests that it has a single or small number of defined sequences. On this basis, a similar approach to sequence the decorin of porcine skin much larger and more structurally complex dermatan sulfate/chondroitin sulfate GAG chain was undertaken. This approach resulted in information on the consistency/variability of its linkage region at the reducing end of the GAG chain, its iduronic acid-rich domain, glucuronic acid-rich domain, and non-reducing end. A general motif for the porcine skin decorin GAG chain was established. A single small decorin GAG chain was sequenced using MS/MS analysis. The data obtained in the study suggest that the decorin GAG chain has a small or a limited number of sequences. PMID:23423381

  4. A Markov Chain Monte Carlo Approach to Confirmatory Item Factor Analysis

    ERIC Educational Resources Information Center

    Edwards, Michael C.

    2010-01-01

    Item factor analysis has a rich tradition in both the structural equation modeling and item response theory frameworks. The goal of this paper is to demonstrate a novel combination of various Markov chain Monte Carlo (MCMC) estimation routines to estimate parameters of a wide variety of confirmatory item factor analysis models. Further, I show…

  5. Detection and analysis of polymerase chain reaction products by mass spectrometry

    SciTech Connect

    Hurst, G.B., Doktycz, M.J., Britt, P.F., Vass, A.A., Buchanan, M.V.

    1997-02-01

    This paper describes recent and ongoing efforts to overcome some of the obstacles to more routine and robust application of MALDI-TOF to analysis of polymerase chain reaction products and other information- bearing nucleic acid molecules. Methods for purifying nucleic acid samples are described, as is the application of delayed extraction TOF mass spectrometry to analysis of short oligonucleotides.

  6. Supply chain analysis of e-tailing versus retailing operation - a case study

    NASA Astrophysics Data System (ADS)

    Kumar, Sameer; Tiffany, Maryellen; Vaidya, Salil

    2016-07-01

    The swift growth of e-commerce or e-tailing as a consumer retail channel has made it a serious competitor to traditional retail channels and is changing consumers' purchasing behaviour. The purpose of this case study, based on Target and Amazon.com, is to analyse the attributes of traditional retailing, e-tailing, and hybrid supply chain models to form conclusions about the feasibility of an idealised supply chain model for the future. An integrated and generalised modelling framework is used that incorporates Six Sigma - define, measure, analyse, improve, control methodology leveraging various tools, including process flow maps, cause and effect diagram, performance efficiency metrics, failure mode and effects analysis (FMEA), and Monte Carlo simulation. Based on this analysis and research, the conclusion is that the idealised supply chain of the future may evolve into a hybrid supply chain, which includes both e-tail and retail channels. The main recommendations from this study include assessing the risks of migrating to such a hybrid supply chain and to leverage the recommended actions provided in the hybrid FMEA. To facilitate more effective and mature processes, this study can guide researchers in exhaustive empirical evaluations of hybrid supply chains, gather experiences and lessons learned for practitioners.

  7. An improved spanning tree approach for the reliability analysis of supply chain collaborative network

    NASA Astrophysics Data System (ADS)

    Lam, C. Y.; Ip, W. H.

    2012-11-01

    A higher degree of reliability in the collaborative network can increase the competitiveness and performance of an entire supply chain. As supply chain networks grow more complex, the consequences of unreliable behaviour become increasingly severe in terms of cost, effort and time. Moreover, it is computationally difficult to calculate the network reliability of a Non-deterministic Polynomial-time hard (NP-hard) all-terminal network using state enumeration, as this may require a huge number of iterations for topology optimisation. Therefore, this paper proposes an alternative approach of an improved spanning tree for reliability analysis to help effectively evaluate and analyse the reliability of collaborative networks in supply chains and reduce the comparative computational complexity of algorithms. Set theory is employed to evaluate and model the all-terminal reliability of the improved spanning tree algorithm and present a case study of a supply chain used in lamp production to illustrate the application of the proposed approach.

  8. Analysis of the sensitivity of a model of terrestrial food chains

    SciTech Connect

    Ganushik, V.; Mitro, A.; Musatova, O.; Sabova, T.

    1985-10-01

    This paper estimates, by means of a sensitivity analysis, the importance of the individual parameters of the model for terrestrial food chains. This method creates the basis for the calculation of the numerical values of the buildup factors of radionuclides in the chain deposited from the atmosphere-the content in food products. The ORB-11 model describes the transportation of radioactive substances through food chains. Several principal food products are considered: wheat, fruits, cucumbers, cabbage, potato, milk, and meat. The coefficient of sensitivity (CS) was computed for each input parameter, radionuclide, contamination route, and given change of input parameter by formula. The data obtained can be used for a stochastic approach to the mnDeling of the transportation of radioactive substances through the food chains, and to the planning of radioecological investigations.

  9. Analysis of liver connexin expression using reverse transcription quantitative real-time polymerase chain reaction

    PubMed Central

    Maes, Michaël; Willebrords, Joost; Crespo Yanguas, Sara; Cogliati, Bruno; Vinken, Mathieu

    2016-01-01

    Summary Although connexin production is mainly regulated at the protein level, altered connexin gene expression has been identified as the underlying mechanism of several pathologies. When studying the latter, appropriate methods to quantify connexin mRNA levels are required. The present chapter describes a well-established reverse transcription quantitative real-time polymerase chain reaction procedure optimized for analysis of hepatic connexins. The method includes RNA extraction and subsequent quantification, generation of complementary DNA, quantitative real-time polymerase chain reaction and data analysis. PMID:27207283

  10. Analysis of Liver Connexin Expression Using Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction.

    PubMed

    Maes, Michaël; Willebrords, Joost; Crespo Yanguas, Sara; Cogliati, Bruno; Vinken, Mathieu

    2016-01-01

    Although connexin production is mainly regulated at the protein level, altered connexin gene expression has been identified as the underlying mechanism of several pathologies. When studying the latter, appropriate methods to quantify connexin RNA levels are required. The present chapter describes a well-established reverse transcription quantitative real-time polymerase chain reaction procedure optimized for analysis of hepatic connexins. The method includes RNA extraction and subsequent quantification, generation of complementary DNA, quantitative real-time polymerase chain reaction, and data analysis. PMID:27207283

  11. Elastic coefficient of a single polymer chain by using Brownian dynamics analysis

    NASA Astrophysics Data System (ADS)

    Horinaka, J.; Maniwa, T.; Oharada, K.; Takigawa, T.

    2007-08-01

    The elastic coefficient of a single polystyrene chain has been experimentally evaluated by using Brownian dynamics analysis. The Brownian motion of the chain is probed using a particle trapped by optical tweezers with a negligibly small spring constant. The displacement of the particle due to Brownian motion is measured by an interferometer assembled using the same laser beam as the optical tweezers. Two methods are employed for Brownian dynamics analysis: (1) the analysis of the time course of the displacement of the particle and (2) the fitting of the power spectrum of Brownian motion with a Lorentzian. The elastic constant of a polystyrene chain in dichloromethane at 21 °C is estimated to be 6.4×10-6 and 1.1×10-5 N/m when methods (1) and (2) are employed, respectively. The elastic constant obtained by approximating the polystyrene chain to a freely jointed chain is in agreement with the experimentally evaluated elastic constant.

  12. Reliability analysis and prediction of mixed mode load using Markov Chain Model

    NASA Astrophysics Data System (ADS)

    Nikabdullah, N.; Singh, S. S. K.; Alebrahim, R.; Azizi, M. A.; K, Elwaleed A.; Noorani, M. S. M.

    2014-06-01

    The aim of this paper is to present the reliability analysis and prediction of mixed mode loading by using a simple two state Markov Chain Model for an automotive crankshaft. The reliability analysis and prediction for any automotive component or structure is important for analyzing and measuring the failure to increase the design life, eliminate or reduce the likelihood of failures and safety risk. The mechanical failures of the crankshaft are due of high bending and torsion stress concentration from high cycle and low rotating bending and torsional stress. The Markov Chain was used to model the two states based on the probability of failure due to bending and torsion stress. In most investigations it revealed that bending stress is much serve than torsional stress, therefore the probability criteria for the bending state would be higher compared to the torsion state. A statistical comparison between the developed Markov Chain Model and field data was done to observe the percentage of error. The reliability analysis and prediction was derived and illustrated from the Markov Chain Model were shown in the Weibull probability and cumulative distribution function, hazard rate and reliability curve and the bathtub curve. It can be concluded that Markov Chain Model has the ability to generate near similar data with minimal percentage of error and for a practical application; the proposed model provides a good accuracy in determining the reliability for the crankshaft under mixed mode loading.

  13. Reliability analysis and prediction of mixed mode load using Markov Chain Model

    SciTech Connect

    Nikabdullah, N.; Singh, S. S. K.; Alebrahim, R.; Azizi, M. A.; K, Elwaleed A.; Noorani, M. S. M.

    2014-06-19

    The aim of this paper is to present the reliability analysis and prediction of mixed mode loading by using a simple two state Markov Chain Model for an automotive crankshaft. The reliability analysis and prediction for any automotive component or structure is important for analyzing and measuring the failure to increase the design life, eliminate or reduce the likelihood of failures and safety risk. The mechanical failures of the crankshaft are due of high bending and torsion stress concentration from high cycle and low rotating bending and torsional stress. The Markov Chain was used to model the two states based on the probability of failure due to bending and torsion stress. In most investigations it revealed that bending stress is much serve than torsional stress, therefore the probability criteria for the bending state would be higher compared to the torsion state. A statistical comparison between the developed Markov Chain Model and field data was done to observe the percentage of error. The reliability analysis and prediction was derived and illustrated from the Markov Chain Model were shown in the Weibull probability and cumulative distribution function, hazard rate and reliability curve and the bathtub curve. It can be concluded that Markov Chain Model has the ability to generate near similar data with minimal percentage of error and for a practical application; the proposed model provides a good accuracy in determining the reliability for the crankshaft under mixed mode loading.

  14. Extraction, purification, methylation and GC-MS analysis of short-chain carboxylic acids for metabolic flux analysis.

    PubMed

    Tivendale, Nathan D; Jewett, Erin M; Hegeman, Adrian D; Cohen, Jerry D

    2016-08-15

    Dynamic metabolic flux analysis requires efficient and effective methods for extraction, purification and analysis of a plethora of naturally-occurring compounds. One area of metabolism that would be highly informative to study using metabolic flux analysis is the tricarboxylic acid (TCA) cycle, which consists of short-chain carboxylic acids. Here, we describe a newly-developed method for extraction, purification, derivatization and analysis of short-chain carboxylic acids involved in the TCA cycle. The method consists of snap-freezing the plant material, followed by maceration and a 12-15h extraction at -80 °C. The extracts are then subject to reduction (to stabilize β-keto acids), purified by strong anion exchange solid phase extraction and methylated with methanolic HCl. This method could also be readily adapted to quantify many other short-chain carboxylic acids. PMID:27348709

  15. Opportunities and Challenges in the Design and Analysis of Biomass Supply Chains

    DOE PAGESBeta

    Lautala, Pasi T.; Hilliard, Michael R.; Webb, Erin; Busch, Ingrid; Richard Hess, J.; Roni, Mohammad S.; Hilbert, Jorge; Handler, Robert M.; Bittencourt, Roger; Valente, Amir; et al

    2015-06-30

    The biomass supply chain is one of the most critical elements of large-scale bioenergy production and in many cases a key barrier for procuring initial funding for new developments on specific energy crops. Most productions rely on complex transforming chains linked to feed and food markets. The term 'supply chain' covers various aspects from cultivation and harvesting of the biomass, to treatment, transportation, and storage. After energy conversion, the product must be delivered to final consumption, whether it is in the form of electricity, heat, or more tangible products, such as pellets and biofuels. Effective supply chains are of utmostmore » importance for bioenergy production, as biomass tends to possess challenging seasonal production cycles and low mass, energy and bulk densities. Additionally, the demand for final products is often also dispersed, further complicating the supply chain. The goal of this paper is to introduce key components of biomass supply chains, examples of related modeling applications, and if/how they address aspects related to environmental metrics and management. The paper will introduce a concept of integrated supply systems for sustainable biomass trade and the factors influencing the bioenergy supply chain landscape, including models that can be used to investigate the factors. Our paper will also cover various aspects of transportation logistics, ranging from alternative modal and multi-modal alternatives to introduction of support tools for transportation analysis. Lastly, gaps and challenges in supply chain research are identified and used to outline research recommendations for the future direction in this area of study.« less

  16. Supply Chain Sustainability Analysis of Three Biofuel Pathways

    SciTech Connect

    Jacob J. Jacobson; Erin Searcy; Kara Cafferty; Jennifer B. Dunn; Michael Johnson; Zhichao Wang; Michael Wang; Mary Biddy; Abhijit Dutta; Daniel Inman; Eric Tan; Sue Jones; Lesley Snowden-Swan

    2013-11-01

    The Department of Energy’s (DOE) Bioenergy Technologies Office (BETO) collaborates with industrial, agricultural, and non-profit partners to develop and deploy biofuels and other biologically-derived products. As part of this effort, BETO and its national laboratory teams conduct in-depth techno-economic assessments (TEA) of technologies to produce biofuels as part state of technology (SOT) analyses. An SOT assesses progress within and across relevant technology areas based on actual experimental results relative to technical targets and cost goals from design cases and includes technical, economic, and environmental criteria as available. Overall assessments of biofuel pathways begin with feedstock production and the logistics of transporting the feedstock from the farm or plantation to the conversion facility or biorefinery. The conversion process itself is modeled in detail as part of the SOT analysis. The teams then develop an estimate of the biofuel minimum selling price (MSP) and assess the cost competitiveness of the biofuel with conventional fuels such as gasoline.

  17. Global analysis of SUMO chain function reveals multiple roles in chromatin regulation

    PubMed Central

    Srikumar, Tharan; Lewicki, Megan C.; Costanzo, Michael; Tkach, Johnny M.; van Bakel, Harm; Tsui, Kyle; Johnson, Erica S.; Brown, Grant W.; Andrews, Brenda J.; Boone, Charles; Giaever, Guri; Nislow, Corey

    2013-01-01

    Like ubiquitin, the small ubiquitin-related modifier (SUMO) proteins can form oligomeric “chains,” but the biological functions of these superstructures are not well understood. Here, we created mutant yeast strains unable to synthesize SUMO chains (smt3allR) and subjected them to high-content microscopic screening, synthetic genetic array (SGA) analysis, and high-density transcript profiling to perform the first global analysis of SUMO chain function. This comprehensive assessment identified 144 proteins with altered localization or intensity in smt3allR cells, 149 synthetic genetic interactions, and 225 mRNA transcripts (primarily consisting of stress- and nutrient-response genes) that displayed a >1.5-fold increase in expression levels. This information-rich resource strongly implicates SUMO chains in the regulation of chromatin. Indeed, using several different approaches, we demonstrate that SUMO chains are required for the maintenance of normal higher-order chromatin structure and transcriptional repression of environmental stress response genes in budding yeast. PMID:23547032

  18. Chain of custody; recommendations for acceptance and analysis of evidentiary geochemical samples

    USGS Publications Warehouse

    Murphy, Christine M.; Briggs, Paul H.; Adrian, Betty M.; Wilson, Steve A.; Hageman, Phil L.; Theodorakos, Pete M.

    1997-01-01

    Personnel from the Analytical Chemistry Services Group (ACSG), Mineral Resource Survey Program, formed a team to determine the policies for acceptance and analysis of geochemical samples. This team contacted law enforcement agencies that handle litigious samples, laboratories that work with samples of special nature, and the Solicitor General, Department of the Interior. Using the knowledge from these agencies as well as the expertise of ACSG personnel, sample control routine procedures, sample control evidentiary procedures, personnel policy governing chain-of-custody samples, and the general polices governing physical security of chain-of custody samples have been enacted.

  19. Rapid quantitative analysis of monoclonal antibody heavy and light chain charge heterogeneity

    PubMed Central

    Vanam, Ram P; Schneider, Michael A; Marlow, Michael S

    2015-01-01

    An alternative method to traditional 2-dimensional gel electrophoresis (2D-PAGE) and its application in characterizing the inherent charge heterogeneity of chromatographically isolated monoclonal antibody heavy and light chains is described. This method, referred to as ChromiCE, utilizes analytical size-exclusion chromatography (SEC), performed under reducing and denaturing conditions, followed by imaged capillary isoelectric focusing (icIEF) of the chromatographically separated heavy and light chains. Under conditions suitable for the subsequent icIEF analysis, the absolute and relative SEC elution volumes of the heavy and light chains were found to be highly pH dependent, a phenomenon that can be exploited in optimizing chromatographic separation. Compared to 2D-PAGE, the ChromiCE method substantially decreases the time and labor needed to complete the analysis, improves reproducibility, and provides fully quantitative assessment of charge heterogeneity. The ChromiCE methodology was applied to a set of diverse monoclonal antibodies to demonstrate suitability for quantitative charge variant analysis of heavy and light chains. A typical application of ChromiCE in extended characterization and stability studies of a purified antibody is shown. PMID:26305772

  20. Marathon: An Open Source Software Library for the Analysis of Markov-Chain Monte Carlo Algorithms.

    PubMed

    Rechner, Steffen; Berger, Annabell

    2016-01-01

    We present the software library marathon, which is designed to support the analysis of sampling algorithms that are based on the Markov-Chain Monte Carlo principle. The main application of this library is the computation of properties of so-called state graphs, which represent the structure of Markov chains. We demonstrate applications and the usefulness of marathon by investigating the quality of several bounding methods on four well-known Markov chains for sampling perfect matchings and bipartite graphs. In a set of experiments, we compute the total mixing time and several of its bounds for a large number of input instances. We find that the upper bound gained by the famous canonical path method is often several magnitudes larger than the total mixing time and deteriorates with growing input size. In contrast, the spectral bound is found to be a precise approximation of the total mixing time. PMID:26824442

  1. Marathon: An Open Source Software Library for the Analysis of Markov-Chain Monte Carlo Algorithms

    PubMed Central

    Rechner, Steffen; Berger, Annabell

    2016-01-01

    We present the software library marathon, which is designed to support the analysis of sampling algorithms that are based on the Markov-Chain Monte Carlo principle. The main application of this library is the computation of properties of so-called state graphs, which represent the structure of Markov chains. We demonstrate applications and the usefulness of marathon by investigating the quality of several bounding methods on four well-known Markov chains for sampling perfect matchings and bipartite graphs. In a set of experiments, we compute the total mixing time and several of its bounds for a large number of input instances. We find that the upper bound gained by the famous canonical path method is often several magnitudes larger than the total mixing time and deteriorates with growing input size. In contrast, the spectral bound is found to be a precise approximation of the total mixing time. PMID:26824442

  2. Improving food safety within the dairy chain: an application of conjoint analysis.

    PubMed

    Valeeva, N I; Meuwissen, M P M; Lansink, A G J M Oude; Huirne, R B M

    2005-04-01

    This study determined the relative importance of attributes of food safety improvement in the production chain of fluid pasteurized milk. The chain was divided into 4 blocks: "feed" (compound feed production and its transport), "farm" (dairy farm), "dairy processing" (transport and processing of raw milk, delivery of pasteurized milk), and "consumer" (retailer/catering establishment and pasteurized milk consumption). The concept of food safety improvement focused on 2 main groups of hazards: chemical (antibiotics and dioxin) and microbiological (Salmonella, Escherichia coli, Mycobacterium paratuberculosis, and Staphylococcus aureus). Adaptive conjoint analysis was used to investigate food safety experts' perceptions of the attributes' importance. Preference data from individual experts (n = 24) on 101 attributes along the chain were collected in a computer-interactive mode. Experts perceived the attributes from the "feed" and "farm" blocks as being more vital for controlling the chemical hazards; whereas the attributes from the "farm" and "dairy processing" were considered more vital for controlling the microbiological hazards. For the chemical hazards, "identification of treated cows" and "quality assurance system of compound feed manufacturers" were considered the most important attributes. For the microbiological hazards, these were "manure supply source" and "action in salmonellosis and M. paratuberculosis cases". The rather high importance of attributes relating to quality assurance and traceability systems of the chain participants indicates that participants look for food safety assurance from the preceding participants. This information has substantial decision-making implications for private businesses along the chain and for the government regarding the food safety improvement of fluid pasteurized milk. PMID:15778330

  3. The Creative Use of Chain Analysis Techniques in Counseling Clients Who Engage in Nonsuicidal Self-Injury

    ERIC Educational Resources Information Center

    Kinch, Stephanie; Kress, Victoria E.

    2012-01-01

    The purpose of this article is to present creative ways that chain analysis techniques, an intervention used in dialectical behavior therapy, can be used to address clients' nonsuicidal self-injurious behaviors. A description and rationale for using chain analysis techniques with clients who self-injure is provided. An illustrative case example is…

  4. Video analysis of sliding chains: A dynamic model based on variable-mass systems

    NASA Astrophysics Data System (ADS)

    Moreno, R.; Page, A.; Riera, J.; Hueso, J. L.

    2015-06-01

    This paper presents an experimental study of the dynamics of a chain sliding off of a table, using video analysis to test a theoretical model. The model consists of two variable-mass subsystems, with friction between the chain and the table and assumes that all links move at the same speed. In order to check the model, the chain position x(t) is obtained using video analysis. The smoothed function x(t) and its derivatives v(t) and a(t) are numerically computed using a local regression algorithm. In this way, the differential equation governing the motion can be directly tested, instead of comparing the position with the solution of the differential equation. Our procedure is very sensitive to deviations between the model and reality, so we can detect the point at which the chain ceases to be in tension and the model is no longer valid. This experiment shows students the limitations of simplified models and offers an opportunity to assess a model's range of validity.

  5. Deriving non-homogeneous DNA Markov chain models by cluster analysis algorithm minimizing multiple alignment entropy.

    PubMed

    Borodovsky, M; Peresetsky, A

    1994-09-01

    Non-homogeneous Markov chain models can represent biologically important regions of DNA sequences. The statistical pattern that is described by these models is usually weak and was found primarily because of strong biological indications. The general method for extracting similar patterns is presented in the current paper. The algorithm incorporates cluster analysis, multiple alignment and entropy minimization. The method was first tested using the set of DNA sequences produced by Markov chain generators. It was shown that artificial gene sequences, which initially have been randomly set up along the multiple alignment panels, are aligned according to the hidden triplet phase. Then the method was applied to real protein-coding sequences and the resulting alignment clearly indicated the triplet phase and produced the parameters of the optimal 3-periodic non-homogeneous Markov chain model. These Markov models were already employed in the GeneMark gene prediction algorithm, which is used in genome sequencing projects. The algorithm can also handle the case in which the sequences to be aligned reveal different statistical patterns, such as Escherichia coli protein-coding sequences belonging to Class II and Class III. The algorithm accepts a random mix of sequences from different classes, and is able to separate them into two groups (clusters), align each cluster separately, and define a non-homogeneous Markov chain model for each sequence cluster. PMID:7952897

  6. Empirical Analysis of Green Supply Chain Management Practices in Indian Automobile Industry

    NASA Astrophysics Data System (ADS)

    Luthra, S.; Garg, D.; Haleem, A.

    2014-04-01

    Environmental sustainability and green environmental issues have an increasing popularity among researchers and supply chain practitioners. An attempt has been made to identify and empirically analyze green supply chain management (GSCM) practices in Indian automobile industry. Six main GSCM practices (having 37 sub practices) and four expected performance outcomes (having 16 performances) have been identified by implementing GSCM practices from literature review. Questionnaire based survey has been made to validate these practices and performance outcomes. 123 complete questionnaires were collected from Indian automobile organizations and used for empirical analysis of GSCM practices in Indian automobile industry. Descriptive statistics have been used to know current implementation status of GSCM practices in Indian automobile industry and multiple regression analysis has been carried out to know the impact on expected organizational performance outcomes by current GSCM practices adopted by Indian automobile industry. The results of study suggested that environmental, economic, social and operational performances improve with the implementation of GSCM practices. This paper may play an important role to understand various GSCM implementation issues and help practicing managers to improve their performances in the supply chain.

  7. The Relationship between Means-End Task Analysis and Context-Specific and Global Self-Efficacy in Emergency Certification Teachers: Exploring a New Model of Teacher Efficacy.

    ERIC Educational Resources Information Center

    Henson, Robin K.; Bennett, D. Tyson; Sienty, Sarah F.; Chambers, Sharon M.

    While consistently related to positive teacher behaviors and student outcomes, teacher efficacy as a construct is currently the subject of debate. The present study examined a new model of teacher efficacy (Tschannen-Moran, Woolfolk Hoy, & Hoy, 1998) that proposes to more clearly define important variables and integrate two theoretical traditions…

  8. Genome-Wide Analysis of Branched-Chain Amino Acid Levels in Arabidopsis Seeds[W

    PubMed Central

    Angelovici, Ruthie; Lipka, Alexander E.; Deason, Nicholas; Gonzalez-Jorge, Sabrina; Lin, Haining; Cepela, Jason; Buell, Robin; Gore, Michael A.; DellaPenna, Dean

    2013-01-01

    Branched-chain amino acids (BCAAs) are three of the nine essential amino acids in human and animal diets and are important for numerous processes in development and growth. However, seed BCAA levels in major crops are insufficient to meet dietary requirements, making genetic improvement for increased and balanced seed BCAAs an important nutritional target. Addressing this issue requires a better understanding of the genetics underlying seed BCAA content and composition. Here, a genome-wide association study and haplotype analysis for seed BCAA traits in Arabidopsis thaliana revealed a strong association with a chromosomal interval containing two BRANCHED-CHAIN AMINO ACID TRANSFERASES, BCAT1 and BCAT2. Linkage analysis, reverse genetic approaches, and molecular complementation analysis demonstrated that allelic variation at BCAT2 is responsible for the natural variation of seed BCAAs in this interval. Complementation analysis of a bcat2 null mutant with two significantly different alleles from accessions Bayreuth-0 and Shahdara is consistent with BCAT2 contributing to natural variation in BCAA levels, glutamate recycling, and free amino acid homeostasis in seeds in an allele-dependent manner. The seed-specific phenotype of bcat2 null alleles, its strong transcription induction during late seed development, and its subcellular localization to the mitochondria are consistent with a unique, catabolic role for BCAT2 in BCAA metabolism in seeds. PMID:24368787

  9. Analysis of Long-Chain Unsaturated Fatty Acids by Ionic Liquid Gas Chromatography.

    PubMed

    Weatherly, Choyce A; Zhang, Ying; Smuts, Jonathan P; Fan, Hui; Xu, Chengdong; Schug, Kevin A; Lang, John C; Armstrong, Daniel W

    2016-02-17

    Four ionic liquid (IL) columns, SLB-IL59, SLB-IL60, SLB-IL65, and SLB-IL111, were evaluated for more rapid analysis or improved resolution of long-chain methyl and ethyl esters of omega-3, omega-6, and additional positional isomeric and stereoisomeric blends of fatty acids found in fish oil, flaxseed oil, and potentially more complicated compositions. The three structurally distinct IL columns provided shorter retention times and more symmetric peak shapes for the fatty acid methyl or ethyl esters than a conventional polyethylene glycol column (PEG), resolving cis- and trans-fatty acid isomers that coeluted on the PEG column. The potential for improved resolution of fatty acid esters is important for complex food and supplement applications, where different forms of fatty acid can be incorporated. Vacuum ultraviolet detection contributed to further resolution for intricate mixtures containing cis- and trans-isomers, as exemplified in a fatty acid blend of shorter chain C18:1 esters with longer chain polyunsaturated fatty acid (PUFA) esters. PMID:26852774

  10. Flow cytometric analysis of expression of interleukin-2 receptor beta chain (p70-75) on various leukemic cells

    SciTech Connect

    Hoshino, S.; Oshimi, K.; Tsudo, M.; Miyasaka, M.; Teramura, M.; Masuda, M.; Motoji, T.; Mizoguchi, H. )

    1990-08-15

    We analyzed the expression of the interleukin-2 receptor (IL-2R) beta chain (p70-75) on various leukemic cells from 44 patients by flow cytometric analysis using the IL-2R beta chain-specific monoclonal antibody, designated Mik-beta 1. Flow cytometric analysis demonstrated the expression of the IL-2R beta chain on granular lymphocytes (GLs) from all eight patients with granular lymphocyte proliferative disorders (GLPDs), on adult T-cell leukemia (ATL) cells from all three patients with ATL, and on T-cell acute lymphoblastic leukemia (T-ALL) cells from one of three patients with T-ALL. Although GLs from all the GLPD patients expressed the IL-2R beta chain alone and not the IL-2R alpha chain (Tac-antigen: p55), ATL and T-ALL cells expressing the beta chain coexpressed the alpha chain. In two of seven patients with common ALL (cALL) and in both patients with B-cell chronic lymphocytic leukemia, the leukemic cells expressed the alpha chain alone. Neither the alpha chain nor the beta chain was expressed on leukemic cells from the remaining 28 patients, including all 18 patients with acute nonlymphocytic leukemia, five of seven patients with cALL, all three patients with multiple myeloma, and two of three patients with T-ALL. These results indicate that three different forms of IL-2R chain expression exist on leukemic cells: the alpha chain alone; the beta chain alone; and both the alpha and beta chains. To examine whether the results obtained by flow cytometric analysis actually reflect functional aspects of the expressed IL-2Rs, we studied the specific binding of 125I-labeled IL-2 (125I-IL-2) to leukemic cells in 18 of the 44 patients. In addition, we performed 125I-IL-2 crosslinking studies in seven patients. The results of IL-2R expression of both 125I-IL-2 binding assay and crosslinking studies were in agreement with those obtained by flow cytometric analysis.

  11. Markov chain Monte Carlo linkage analysis of a complex qualitative phenotype.

    PubMed

    Hinrichs, A; Lin, J H; Reich, T; Bierut, L; Suarez, B K

    1999-01-01

    We tested a new computer program, LOKI, that implements a reversible jump Markov chain Monte Carlo (MCMC) technique for segregation and linkage analysis. Our objective was to determine whether this software, designed for use with continuously distributed phenotypes, has any efficacy when applied to the discrete disease states of the simulated data from the Mordor data from GAW Problem 1. Although we were able to identify the genomic location for two of the three quantitative trait loci by repeated application of the software, the MCMC sampler experienced significant mixing problems indicating that the method, as currently formulated in LOKI, was not suitable for the discrete phenotypes in this data set. PMID:10597502

  12. Loss of PEG chain in routine SDS-PAGE analysis of PEG-maleimide modified protein.

    PubMed

    Zhang, Chun; Liu, Yongdong; Feng, Cui; Wang, Qi; Shi, Hong; Zhao, Dawei; Yu, Rong; Su, Zhiguo

    2015-01-01

    SDS-PAGE represents a quick and simple method for qualitative and quantitative analysis of protein and protein-containing conjugates, mostly pegylated proteins. PEG-maleimide (MAL) is frequently used to site-specifically pegylate therapeutic proteins via free cysteine residue by forming a thiosuccinimide structure for pursuing homogeneous products. The C-S linkage between protein and PEG-MAL is generally thought to be relatively stable. However, loss of intact PEG chain in routine SDS-PAGE analysis of PEG-maleimide modified protein was observed. It is a thiol-independent thioether cleavage and the shedding of PEG chain exclusively happens to PEG-MAL modified conjugates although PEG-vinylsulfone conjugates to thiol-containing proteins also through a C-S linkage. Cleavage kinetics of PEG40k-MAL modified ciliary neurotrophic factor showed this kind of degradation could immediately happen even in 1 min incubation at high temperature and could be detected at physiological temperature and pH, although the rate was relatively slow. This may provide another degradation route for maleimide-thiol conjugate irrespective of reactive thiol, although the specific mechanism is still not very clear for us. It would also offer a basis for accurate characterization of PEG-MAL modified protein/peptide by SDS-PAGE analysis. PMID:25265901

  13. Brief Communication: Earthquake sequencing: analysis of time series constructed from the Markov chain model

    NASA Astrophysics Data System (ADS)

    Cavers, M. S.; Vasudevan, K.

    2015-10-01

    Directed graph representation of a Markov chain model to study global earthquake sequencing leads to a time series of state-to-state transition probabilities that includes the spatio-temporally linked recurrent events in the record-breaking sense. A state refers to a configuration comprised of zones with either the occurrence or non-occurrence of an earthquake in each zone in a pre-determined time interval. Since the time series is derived from non-linear and non-stationary earthquake sequencing, we use known analysis methods to glean new information. We apply decomposition procedures such as ensemble empirical mode decomposition (EEMD) to study the state-to-state fluctuations in each of the intrinsic mode functions. We subject the intrinsic mode functions, derived from the time series using the EEMD, to a detailed analysis to draw information content of the time series. Also, we investigate the influence of random noise on the data-driven state-to-state transition probabilities. We consider a second aspect of earthquake sequencing that is closely tied to its time-correlative behaviour. Here, we extend the Fano factor and Allan factor analysis to the time series of state-to-state transition frequencies of a Markov chain. Our results support not only the usefulness of the intrinsic mode functions in understanding the time series but also the presence of power-law behaviour exemplified by the Fano factor and the Allan factor.

  14. Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis.

    PubMed Central

    Telenti, A; Marchesi, F; Balz, M; Bally, F; Böttger, E C; Bodmer, T

    1993-01-01

    A method for the rapid identification of mycobacteria to the species level was developed on the basis of evaluation by the polymerase chain reaction (PCR) of the gene encoding for the 65-kDa protein. The method involves restriction enzyme analysis of PCR products obtained with primers common to all mycobacteria. Using two restriction enzymes, BstEII and HaeIII, medically relevant and other frequent laboratory isolates were differentiated to the species or subspecies level by PCR-restriction enzyme pattern analysis. PCR-restriction enzyme pattern analysis was performed on isolates (n = 330) from solid and fluid culture media, including BACTEC, or from frozen and lyophilized stocks. The procedure does not involve hybridization steps or the use of radioactivity and can be completed within 1 working day. Images PMID:8381805

  15. Stability and Bifurcation Analysis of a Three-Species Food Chain Model with Delay

    NASA Astrophysics Data System (ADS)

    Pal, Nikhil; Samanta, Sudip; Biswas, Santanu; Alquran, Marwan; Al-Khaled, Kamel; Chattopadhyay, Joydev

    In the present paper, we study the effect of gestation delay on a tri-trophic food chain model with Holling type-II functional response. The essential mathematical features of the proposed model are analyzed with the help of equilibrium analysis, stability analysis, and bifurcation theory. Considering time-delay as the bifurcation parameter, the Hopf-bifurcation analysis is carried out around the coexisting equilibrium. The direction of Hopf-bifurcation and the stability of the bifurcating periodic solutions are determined by applying the normal form theory and center manifold theorem. We observe that if the magnitude of the delay is increased, the system loses stability and shows limit cycle oscillations through Hopf-bifurcation. The system also shows the chaotic dynamics via period-doubling bifurcation for further enhancement of time-delay. Our analytical findings are illustrated through numerical simulations.

  16. U.S. Wind Energy Manufacturing and Supply Chain: A Competitiveness Analysis

    SciTech Connect

    Fullenkamp, Patrick H; Holody, Diane S

    2014-06-15

    The goal of the project was to develop a greater understanding of the key factors determining wind energy component manufacturing costs and pricing on a global basis in order to enhance the competitiveness of U.S. manufacturers, and to reduce installed systems cost. Multiple stakeholders including DOE, turbine OEMs, and large component manufactures will all benefit by better understanding the factors determining domestic competitiveness in the emerging offshore and next generation land-based wind industries. Major objectives of this project were to: 1. Carry out global cost and process comparisons for 5MW jacket foundations, blades, towers, and permanent magnet generators; 2. Assess U.S. manufacturers’ competitiveness and potential for cost reduction; 3. Facilitate informed decision-making on investments in U.S. manufacturing; 4. Develop an industry scorecard representing the readiness of the U.S. manufacturers’ to produce components for the next generations of wind turbines, nominally 3MW land-based and 5MW offshore; 5. Disseminate results through the GLWN Wind Supply Chain GIS Map, a free website that is the most comprehensive public database of U.S. wind energy suppliers; 6. Identify areas and develop recommendations to DOE on potential R&D areas to target for increasing domestic manufacturing competitiveness, per DOE’s Clean Energy Manufacturing Initiative (CEMI). Lists of Deliverables 1. Cost Breakdown Competitive Analyses of four product categories: tower, jacket foundation, blade, and permanent magnet (PM) generator. The cost breakdown for each component includes a complete Bill of Materials with net weights; general process steps for labor; and burden adjusted by each manufacturer for their process categories of SGA (sales general and administrative), engineering, logistics cost to a common U.S. port, and profit. 2. Value Stream Map Competitiveness Analysis: A tool that illustrates both information and material flow from the point of getting a

  17. A Markov Chain Analysis of Fish Movements to Determine Entrainment Zones

    SciTech Connect

    Johnson, Gary E.; Hedgepeth, J; Skalski, John R.; Giorgi, Albert E.

    2004-10-01

    Fish can become entrained at water withdrawal locations such as fish bypasses or cooling water intakes. Accordingly, the size of a fish entrainment zone (FEZ) is often of interest to fisheries managers and facility operators. This study developed a new technique to map the FEZ, defined here as the region immediately upstream of a portal where the probability of fish movement toward the portal is greater than 90%. To map the FEZ, we applied a Markov chain analysis to fish movement data collected with an active tracking sonar. This device locks onto and follows a target, recording positions through a set of volumetric cells comprising the sampled volume. The probability of a fish moving from one cell to another was calculated from fish position data, which was used to populate a Markov transition matrix. We developed and applied the technique using data on salmon smolts migrating near the ice/trash sluiceway at The Dalles Dam on the Columbia River. The FEZ of the sluiceway entrance in 2000 as determined with this procedure was approximately 5 m across and extended 6-8 m out from the face of the dam in the surface layer 2-3 m deep. In conclusion, using a Markov chain analysis of fish track data we were able to describe and quantify the FEZ of the sluiceway at The Dalles Dam. This technique for FEZ mapping is applicable to other bioengineering efforts aimed at protecting fish populations affected by water withdrawals.

  18. An example of neutronic penalizations in reactivity transient analysis using 3D coupled chain HEMERA

    SciTech Connect

    Dubois, F.; Normand, B.; Sargeni, A.

    2012-07-01

    HEMERA (Highly Evolutionary Methods for Extensive Reactor Analyses), is a fully coupled 3D computational chain developed jointly by IRSN and CEA. It is composed of CRONOS2 (core neutronics, cross sections library from APOLLO2), FLICA4 (core thermal-hydraulics) and the system code CATHARE. Multi-level and multi-dimensional models are developed to account for neutronics, core thermal-hydraulics, fuel thermal analysis and system thermal-hydraulics, dedicated to best-estimate, conservative simulations and sensitivity analysis. In IRSN, the HEMERA chain is widely used to study several types of reactivity accidents and for sensitivity studies. Just as an example of the HEMERA possibilities, we present here two types of neutronic penalizations and their impact on a power transient due to a REA (Rod Ejection Accident): in the first one, we studied a bum-up distribution modification and in the second one, a delayed-neutron fraction modification. Both modifications are applied to the whole core or localized in a few assemblies. Results show that it is possible to use global or local changes but 1) in case of bum-up modification, the total core power can increase when assembly peak power decrease so, care has to be taken if the goal is to maximize a local power peak and 2) for delayed-neutron fraction, a local modification can have the same effect as the one on the whole core, provided that it is large enough. (authors)

  19. Stochastic Analysis of Contaminant Transport in Porous Media: Analysis of a Two-Member Radionuclide Chain

    NASA Astrophysics Data System (ADS)

    Bonano, Evaristo J.; Shipers, Larry R.; Gutjahr, Allan L.

    1987-06-01

    In this study we extend previous stochastic analyses of contaminant transport in geologic media for a single species to a chain of two species. Our particular application is the quantification of uncertainties due to lack of characterization of the spatial variability of hydrologic parameters on transport of radionuclides from a high-level waste repository to the biosphere. Radionuclide chains can have a significant impact on demonstrating compliance (or violation) of standards regulating the release to the environment accessible to humans. Two approaches for determining the cross-covariance terms in the mean concentration equations are presented. One uses a Taylor expansion to obtain the cross-covariance between the velocity and concentration fluctuations, while the other is based on a Fourier-Laplace double transform method. For the conditions of interest here, the differences between these two approaches are expected to be small. In addition, the variances are calculated in a unique way by solving another associated partial differential equation. A parametric study is carried out to examine the sensitivity of the mean concentration of the two species and their corresponding variances and cross-covariance on the parameters associated with the structure of the stochastic velocity field. It is found that the dependent variables are most sensitive to the intensity and correlation length of the velocity fluctuations. The magnitude of the variances and cross-covariance of the concentrations are proportional to the magnitude of the mean concentrations which depend on inlet concentration boundary conditions.

  20. Comparative Analysis of Immune Repertoires between Bactrian Camel's Conventional and Heavy-Chain Antibodies.

    PubMed

    Li, Xinyang; Duan, Xiaobo; Yang, Kai; Zhang, Wei; Zhang, Changjiang; Fu, Longfei; Ren, Zhe; Wang, Changxi; Wu, Jinghua; Lu, Ruxue; Ye, Yanrui; He, Mengying; Nie, Chao; Yang, Naibo; Wang, Jian; Yang, Huanming; Liu, Xiao; Tan, Wen

    2016-01-01

    Compared to classical antibodies, camel heavy chain antibodies (HCAbs) are smaller in size due to lack of the light chain and the first constant domain of the heavy chain (CH1 region). The variable regions of HCAbs (VHHs) are more soluble and stable than that of conventional antibodies (VHs). Even with such simple structure, they are still functional in antigen binding. Although HCAbs have been extensively investigated over the past two decades, most efforts have been based upon low throughput sequence analysis, and there are only limited reports trying to analyze and describe the complete immune repertoire (IR) of camel HCAbs. Here we leveraged the high-throughput data generated by Next Generation Sequencing (NGS) of the variable domains of the antibody heavy chains from three Bactrian camels to conduct in-depth comparative analyses of the immunoglobulin repertoire. These include analyses of the complementary determining region 3 (CDR3) length and distribution, mutation rate, antibody characteristic amino acids, the distribution of the cysteine (Cys) codons, and the non-classical VHHs. We found that there is higher diversity in the CDR2 than in the other sub-regions, and there is a higher mutation rate in the VHHs than in the VHs (P < 0.05). In addition to substitutions at amino acid (AA) residue positions NO.49/50/52 between VH and VHH clones, we also observed other substitutions at the positions NO.40/54/57/96/101 that could lead to additional structural alterations. We also found that VH-derived VHH clones, referred to as non-classical VHH clones in this study, accounted for about 8% of all clones. Further, only 5%-10% clones had the Trp > Arg AA substitution at the first position of framework 4 for all types of clones. We present, for the first time, a relatively complete picture of the Bactrian camel antibody immune repertoire, including conventional antibody (Ab) and HCAbs, using PCR and in silico analysis based on high-throughput NGS data. PMID:27588755

  1. Analysis of myosin heavy chain mRNA expression by RT-PCR

    NASA Technical Reports Server (NTRS)

    Wright, C.; Haddad, F.; Qin, A. X.; Baldwin, K. M.

    1997-01-01

    An assay was developed for rapid and sensitive analysis of myosin heavy chain (MHC) mRNA expression in rodent skeletal muscle. Only 2 microg of total RNA were necessary for the simultaneous analysis of relative mRNA expression of six different MHC genes. We designed synthetic DNA fragments as internal standards, which contained the relevant primer sequences for the adult MHC mRNAs type I, IIa, IIx, IIb as well as the embryonic and neonatal MHC mRNAs. A known amount of the synthetic fragment was added to each polymerase chain reaction (PCR) and yielded a product of different size than the amplified MHC mRNA fragment. The ratio of amplified MHC fragment to synthetic fragment allowed us to calculate percentages of the gene expression of the different MHC genes in a given muscle sample. Comparison with the traditional Northern blot analysis demonstrated that our reverse transcriptase-PCR-based assay was reliable, fast, and quantitative over a wide range of relative MHC mRNA expression in a spectrum of adult and neonatal rat skeletal muscles. Furthermore, the high sensitivity of the assay made it very useful when only small quantities of tissue were available. Statistical analysis of the signals for each MHC isoform across the analyzed samples showed a highly significant correlation between the PCR and the Northern signals as Pearson correlation coefficients ranged between 0.77 and 0.96 (P < 0.005). This assay has potential use in analyzing small muscle samples such as biopsies and samples from pre- and/or neonatal stages of development.

  2. Health supply chain management.

    PubMed

    Zimmerman, Rolf; Gallagher, Pat

    2010-01-01

    This chapter gives an educational overview of: * The actual application of supply chain practice and disciplines required for service delivery improvement within the current health environment. * A rationale for the application of Supply Chain Management (SCM) approaches to the Health sector. * The tools and methods available for supply chain analysis and benchmarking. * Key supply chain success factors. PMID:20407173

  3. Empirical Study on Relationship Capital in Supply Chain-Based on Analysis of Enterprises in Hunan Province

    NASA Astrophysics Data System (ADS)

    Shan, Lu; Qiang-Bin, Ou-Yang

    Based on the existing theories and studies, this thesis aims to propose a theoretical model for describing the relationship between the relationship capital in the supply chain and its influencing factors, and meanwhile, the EFA (exploratory factor analysis) and CFA (confirmatory factor analysis) are carried out on 188 sample data. Through the evaluation of goodness of fit on the structure model as well as assumption testing, it turns out that there are four influencing factors for the relationship capital in the supply chain, namely, capability and reputation of the cooperation companies in the supply chain, input in specific assets and transfer cost, which are in a positive correlation with relationship capital separately. Then a decision-making basis is provided for the practice of relationship capital in the supply chain.

  4. Evaluation of Supply Chain Efficiency Based on a Novel Network of Data Envelopment Analysis Model

    NASA Astrophysics Data System (ADS)

    Fu, Li Fang; Meng, Jun; Liu, Ying

    2015-12-01

    Performance evaluation of supply chain (SC) is a vital topic in SC management and inherently complex problems with multilayered internal linkages and activities of multiple entities. Recently, various Network Data Envelopment Analysis (NDEA) models, which opened the “black box” of conventional DEA, were developed and applied to evaluate the complex SC with a multilayer network structure. However, most of them are input or output oriented models which cannot take into consideration the nonproportional changes of inputs and outputs simultaneously. This paper extends the Slack-based measure (SBM) model to a nonradial, nonoriented network model named as U-NSBM with the presence of undesirable outputs in the SC. A numerical example is presented to demonstrate the applicability of the model in quantifying the efficiency and ranking the supply chain performance. By comparing with the CCR and U-SBM models, it is shown that the proposed model has higher distinguishing ability and gives feasible solution in the presence of undesirable outputs. Meanwhile, it provides more insights for decision makers about the source of inefficiency as well as the guidance to improve the SC performance.

  5. Markov chain modelling of reliability analysis and prediction under mixed mode loading

    NASA Astrophysics Data System (ADS)

    Singh, Salvinder; Abdullah, Shahrum; Nik Mohamed, Nik Abdullah; Mohd Noorani, Mohd Salmi

    2015-03-01

    The reliability assessment for an automobile crankshaft provides an important understanding in dealing with the design life of the component in order to eliminate or reduce the likelihood of failure and safety risks. The failures of the crankshafts are considered as a catastrophic failure that leads towards a severe failure of the engine block and its other connecting subcomponents. The reliability of an automotive crankshaft under mixed mode loading using the Markov Chain Model is studied. The Markov Chain is modelled by using a two-state condition to represent the bending and torsion loads that would occur on the crankshaft. The automotive crankshaft represents a good case study of a component under mixed mode loading due to the rotating bending and torsion stresses. An estimation of the Weibull shape parameter is used to obtain the probability density function, cumulative distribution function, hazard and reliability rate functions, the bathtub curve and the mean time to failure. The various properties of the shape parameter is used to model the failure characteristic through the bathtub curve is shown. Likewise, an understanding of the patterns posed by the hazard rate onto the component can be used to improve the design and increase the life cycle based on the reliability and dependability of the component. The proposed reliability assessment provides an accurate, efficient, fast and cost effective reliability analysis in contrast to costly and lengthy experimental techniques.

  6. Improving Bayesian analysis for LISA Pathfinder using an efficient Markov Chain Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Ferraioli, Luigi; Porter, Edward K.; Armano, Michele; Audley, Heather; Congedo, Giuseppe; Diepholz, Ingo; Gibert, Ferran; Hewitson, Martin; Hueller, Mauro; Karnesis, Nikolaos; Korsakova, Natalia; Nofrarias, Miquel; Plagnol, Eric; Vitale, Stefano

    2014-02-01

    We present a parameter estimation procedure based on a Bayesian framework by applying a Markov Chain Monte Carlo algorithm to the calibration of the dynamical parameters of the LISA Pathfinder satellite. The method is based on the Metropolis-Hastings algorithm and a two-stage annealing treatment in order to ensure an effective exploration of the parameter space at the beginning of the chain. We compare two versions of the algorithm with an application to a LISA Pathfinder data analysis problem. The two algorithms share the same heating strategy but with one moving in coordinate directions using proposals from a multivariate Gaussian distribution, while the other uses the natural logarithm of some parameters and proposes jumps in the eigen-space of the Fisher Information matrix. The algorithm proposing jumps in the eigen-space of the Fisher Information matrix demonstrates a higher acceptance rate and a slightly better convergence towards the equilibrium parameter distributions in the application to LISA Pathfinder data. For this experiment, we return parameter values that are all within ˜1 σ of the injected values. When we analyse the accuracy of our parameter estimation in terms of the effect they have on the force-per-unit of mass noise, we find that the induced errors are three orders of magnitude less than the expected experimental uncertainty in the power spectral density.

  7. Western thymomas lack Epstein-Barr virus by Southern blotting analysis and by polymerase chain reaction.

    PubMed Central

    Inghirami, G.; Chilosi, M.; Knowles, D. M.

    1990-01-01

    The authors investigated 16 western thymomas, 9 from the United States and 7 from Europe, for the presence of Epstein-Barr virus (EBV) DNA sequences by both Southern blot hybridization analysis and polymerase chain reaction using EBV-specific DNA probes that detect the long internal repeat and terminal repeat regions and the EBNA-1 gene. None of the 16 thymomas contained evidence of the EBV genome, even though we could detect EBV by Southern blotting when EBV DNA represents less than or equal to 1% of the total DNA and by polymerase chain reaction when a single EBV-positive cell is present among 10(5) EBV-negative cells. These results fail to demonstrate EBV genome in western thymomas and stand in contrast to those of McGuire et al (Am J Pathol 1988, 131:385) who previously reported that the EBV genome is present in thymomas occurring in southern Chinese patients. Therefore EBV does not appear to be implicated in the pathogenesis of all thymomas. The presence of EBV in eastern thymomas, regions where EBV is endemic may be due to epidemiologic factors and/or genetic predispositions. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:2162629

  8. A Benchmarking Analysis for Five Radionuclide Vadose Zone Models (Chain, Multimed{_}DP, Fectuz, Hydrus, and Chain 2D) in Soil Screening Level Calculations

    SciTech Connect

    Chen, J-S.; Drake, R.; Lin, Z.; Jewett, D. G.

    2002-02-26

    Five vadose zone models with different degrees of complexity (CHAIN, MULTIMED{_}DP, FECTUZ, HYDRUS, and CHAIN 2D) were selected for use in radionuclide soil screening level (SSL) calculations. A benchmarking analysis between the models was conducted for a radionuclide ({sup 99}Tc) release scenario at the Las Cruces Trench Site in New Mexico. Sensitivity of three model outputs to the input parameters were evaluated and compared among the models. The three outputs were peak contaminant concentrations, time to peak concentrations at the water table, and time to exceed the contaminants maximum critical level at a representative receptor well. Model parameters investigated include soil properties such as bulk density, water content, soil water retention parameters and hydraulic conductivity. Chemical properties examined include distribution coefficient, radionuclide half-life, dispersion coefficient, and molecular diffusion. Other soil characteristics, such as recharge rate, also were examined. Model sensitivity was quantified in the form of sensitivity and relative sensitivity coefficients. Relative sensitivities were used to compare the sensitivities of different parameters. The analysis indicates that soil water content, recharge rate, saturated soil water content, and soil retention parameter, {beta}, have a great influence on model outputs. In general, the results of sensitivities and relative sensitivities using five models are similar for a specific scenario. Slight differences were observed in predicted peak contaminant concentrations due to different mathematical treatment among models. The results of benchmarking and sensitivity analysis would facilitate the model selection and application of the model in SSL calculations.

  9. Tissue extraction of DNA and RNA and analysis by the polymerase chain reaction.

    PubMed Central

    Jackson, D P; Lewis, F A; Taylor, G R; Boylston, A W; Quirke, P

    1990-01-01

    Several DNA extraction techniques were quantitatively and qualitatively compared using both fresh and paraffin wax embedded tissue and their suitability investigated for providing DNA and RNA for the polymerase chain reaction (PCR). A one hour incubation with proteinase K was the most efficient DNA extraction procedure for fresh tissue. For paraffin wax embedded tissue a five day incubation with proteinase K was required to produce good yields of DNA. Incubation with sodium dodecyl sulphate produced very poor yields, while boiling produced 20% as much DNA as long enzyme digestion. DNA extracted by these methods was suitable for the PCR amplification of a single copy gene. Proteinase K digestion also produced considerable amounts of RNA which has previously been shown to be suitable for PCR analysis. A delay before fixation had no effect on the amount of DNA obtained while fixation in Carnoy's reagent results in a much better preservation of DNA than formalin fixation, allowing greater yields to be extracted. Images PMID:1696290

  10. Single Quantum Dot Analysis Enables Multiplexed Point Mutation Detection by Gap Ligase Chain Reaction

    PubMed Central

    Song, Yunke; Zhang, Yi; Wang, Tza-Huei

    2014-01-01

    Gene point mutations present important biomarkers for genetic diseases. However, existing point mutation detection methods suffer from low sensitivity, specificity, and tedious assay processes. In this report, we propose an assay technology which combines the outstanding specificity of gap ligase chain reaction (Gap-LCR), the high sensitivity of single molecule coincidence detection and superior optical properties of quantum dots (QDs) for multiplexed detection of point mutations in genomic DNA. Mutant-specific ligation products are generated by Gap-LCR and subsequently captured by QDs to form DNA-QD nanocomplexes that are detected by single molecule spectroscopy (SMS) through multi-color fluorescence burst coincidence analysis, allowing for multiplexed mutation detection in a separation-free format. The proposed assay is capable of detecting zeptomoles of KRAS codon 12 mutation variants with near 100% specificity. Its high sensitivity allows direct detection of KRAS mutation in crude genomic DNA without PCR pre-amplification. PMID:23239594

  11. Analysis of BRCA2 loss of heterozygosity in tumor tissue using droplet digital polymerase chain reaction.

    PubMed

    Cochran, Rory L; Cravero, Karen; Chu, David; Erlanger, Bracha; Toro, Patricia Valda; Beaver, Julia A; Zabransky, Daniel J; Wong, Hong Yuen; Cidado, Justin; Croessmann, Sarah; Parsons, Heather A; Kim, Minsoo; Wheelan, Sarah J; Argani, Pedram; Park, Ben Ho

    2014-07-01

    Loss-of-heterozygosity (LOH) analysis of archival tumor tissue can aid in determining the clinical significance of BRCA variants. Here we describe an approach for assessing LOH in formalin-fixed, paraffin-embedded (FFPE) tissues using variant-specific probes and droplet digital polymerase chain reaction (ddPCR). We evaluated LOH in 2 related breast cancer patients harboring a rare missense BRCA2 variant of unknown clinical significance (c.6966G>T; M2322I). Conventional PCR followed by Sanger sequencing suggested a change in allelic abundance in the FFPE specimens. However, we found no evidence of LOH as determined by the allelic ratio (wild type-variant) for BRCA2 in both patients' archival tumor specimens and adjacent normal control tissues using ddPCR. In summary, these experiments demonstrate the utility of ddPCR to quickly and accurately assess LOH in archival FFPE tumor tissue. PMID:24824029

  12. Gene analysis of multiple oral bacteria by the polymerase chain reaction coupled with capillary polymer electrophoresis.

    PubMed

    Liu, Chenchen; Yamaguchi, Yoshinori; Sekine, Shinichi; Ni, Yi; Li, Zhenqing; Zhu, Xifang; Dou, Xiaoming

    2016-03-01

    Capillary polymer electrophoresis is identified as a promising technology for the analysis of DNA from bacteria, virus and cell samples. In this paper, we propose an innovative capillary polymer electrophoresis protocol for the quantification of polymerase chain reaction products. The internal standard method was modified and applied to capillary polymer electrophoresis. The precision of our modified internal standard protocol was evaluated by measuring the relative standard deviation of intermediate capillary polymer electrophoresis experiments. Results showed that the relative standard deviation was reduced from 12.4-15.1 to 0.6-2.3%. Linear regression tests were also implemented to validate our protocol. The modified internal standard method showed good linearity and robust properties. Finally, the ease of our method was illustrated by analyzing a real clinical oral sample using a one-run capillary polymer electrophoresis experiment. PMID:26648455

  13. Uncertainty analysis of the modelling chain from GCM to flood inundation

    NASA Astrophysics Data System (ADS)

    Wetterhall, F.; He, Y.; Freer, J. F.; Cloke, H.; Pappenberger, F.; Wilson, M.; McGregor, G.

    2010-05-01

    This study aims to set up novel techniques for tracking uncertainties through a modelling framework of extreme floods under a climate change. More specifically, thestudy will attempts to (1) assess future flood inundation impacts and extent as well as its hazards and (2) quantifying the cascading uncertainties in a modelling framework. The modeling framework consists of statistically and dynamically downscaled meteorological input from an ensemble of GCMs and RCMs. The climate input is further driving a set of rainfall-runoff models, in this case LISFLOOD-RR and HBV. The hydrological models provide modelled discharges which are fed through two flood inundation models, LISFLOOD-FP and HECRAS. Uncertainties in climate impact modelling are many, for example input errors in observations, impact model parameter and structural uncertainties, parameterisation and resolution errors in climate models and the underlying future scenarios. The uncertainties are cascaded through the modelling chain and it is important to rigorously estimate this uncertainty at all levels. The main aim of this project is to incorporate all these uncertainties at the very end of the chain in a flood risk map. The main research questions of this study are (1) how sensitive is the cascade setup to the downscaled meteorological input from the GCMs, particularly with respect to extreme events; (2) how is the climate change signal affected by the downscaling technique; (3) how can we quantify the sources and magnitude of uncertainties when simulating flood inundation within the context of climate change; (4) how do we deal with multi-scale multi-source uncertainties whilst taking into account the limitations of our observed measurements; (5) how do we develop strategies that improve the efficiency of sampling such a cascaded modeling structure to characterise the uncertainties and most importantly; (6) how do we convey the information to stake holders and policy makers? The analysis is done in three

  14. Analysis of N-linked oligosaccharide chains of glycoproteins on nitrocellulose sheets using lectin-peroxidase reagents.

    PubMed

    Kijimoto-Ochiai, S; Katagiri, Y U; Ochiai, H

    1985-05-15

    A rapid and convenient method was established for analysis of the N-linked carbohydrate chains of glycoproteins on nitrocellulose sheets. Proteins were separated by polyacrylamide gel electrophoresis, transferred to nitrocellulose sheets, reacted with peroxidase-coupled lectins, and detected by color development of the enzyme reaction. Four glycoproteins having N-linked oligosaccharide chains were used as test materials: Taka-amylase A (which has a high-mannose-type chain), ovalbumin (high-mannose-type chains and hybrid-type chains), transferrin (biantennary chains of complex type), and fetuin (triantennary chains of complex type and O-linked-type chains). Concanavalin A interacted with Taka-amylase A, transferrin, and ovalbumin but barely interacted with fetuin. After treatment of the glycoproteins on a nitrocellulose sheet with endo-beta-N-acetylglucosaminidase H, transferrin reacted with concanavalin A but Taka-amylase A and ovalbumin did not. Wheat germ agglutinin interacted with Taka-amylase A but not ovalbumin; therefore, they were distinguishable from each other. Fetuin and transferrin were detected by Ricinus communis agglutinin or peanut agglutinin after removal of sialic acid by treatment with neuraminidase or by weak-acid hydrolysis. Erythroagglutinating Phaseolus vulgaris agglutinin detected fetuin and transferrin. Thus, the combined use of these procedures distinguished the four different types of N-linked glycoproteins. This method was also applied to the analysis of membrane glycoproteins from sheep red blood cells. The terminally positioned sugars of sialic acid, alpha-fucose, alpha-galactose, and alpha-N-acetylgalactosamine were also detected with lectins from Limulus polyphemus, Lotus tetragonolobus, Maclura pomifera, and Dolichos biflorus, respectively. PMID:2411164

  15. BMI Affects the Relationship between Long Chain N-3 Polyunsaturated Fatty Acid Intake and Stroke Risk: a Meta-Analysis.

    PubMed

    Cheng, Pengfei; Huang, Wen; Bai, Shunjie; Wu, Yu; Yu, Jia; Zhu, Xiaofeng; Qi, Zhiguo; Shao, Weihua; Xie, Peng

    2015-01-01

    We performed a meta-analysis to clarify the relationship between long chain n-3 polyunsaturated fatty acid (PUFA) intake and stroke risk. Relevant studies were identified by searching online databases through May 2015. Log relative risks (RRs) of the highest versus the lowest for cohort studies were weighed by the inverse variance method to obtain pooled RRs. Fourteen prospective cohort studies including 514,483 individuals and 9,065 strokes were included. The pooled RR of overall stroke risk for long chain n-3 PUFA intake was 0.87 [95% confidence interval (CI), 0.79-0.95]. Stratification analysis showed that higher long chain n-3 PUFAs intake was associated with reduced fatal stroke risk (RR = 0.84; 95% CI, 0.73-0.97), reduced stroke risk for BMI < 24 (RR = 0.86; 95% CI, 0.75-0.98) and reduced stroke risk for females (RR = 0.81; 95% CI, 0.71-0.92), but was not associated with stroke risk for either BMI ≥ 24 or men. This meta-analysis reveals that higher long chain n-3 PUFA intake is inversely associated with risk of stroke morbidity and mortality with BMI and sex as key factors influencing this risk. Individuals should be encouraged to manage their body weight while increasing their intake of long chain n-3 PUFAs. PMID:26369699

  16. BMI Affects the Relationship between Long Chain N-3 Polyunsaturated Fatty Acid Intake and Stroke Risk: a Meta-Analysis

    PubMed Central

    Cheng, Pengfei; Huang, Wen; Bai, Shunjie; Wu, Yu; Yu, Jia; Zhu, Xiaofeng; Qi, Zhiguo; Shao, Weihua; Xie, Peng

    2015-01-01

    We performed a meta-analysis to clarify the relationship between long chain n-3 polyunsaturated fatty acid (PUFA) intake and stroke risk. Relevant studies were identified by searching online databases through May 2015. Log relative risks (RRs) of the highest versus the lowest for cohort studies were weighed by the inverse variance method to obtain pooled RRs. Fourteen prospective cohort studies including 514,483 individuals and 9,065 strokes were included. The pooled RR of overall stroke risk for long chain n-3 PUFA intake was 0.87 [95% confidence interval (CI), 0.79–0.95]. Stratification analysis showed that higher long chain n-3 PUFAs intake was associated with reduced fatal stroke risk (RR = 0.84; 95% CI, 0.73–0.97), reduced stroke risk for BMI < 24 (RR = 0.86; 95% CI, 0.75–0.98) and reduced stroke risk for females (RR = 0.81; 95% CI, 0.71–0.92), but was not associated with stroke risk for either BMI ≥ 24 or men. This meta-analysis reveals that higher long chain n-3 PUFA intake is inversely associated with risk of stroke morbidity and mortality with BMI and sex as key factors influencing this risk. Individuals should be encouraged to manage their body weight while increasing their intake of long chain n-3 PUFAs. PMID:26369699

  17. Effects of tour boats on dolphin activity examined with sensitivity analysis of Markov chains.

    PubMed

    Dans, Silvana Laura; Degrati, Mariana; Pedraza, Susana Noemí; Crespo, Enrique Alberto

    2012-08-01

    In Patagonia, Argentina, watching dolphins, especially dusky dolphins (Lagenorhynchus obscurus), is a new tourist activity. Feeding time decreases and time to return to feeding after feeding is abandoned and time it takes a group of dolphins to feed increase in the presence of boats. Such effects on feeding behavior may exert energetic costs on dolphins and thus reduce an individual's survival and reproductive capacity or maybe associated with shifts in distribution. We sought to predict which behavioral changes modify the activity pattern of dolphins the most. We modeled behavioral sequences of dusky dolphins with Markov chains. We calculated transition probabilities from one activity to another and arranged them in a stochastic matrix model. The proportion of time dolphins dedicated to a given activity (activity budget) and the time it took a dolphin to resume that activity after it had been abandoned (recurrence time) were calculated. We used a sensitivity analysis of Markov chains to calculate the sensitivity of the time budget and the activity-resumption time to changes in behavioral transition probabilities. Feeding-time budget was most sensitive to changes in the probability of dolphins switching from traveling to feeding behavior and of maintaining feeding behavior. Thus, an increase in these probabilities would be associated with the largest reduction in the time dedicated to feeding. A reduction in the probability of changing from traveling to feeding would also be associated with the largest increases in the time it takes dolphins to resume feeding. To approach dolphins when they are traveling would not affect behavior less because presence of the boat may keep dolphins from returning to feeding. Our results may help operators of dolphin-watching vessels minimize negative effects on dolphins. PMID:22624561

  18. Accuracy of mucocutaneous leishmaniasis diagnosis using polymerase chain reaction: systematic literature review and meta-analysis

    PubMed Central

    Gomes, Ciro Martins; Mazin, Suleimy Cristina; dos Santos, Elisa Raphael; Cesetti, Mariana Vicente; Bächtold, Guilherme Albergaria Brízida; Cordeiro, João Henrique de Freitas; Theodoro, Fabrício Claudino Estrela Terra; Damasco, Fabiana dos Santos; Carranza, Sebastián Andrés Vernal; Santos, Adriana de Oliveira; Roselino, Ana Maria; Sampaio, Raimunda Nonata Ribeiro

    2015-01-01

    The diagnosis of mucocutaneous leishmaniasis (MCL) is hampered by the absence of a gold standard. An accurate diagnosis is essential because of the high toxicity of the medications for the disease. This study aimed to assess the ability of polymerase chain reaction (PCR) to identify MCL and to compare these results with clinical research recently published by the authors. A systematic literature review based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses: the PRISMA Statement was performed using comprehensive search criteria and communication with the authors. A meta-analysis considering the estimates of the univariate and bivariate models was performed. Specificity near 100% was common among the papers. The primary reason for accuracy differences was sensitivity. The meta-analysis, which was only possible for PCR samples of lesion fragments, revealed a sensitivity of 71% [95% confidence interval (CI) = 0.59; 0.81] and a specificity of 93% (95% CI = 0.83; 0.98) in the bivariate model. The search for measures that could increase the sensitivity of PCR should be encouraged. The quality of the collected material and the optimisation of the amplification of genetic material should be prioritised. PMID:25946238

  19. Long-chain polyunsaturated fatty acid status in obesity: a systematic review and meta-analysis.

    PubMed

    Fekete, K; Györei, E; Lohner, S; Verduci, E; Agostoni, C; Decsi, T

    2015-06-01

    Long-chain polyunsaturated fatty acid (LCPUFA) status has recently been related to the pathogenesis of obesity. Our aims were to systematically review observational studies investigating LCPUFA status from different blood compartments in overweight or obese subjects and to assess the relationship between LCPUFA profile and obesity. The Ovid MEDLINE, Scopus and Cochrane Library CENTRAL databases were searched from inception to January 2014. The meta-analysis showed significant differences in the LCPUFA composition of total plasma lipids, plasma phospholipids and plasma cholesteryl esters between overweight or obese subjects and controls. Dihomo-γ-linolenic acid (DGLA) values were significantly higher in overweight or obese subjects compared with controls in all the investigated biomarkers. In addition, the DGLA/linoleic acid ratio (surrogate parameter for Δ6 desaturase activity) in plasma phospholipids was significantly elevated (mean difference [MD]: 0.05; 95% confidence interval [CI]: 0.02, 0.08; n = 280), while the arachidonic acid/DGLA ratio (surrogate parameter for Δ5 desaturase activity) was significantly decreased (MD: -0.55; 95% CI: -0.71, -0.39; n = 347) in overweight or obese subjects compared with controls. The results of the present meta-analysis confirm that LCPUFA profile is altered in obesity and suggest that the differences observed in desaturase activities may be responsible for the disturbed LCPUFA metabolism in obesity. PMID:25828602

  20. STRUCTURAL ANALYSIS OF ALTERNATIVE COMPLEX III IN THE PHOTOSYNTHETIC ELECTRON TRANSFER CHAIN OF CHLOROFLEXUS AURANTIACUS

    PubMed Central

    Gao, Xinliu; Xin, Yueyong; Bell, Patrick D.; Wen, Jianzhong; Blankenship, Robert E.

    2010-01-01

    The green photosynthetic bacterium Chloroflexus aurantiacus, which belongs to the phylum of filamentous anoxygenic phototrophs, does not contain a cytochrome bc or bf type complex as is found in all other known groups of phototrophs. This suggests that a functional replacement exists to link the reaction center photochemistry to cyclic electron transfer as well as respiration. Earlier work identified a potential substitute of the cytochrome bc complex, now named alternative complex III (ACIII), which has been purified, identified and characterized from C. aurantiacus. ACIII functions as a menaquinol:auracyanin oxidoreductase in the photosynthetic electron transfer chain, and a related but distinct complex functions in respiratory electron flow to a terminal oxidase. In this work, we focus on elucidating the structure of the photosynthetic ACIII. We found that AC III is an integral-membrane protein complex of around 300 kDa that consists of 8 subunits of 7 different types. Among them, there are 4 metalloprotein subunits, including a 113 kDa iron-sulfur cluster-containing polypeptide, a 25 kDa penta-heme c-containing subunit and two 20 kDa mono-heme c-containing subunits in the form of a homodimer. A variety of analytical techniques were employed in determining the ACIII substructure, including HPLC combined with ESI-MS, metal analysis, potentiometric titration and intensity analysis of heme-staining SDS-PAGE. A preliminary structural model of the ACIII complex is proposed based on the analytical data and chemical cross-linking in tandem with mass analysis using MALDI-TOF, as well as transmembrane and transit peptide analysis. PMID:20614874

  1. Multistationary and Oscillatory Modes of Free Radicals Generation by the Mitochondrial Respiratory Chain Revealed by a Bifurcation Analysis

    PubMed Central

    Selivanov, Vitaly A.; Cascante, Marta; Friedman, Mark; Schumaker, Mark F.; Trucco, Massimo; Votyakova, Tatyana V.

    2012-01-01

    The mitochondrial electron transport chain transforms energy satisfying cellular demand and generates reactive oxygen species (ROS) that act as metabolic signals or destructive factors. Therefore, knowledge of the possible modes and bifurcations of electron transport that affect ROS signaling provides insight into the interrelationship of mitochondrial respiration with cellular metabolism. Here, a bifurcation analysis of a sequence of the electron transport chain models of increasing complexity was used to analyze the contribution of individual components to the modes of respiratory chain behavior. Our algorithm constructed models as large systems of ordinary differential equations describing the time evolution of the distribution of redox states of the respiratory complexes. The most complete model of the respiratory chain and linked metabolic reactions predicted that condensed mitochondria produce more ROS at low succinate concentration and less ROS at high succinate levels than swelled mitochondria. This prediction was validated by measuring ROS production under various swelling conditions. A numerical bifurcation analysis revealed qualitatively different types of multistationary behavior and sustained oscillations in the parameter space near a region that was previously found to describe the behavior of isolated mitochondria. The oscillations in transmembrane potential and ROS generation, observed in living cells were reproduced in the model that includes interaction of respiratory complexes with the reactions of TCA cycle. Whereas multistationarity is an internal characteristic of the respiratory chain, the functional link of respiration with central metabolism creates oscillations, which can be understood as a means of auto-regulation of cell metabolism. PMID:23028295

  2. [Analysis of the vegetable productive chain in Ribeirão Preto, SP].

    PubMed

    Takayanagui, Osvaldo M; Capuano, Divani M; Oliveira, Carlos A D; Bergamini, Alzira M M; Okino, Madalena H T; Castro e Silva, Ana A M C; Oliveira, Maria A; Ribeiro, Eliana G A; Takayanagui, Angela M M

    2006-01-01

    With the aim of assessing the cumulative risk of lettuce contamination, 45 production chains were investigated. The presence of thermotolerant coliforms, Salmonella and/or parasites was detected in 69% of these, in all steps of the production chain. Quality control in all steps of the lettuce production process should be intensified. PMID:16699655

  3. Falling Chains as Variable-Mass Systems: Theoretical Model and Experimental Analysis

    ERIC Educational Resources Information Center

    de Sousa, Celia A.; Gordo, Paulo M.; Costa, Pedro

    2012-01-01

    In this paper, we revisit, theoretically and experimentally, the fall of a folded U-chain and of a pile-chain. The model calculation implies the division of the whole system into two subsystems of variable mass, allowing us to explore the role of tensional contact forces at the boundary of the subsystems. This justifies, for instance, that the…

  4. Regeneration and Fixed-Width Analysis of Markov Chain Monte Carlo Algorithms

    NASA Astrophysics Data System (ADS)

    Latuszynski, Krzysztof

    2009-07-01

    In the thesis we take the split chain approach to analyzing Markov chains and use it to establish fixed-width results for estimators obtained via Markov chain Monte Carlo procedures (MCMC). Theoretical results include necessary and sufficient conditions in terms of regeneration for central limit theorems for ergodic Markov chains and a regenerative proof of a CLT version for uniformly ergodic Markov chains with E_{π}f^2< infty. To obtain asymptotic confidence intervals for MCMC estimators, strongly consistent estimators of the asymptotic variance are essential. We relax assumptions required to obtain such estimators. Moreover, under a drift condition, nonasymptotic fixed-width results for MCMC estimators for a general state space setting (not necessarily compact) and not necessarily bounded target function f are obtained. The last chapter is devoted to the idea of adaptive Monte Carlo simulation and provides convergence results and law of large numbers for adaptive procedures under path-stability condition for transition kernels.

  5. Automated Microfluidic Platform for Serial Polymerase Chain Reaction and High-Resolution Melting Analysis.

    PubMed

    Cao, Weidong; Bean, Brian; Corey, Scott; Coursey, Johnathan S; Hasson, Kenton C; Inoue, Hiroshi; Isano, Taisuke; Kanderian, Sami; Lane, Ben; Liang, Hongye; Murphy, Brian; Owen, Greg; Shinoda, Nobuhiko; Zeng, Shulin; Knight, Ivor T

    2016-06-01

    We report the development of an automated genetic analyzer for human sample testing based on microfluidic rapid polymerase chain reaction (PCR) with high-resolution melting analysis (HRMA). The integrated DNA microfluidic cartridge was used on a platform designed with a robotic pipettor system that works by sequentially picking up different test solutions from a 384-well plate, mixing them in the tips, and delivering mixed fluids to the DNA cartridge. A novel image feedback flow control system based on a Canon 5D Mark II digital camera was developed for controlling fluid movement through a complex microfluidic branching network without the use of valves. The same camera was used for measuring the high-resolution melt curve of DNA amplicons that were generated in the microfluidic chip. Owing to fast heating and cooling as well as sensitive temperature measurement in the microfluidic channels, the time frame for PCR and HRMA was dramatically reduced from hours to minutes. Preliminary testing results demonstrated that rapid serial PCR and HRMA are possible while still achieving high data quality that is suitable for human sample testing. PMID:25827436

  6. A Markov chain analysis of fish movements to determine entrainment zones

    SciTech Connect

    Johnson, Gary E.; Hedgepeth, J.; Skalski, John R.; Giorgi, Albert E.

    2004-06-01

    The extent of the biological zone of influence (BZI) of a water withdrawal port, such as a cooling water intake or a smolt bypass, directly reflects its local effect on fish. This study produced a new technique to determine the BZI, defined as the region immediately upstream of a portal where the probability of fish movement toward the portal is greater than 90%. We developed and applied the technique at The Dalles Dam on the Columbia River, where the ice/trash sluiceway functions as a surface flow smolt bypass. To map the BZI, we applied a Markov-Chain analysis to smolt movement data collected with an active fish tracking sonar system. Probabilities of fish movement from cell to cell in the sample volume, calculated from tracked fish data, formed a Markov transition matrix. Multiplying this matrix by itself many times with absorption at the boundaries produced estimates of probability of passage out each side of the sample volume from the cells within. The BZI of a sluiceway entrance at The Dalles Dam was approximately 5 m across and extended 6-8 m out from the face of the dam in the surface layer 2-3 m deep. BZI mapping is applicable to many bioengineering efforts to protect fish populations.

  7. Applications of constant denaturant capillary electrophoresis/high-fidelity polymerase chain reaction to human genetic analysis.

    PubMed

    Li-Sucholeiki, X C; Khrapko, K; André, P C; Marcelino, L A; Karger, B L; Thilly, W G

    1999-06-01

    Constant denaturant capillary electrophoresis (CDCE) permits high-resolution separation of single-base variations occurring in an approximately 100 bp isomelting DNA sequence based on their differential melting temperatures. By coupling CDCE for highly efficient enrichment of mutants with high-fidelity polymerase chain reaction (hifi PCR), we have developed an analytical approach to detecting point mutations at frequencies equal to or greater than 10(-6) in human genomic DNA. In this article, we present several applications of this approach in human genetic studies. We have measured the point mutational spectra of a 100 bp mitochondrial DNA sequence in human tissues and cultured cells. The observations have led to the conclusion that the primary causes of mutation in human mitochondrial DNA are spontaneous in origin. In the course of studying the mitochondrial somatic mutations, we have also identified several nuclear pseudogenes homologous to the analyzed mitochondrial DNA fragment. Recently, through developments of the means to isolate the desired target sequences from bulk genomic DNA and to increase the loading capacity of CDCE, we have extended the CDCE/hifi PCR approach to study a chemically induced mutational spectrum in a single-copy nuclear sequence. Future applications of the CDCE/hifi PCR approach to human genetic analysis include studies of somatic mitochondrial mutations with respect to aging, measurement of mutational spectra of nuclear genes in healthy human tissues and population screening for disease-associated single nucleotide polymorphisms (SNPs) in large pooled samples. PMID:10380762

  8. Markov chain Monte Carlo analysis to constrain dark matter properties with directional detection

    SciTech Connect

    Billard, J.; Mayet, F.; Santos, D.

    2011-04-01

    Directional detection is a promising dark matter search strategy. Indeed, weakly interacting massive particle (WIMP)-induced recoils would present a direction dependence toward the Cygnus constellation, while background-induced recoils exhibit an isotropic distribution in the Galactic rest frame. Taking advantage of these characteristic features, and even in the presence of a sizeable background, it has recently been shown that data from forthcoming directional detectors could lead either to a competitive exclusion or to a conclusive discovery, depending on the value of the WIMP-nucleon cross section. However, it is possible to further exploit these upcoming data by using the strong dependence of the WIMP signal with: the WIMP mass and the local WIMP velocity distribution. Using a Markov chain Monte Carlo analysis of recoil events, we show for the first time the possibility to constrain the unknown WIMP parameters, both from particle physics (mass and cross section) and Galactic halo (velocity dispersion along the three axis), leading to an identification of non-baryonic dark matter.

  9. Polymerase chain reaction analysis of aqueous humour samples in necrotising retinitis

    PubMed Central

    Tran, T H C; Rozenberg, F; Cassoux, N; Rao, N A; LeHoang, P; Bodaghi, B

    2003-01-01

    Aim: To evaluate the diagnostic value of polymerase chain reaction (PCR) performed on aqueous humour for the detection of viral DNA in patients with necrotising herpetic retinitis. Methods: The clinical features and laboratory results of 22 patients (29 eyes) presenting with necrotising herpetic retinitis between March 1999 and June 2001 were reviewed retrospectively. Aqueous humour was obtained after anterior chamber paracentesis and PCR was performed in all cases. Results: Viral DNA was detected in the aqueous humour of 19 patients (86.4%). Epstein-Barr virus (EBV) seroconversion was evidenced in one additional patient. In the acute retinal necrosis (ARN) group (n = 19), varicella zoster virus (VZV) DNA was identified in six patients, herpes simplex virus 1 (HSV-1) DNA in two patients, herpes simplex virus 2 (HSV-2) DNA in four patients, and cytomegalovirus (CMV) genome in four patients. In the progressive outer retinal necrosis (PORN) group (n = 3), VZV DNA was detected in all patients. No sample was positive for more than one virus. Conclusions: PCR analysis of aqueous humour in patients with clinical features of necrotising viral retinitis can provide specific aetiological orientation and the method appears to be safe and highly sensitive. PMID:12488268

  10. Assessment of the Cotton Industry Using the Global Commodity Chain Analysis Approach in Katsina State, Nigeria

    NASA Astrophysics Data System (ADS)

    Kudi, T. M.; Akpoko, J. G.; Abdulsalam, Z.

    The study examines the cotton commodity chain and assessed the share of each actor in the cotton industry and identified the constraints encountered in cotton production, marketing and processing. A sample of thirty cotton producers, 50 traders, 500 agents and 3 ginneries were selected from Funtua Local Government Area of Katsina State using both random and purposive sampling techniques. Both qualitative and quantitative data were collected from the participants using focus group discussion and structured questionnaire during the 2004/2005 cropping season. Analysis of the data was done using descriptive statistics and budgeting technique. The farmersN budget analysis indicated that from an investment cost of N 33,146.00 ha-1, farmers obtained a revenue of N 44,544-00 ha-1, thus making a net income of N 11,398 ha-1, while the agent analysis shows that an agent is paid a commission of N 500.00 ton-1 of seed cotton purchase on behalf of the merchant. The analysis of the tradersN budget revealed that from an investment cost of N 36,746.00 ton-1 of seed cotton purchased, traders` N 41,700.00 (lint + seed) and a net profit of N 4,954.00 ton h-1 of seed cotton. The analysis of the ginnery budget revealed that from one ton of seed cotton processed, a ginnery is making a net profit of N 2,178.00. These analyses indicated that cotton production, marketing and processing under the current price and cost setting is profitable. In spite of the profitability in cotton business, the following problems were identified: adulteration of seed cotton with foreign materials, heterogeneous seeds resale in the market, inappropriate packaging systems, no good prices for improving the quality and no mechanism for ensuring transparency in the quality (trust between actors). There is the need for intensification and expansion of the cotton sector in terms of provision of high quality inputs, clean seed cotton, introduction of jute bags for packaging, introduction of quality control

  11. Human von Willebrand factor gene and pseudogene: Structural analysis and differentiation by polymerase chain reaction

    SciTech Connect

    Mancuso, D.J.; Tuley, E.A.; Westfield, L.A.; Lester-Mancuso, T.L.; Sorace, J.M.; Sadler, J.E. ); Le Beau, M.M. )

    1991-01-01

    Structural analysis of the von Willebrand factor gene located on chromosome 12 is complicated by the presence of a partial unprocessed pseudogene on chromosome 22q11-13. The structures of the von Willebrand factor pseudogene and corresponding segment of the gene were determined, and methods were developed for the rapid differentiation of von Willebrand factor gene and pseudogene sequences. The pseudogene is 21-29 kilobases in length and corresponds to 12 exons (exons 23-34) of the von Willebrand factor gene. Approximately 21 kilobases of the gene and pseudogene were sequenced, including the 5{prime} boundary of the pseudogene. The 3{prime} boundary of the pseudogene lies within an 8-kb region corresponding to intron 34 of the gene. The presence of splice site and nonsense mutations suggests that the pseudogene cannot yield functional transcripts. The pseudogene has diverged {approximately}3.1{percent} in nucleotide sequence from the gene. This suggests a recent evolutionary origin {approximately}19-29 million years ago, near the time of divergence of humans and apes from monkeys. Several repetitive sequences were identified, including 4 Alu, one Line-1, and several short simple sequence repeats. Several of these simple repeats differ in length between the gene and pseudogene and provide useful markers for distinguishing these loci. Sequence differences between the gene and pseudogene were exploited to design oligonucleotide primers for use in the polymerase chain reaction to selectivity amplify sequences corresponding to exons 23-34 from either the von Willebrand factor gene or the pseudogene. This method is useful for the analysis of gene defects in patients with von Willebrand disease, without interference from homologous sequences in the pseudogene.

  12. Dynamic Models and Coordination Analysis of Reverse Supply Chain with Remanufacturing

    NASA Astrophysics Data System (ADS)

    Yan, Nina

    In this paper, we establish a reverse chain system with one manufacturer and one retailer under demand uncertainties. Distinguishing between the recycling process of the retailer and the remanufacturing process of the manufacturer, we formulate a two-stage dynamic model for reverse supply chain based on remanufacturing. Using buyback contract as coordination mechanism and applying dynamic programming the optimal decision problems for each stage are analyzed. It concluded that the reverse supply chain system could be coordinated under the given condition. Finally, we carry out numerical calculations to analyze the expected profits for the manufacturer and the retailer under different recovery rates and recovery prices and the outcomes validate the theoretical analyses.

  13. Pulse-chase analysis of N-linked sugar chains from glycoproteins in mammalian cells.

    PubMed

    Avezov, Edward; Ron, Efrat; Izenshtein, Yana; Adan, Yosef; Lederkremer, Gerardo Z

    2010-01-01

    Attachment of the Glc3Man9GlcNAc2 precursor oligosaccharide to nascent polypeptides in the ER is a common modification for secretory proteins. Although this modification was implicated in several biological processes, additional aspects of its function are emerging, with recent evidence of its role in the production of signals for glycoprotein quality control and trafficking. Thus, phenomena related to N-linked glycans and their processing are being intensively investigated. Methods that have been recently developed for proteomic analysis have greatly improved the characterization of glycoprotein N-linked glycans. Nevertheless, they do not provide insight into the dynamics of the sugar chain processing involved. For this, labeling and pulse-chase analysis protocols are used that are usually complex and give very low yields. We describe here a simple method for the isolation and analysis of metabolically labeled N-linked oligosaccharides. The protocol is based on labeling of cells with [2-(3)H] mannose, denaturing lysis and enzymatic release of the oligosaccharides from either a specifically immunoprecipitated protein of interest or from the general glycoprotein pool by sequential treatments with endo H and N-glycosidase F, followed by molecular filtration (Amicon). In this method the isolated oligosaccharides serve as an input for HPLC analysis, which allows discrimination between various glycan structures according to the number of monosaccharide units comprising them, with a resolution of a single monosaccharide. Using this method we were able to study high mannose N-linked oligosaccharide profiles of total cell glycoproteins after pulse-chase in normal conditions and under proteasome inhibition. These profiles were compared to those obtained from an immunoprecipitated ER-associated degradation (ERAD) substrate. Our results suggest that most NIH 3T3 cellular glycoproteins are relatively stable and that most of their oligosaccharides are trimmed to Man9-8GlcNAc2

  14. Immunoglobulin analysis tool: a novel tool for the analysis of human and mouse heavy and light chain transcripts.

    PubMed

    Rogosch, Tobias; Kerzel, Sebastian; Hoi, Kam Hon; Zhang, Zhixin; Maier, Rolf F; Ippolito, Gregory C; Zemlin, Michael

    2012-01-01

    Sequence analysis of immunoglobulin (Ig) heavy and light chain transcripts can refine categorization of B cell subpopulations and can shed light on the selective forces that act during immune responses or immune dysregulation, such as autoimmunity, allergy, and B cell malignancy. High-throughput sequencing yields Ig transcript collections of unprecedented size. The authoritative web-based IMGT/HighV-QUEST program is capable of analyzing large collections of transcripts and provides annotated output files to describe many key properties of Ig transcripts. However, additional processing of these flat files is required to create figures, or to facilitate analysis of additional features and comparisons between sequence sets. We present an easy-to-use Microsoft(®) Excel(®) based software, named Immunoglobulin Analysis Tool (IgAT), for the summary, interrogation, and further processing of IMGT/HighV-QUEST output files. IgAT generates descriptive statistics and high-quality figures for collections of murine or human Ig heavy or light chain transcripts ranging from 1 to 150,000 sequences. In addition to traditionally studied properties of Ig transcripts - such as the usage of germline gene segments, or the length and composition of the CDR-3 region - IgAT also uses published algorithms to calculate the probability of antigen selection based on somatic mutational patterns, the average hydrophobicity of the antigen-binding sites, and predictable structural properties of the CDR-H3 loop according to Shirai's H3-rules. These refined analyses provide in-depth information about the selective forces acting upon Ig repertoires and allow the statistical and graphical comparison of two or more sequence sets. IgAT is easy to use on any computer running Excel(®) 2003 or higher. Thus, IgAT is a useful tool to gain insights into the selective forces and functional properties of small to extremely large collections of Ig transcripts, thereby assisting a researcher to mine a data set

  15. The Analysis of Rush Orders Risk in Supply Chain: A Simulation Approach

    NASA Technical Reports Server (NTRS)

    Mahfouz, Amr; Arisha, Amr

    2011-01-01

    Satisfying customers by delivering demands at agreed time, with competitive prices, and in satisfactory quality level are crucial requirements for supply chain survival. Incidence of risks in supply chain often causes sudden disruptions in the processes and consequently leads to customers losing their trust in a company's competence. Rush orders are considered to be one of the main types of supply chain risks due to their negative impact on the overall performance, Using integrated definition modeling approaches (i.e. IDEF0 & IDEF3) and simulation modeling technique, a comprehensive integrated model has been developed to assess rush order risks and examine two risk mitigation strategies. Detailed functions sequence and objects flow were conceptually modeled to reflect on macro and micro levels of the studied supply chain. Discrete event simulation models were then developed to assess and investigate the mitigation strategies of rush order risks, the objective of this is to minimize order cycle time and cost.

  16. RFID Application Strategy in Agri-Food Supply Chain Based on Safety and Benefit Analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Min; Li, Peichong

    Agri-food supply chain management (SCM), a management method to optimize internal costs and productivities, has evolved as an application of e-business technologies. These days, RFID has been widely used in many fields. In this paper, we analyze the characteristics of agri-food supply chain. Then the disadvantages of RFID are discussed. After that, we study the application strategies of RFID based on benefit and safety degree.

  17. Supply Chain Sustainability Analysis of Indirect Liquefaction of Blended Biomass to Produce High Octane Gasoline

    SciTech Connect

    Cai, Hao; Canter, Christina E.; Dunn, Jennifer B.; Tan, Eric; Biddy, Mary; Talmadge, Michael; Hartley, Damon S.; Snowden-Swan, Lesley

    2015-09-01

    The Department of Energy’s (DOE) Bioenergy Technologies Office (BETO) aims at developing and deploying technologies to transform renewable biomass resources into commercially viable, high-performance biofuels, bioproducts and biopower through public and private partnerships (DOE, 2015). BETO also performs a supply chain sustainability analysis (SCSA). This report describes the SCSA of the production of renewable high octane gasoline (HOG) via indirect liquefaction (IDL) of lignocellulosic biomass. This SCSA was developed for the 2017 design case for feedstock logistics (INL, 2014) and for the 2022 target case for HOG production via IDL (Tan et al., 2015). The design includes advancements that are likely and targeted to be achieved by 2017 for the feedstock logistics and 2022 for the IDL conversion process. The 2017 design case for feedstock logistics demonstrated a delivered feedstock cost of $80 per dry U.S. short ton by the year 2017 (INL, 2014). The 2022 design case for the conversion process, as modeled in Tan et al. (2015), uses the feedstock 2017 design case blend of biomass feedstocks consisting of pulpwood, wood residue, switchgrass, and construction and demolition waste (C&D) with performance properties consistent with a sole woody feedstock type (e.g., pine or poplar). The HOG SCSA case considers the 2017 feedstock design case (the blend) as well as individual feedstock cases separately as alternative scenarios when the feedstock blend ratio varies as a result of a change in feedstock availability. These scenarios could be viewed as bounding SCSA results because of distinctive requirements for energy and chemical inputs for the production and logistics of different components of the blend feedstocks.

  18. Plasma lipidomics analysis finds long chain cholesteryl esters to be associated with Alzheimer's disease

    PubMed Central

    Proitsi, P; Kim, M; Whiley, L; Pritchard, M; Leung, R; Soininen, H; Kloszewska, I; Mecocci, P; Tsolaki, M; Vellas, B; Sham, P; Lovestone, S; Powell, J F; Dobson, R J B; Legido-Quigley, C

    2015-01-01

    There is an urgent need for the identification of Alzheimer's disease (AD) biomarkers. Studies have now suggested the promising use of associations with blood metabolites as functional intermediate phenotypes in biomedical and pharmaceutical research. The aim of this study was to use lipidomics to identify a battery of plasma metabolite molecules that could predict AD patients from controls. We performed a comprehensive untargeted lipidomic analysis, using ultra-performance liquid chromatography/mass spectrometry on plasma samples from 35 AD patients, 40 elderly controls and 48 individuals with mild cognitive impairment (MCI) and used multivariate analysis methods to identify metabolites associated with AD status. A combination of 10 metabolites could discriminate AD patients from controls with 79.2% accuracy (81.8% sensitivity, 76.9% specificity and an area under curve of 0.792) in a novel test set. Six of the metabolites were identified as long chain cholesteryl esters (ChEs) and were reduced in AD (ChE 32:0, odds ratio (OR)=0.237, 95% confidence interval (CI)=0.10–0.48, P=4.19E−04; ChE 34:0, OR=0.152, 95% CI=0.05–0.37, P=2.90E−04; ChE 34:6, OR=0.126, 95% CI=0.03–0.35, P=5.40E−04; ChE 32:4, OR=0.056, 95% CI=0.01–0.24, P=6.56E−04 and ChE 33:6, OR=0.205, 95% CI=0.06–0.50, P=2.21E−03, per (log2) metabolite unit). The levels of these metabolites followed the trend control>MCI>AD. We, additionally, found no association between cholesterol, the precursor of ChE and AD. This study identified new ChE molecules, involved in cholesterol metabolism, implicated in AD, which may help identify new therapeutic targets; although, these findings need to be replicated in larger well-phenotyped cohorts. PMID:25585166

  19. Quantitative Polymerase Chain Reaction Analysis of the Mouse Cyp2j Subfamily: Tissue Distribution and Regulation.

    PubMed

    Graves, Joan P; Gruzdev, Artiom; Bradbury, J Alyce; DeGraff, Laura M; Li, Huiling; House, John S; Hoopes, Samantha L; Edin, Matthew L; Zeldin, Darryl C

    2015-08-01

    Members of the cytochrome P450 CYP2J subfamily are expressed in multiple tissues in mice and humans. These enzymes are active in the metabolism of fatty acids to generate bioactive compounds. Herein we report new methods and results for quantitative polymerase chain reaction (qPCR) analysis for the seven genes (Cyp2j5, Cyp2j6, Cyp2j8, Cyp2j9, Cyp2j11, Cyp2j12, and Cyp2j13) of the mouse Cyp2j subfamily. SYBR Green primer sets were developed and compared with commercially available TaqMan primer/probe assays for specificity toward mouse Cyp2j cDNA, and analysis of tissue distribution and regulation of Cyp2j genes. Each TaqMan primer/probe set and SYBR Green primer set were shown to be specific for their intended mouse Cyp2j cDNA. Tissue distribution of the mouse Cyp2j isoforms confirmed similar patterns of expression between the two qPCR methods. Cyp2j5 and Cyp2j13 were highly expressed in male kidneys, and Cyp2j11 was highly expressed in both male and female kidneys. Cyp2j6 was expressed in multiple tissues, with the highest expression in the small intestine and duodenum. Cyp2j8 was detected in various tissues, with highest expression found in the skin. Cyp2j9 was highly expressed in the brain, liver, and lung. Cyp2j12 was predominately expressed in the brain. We also determined the Cyp2j isoform expression in Cyp2j5 knockout mice to determine whether there was compensatory regulation of other Cyp2j isoforms, and we assessed Cyp2j isoform regulation during various inflammatory models, including influenza A, bacterial lipopolysaccharide, house dust mite allergen, and corn pollen. Both qPCR methods detected similar suppression of Cyp2j6 and Cyp2j9 during inflammation in the lung. PMID:25994032

  20. Heterogeneity of lipopolysaccharides from Pseudomonas aeruginosa: analysis of lipopolysaccharide chain length.

    PubMed Central

    Rivera, M; Bryan, L E; Hancock, R E; McGroarty, E J

    1988-01-01

    Lipopolysaccharide (LPS) from smooth strains of Pseudomonas aeruginosa 503, PAZ1, PAO1715, PAO1716, and Z61 was fractionated by gel filtration chromatography. LPS samples from the first four strains, all PAO1 derivatives, separated into three major size populations, whereas LPS from strain Z61, a Pac K799/WT mutant strain, separated into two size populations. When column fractions were applied to sodium dodecyl sulfate-polyacrylamide gels in their order of elution, molecules of decreasing size were resolved, and the ladder of molecules with different-length O antigens formed a diagonal across the gel. The LPS from the PAO1 derivatives contained two distinct sets of bands, distinguished on the gels as two sets of diagonals. The set of bands with the faster mobility, the B bands, was found in column fractions comprising the three major amino sugar-containing peaks. In the sample from strain 503, a fourth minor peak which contained B bands was resolved. The slower-moving set of bands, the A bands, were recovered in a minor peak. LPS from strain Z61 contained only one set of bands, with the higher-molecular-weight molecules eluting from the column in a volume similar to that of the B bands of the PAO1 strains. Analysis of the fractions of LPS from all strains indicated that less than 8% of the LPS molecules had a long, attached O antigen. Analysis of the peak that contained mainly A bands indicated a lack of reactive amino sugar and phosphate, although heptose and 2-keto-3-deoxyoctulosonic acid were detected. Reaction of isolated fractions with monoclonal antibody specific for the PAO1 O-antigen side chain indicated that only the B bands from the PAO1 strains were antigenically reactive. The bands from strain Z61 showed no reactivity. The data suggest that the A and B bands from the PAO1 strains are antigenically distinct. We propose that PAO1 strains synthesize two types of molecules that are antigenically different. Images PMID:3123455

  1. Scalability analysis of the synchronizability for ring or chain networks with dense clusters

    NASA Astrophysics Data System (ADS)

    Lu, Jun-An; Zhang, Yong; Chen, Juan; Lü, Jinhu

    2014-03-01

    It is well known that most real-world complex networks, such as the Internet and the World Wide Web, are evolving networks. An interesting fundamental question is: how do some important functions or dynamical behaviors of complex networks evolve with increasing network scale? This paper aims at investigating the scalability of the synchronizability for ring or chain networks with dense clusters as the network size increases. We discover some interesting phenomena as follows: (i) the synchronizability of ring or chain networks with clusters decreases with increasing network scale regardless of the inner structures of all communities; (ii) for the same network scale, the network synchronizability decreases more quickly with increasing number of cluster blocks than with increasing number of nodes within the cluster block; (iii) the number of rings or chains has a much more significant influence on the network synchronizability than the size of the rings or chains. Our results indicate that network synchronizability can be maintained with increasing network scale by avoiding ring and chain structures.

  2. Time-based analysis of the apheresis platelet supply chain in England.

    PubMed

    Wilding, R; Cotton, S; Dobbin, J; Chapman, J; Yates, N

    2011-10-01

    During 2009/2010 loss of platelets within NHS Blood and Transplant (NHSBT) due to time expiry was 9.3%. Hospitals remain reluctant to hold stocks of platelets due to the poor shelf life at issue. The purpose of this study was to identify areas for time compression in the apheresis platelet supply chain to extend the shelf life available for hospitals and reduce wastage in NHSBT. This was done within the context of NHSBT reconfiguring their supply chain and moving towards a consolidated and centralised approach. Time based process mapping was applied to identify value and non-value adding time in two manufacturing models. A large amount of the non-value adding time in the apheresis platelet supply chain is due to transportation and waiting for the next process in the manufacturing process to take place. Time based process mapping provides an effective 'lens' for supply chain professionals to identify opportunities for improvement in the platelet supply chain. PMID:21521234

  3. The food chain as a source of human exposure from municipal waste combustion: An uncertainty analysis

    SciTech Connect

    Belcher, G.D.; Travis, C.C.; Bruins, R.J.F.; Environmental Protection Agency, Cincinnati, OH . Office of Environmental Criteria and Assessment)

    1989-01-01

    The current installed incineration capacity of municipal waste combustors (MWCs) in the United States has reached approximately 50 thousand tons per day and is projected to triple over the next decade. As the use of MWCs as a waste management alternative has increased, public concern over possible environmental and human health effects has also increased. Of particular concern are health risks associated with potential exposures through the food chain. The food chain is the primary pathway of human exposure for a large class of organics, such as dioxin, PCBs, DDT, and other pesticides. Because many pollutants emitted by MWCs are lipophilic, extremely persistent compounds, they tend to sorb strong to air particles, soil, and sediment and to bioaccumulate in living organisms. As a result, the food chain can be a major pathway of exposure to pollutants emitted by MWCs. It is the purpose of this paper to assess the magnitude of human exposure through the food chain for two pollutants released by MWCs: cadmium and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), commonly referred to as dioxin. These pollutants were chosen as representative of two chemical classes: metals and organics. Cadmium is a metal which presumably will enter the food chain primarily through vegetative root uptake, while dioxin is an extremely lipophilic compound which will bioconcentrate in beef and milk. 57 refs., 7 figs., 14 tabs.

  4. Optimization of Serum Immunoglobulin Free Light Chain Analysis for Subclassification of Cardiac Amyloidosis.

    PubMed

    Halushka, Marc K; Eng, George; Collins, A Bernard; Judge, Daniel P; Semigran, Marc J; Stone, James R

    2015-06-01

    Accurate and rapid classification of cardiac amyloidosis is important for patient management. We have optimized the use of serum free light chain kappa and lambda values to differentiate immunoglobulin light chain amyloid (AL) amyloidosis from transthyretin amyloid and amyloid A using 85 cases of tissue-proven cardiac amyloidosis, in which there was direct classification of amyloidosis by mass spectrometry or immunofluorescence. The serum free light chain kappa/lambda ratios were non-overlapping for the three major groups: AL-lambda (0.01-0.41, n = 30), non-AL (0.52-2.7, n = 43), and AL-kappa (6.7-967, n = 12). A kappa/lambda ratio value between 0.5 and 5.0 had 100 % sensitivity and 100 % specificity for distinguishing AL amyloidosis from non-AL amyloidosis. This optimized range for serum light chain kappa/lambda ratio provides extremely robust classification of cardiac amyloidosis. Cases of cardiac amyloidosis in which the serum kappa/lambda free light chain ratio falls close to these new cutoff values may benefit most from direct amyloid subtyping. PMID:25925232

  5. A comparative analysis of accident risks in fossil, hydro, and nuclear energy chains

    SciTech Connect

    Burgherr, P.; Hirschberg, S.

    2008-07-01

    This study presents a comparative assessment of severe accident risks in the energy sector, based on the historical experience of fossil (coal, oil, natural gas, and LPG (Liquefied Petroleum Gas)) and hydro chains contained in the comprehensive Energy-related Severe Accident Database (ENSAD), as well as Probabilistic Safety Assessment (PSA) for the nuclear chain. Full energy chains were considered because accidents can take place at every stage of the chain. Comparative analyses for the years 1969-2000 included a total of 1870 severe ({>=} 5 fatalities) accidents, amounting to 81,258 fatalities. Although 79.1% of all accidents and 88.9% of associated fatalities occurred in less developed, non-OECD countries, industrialized OECD countries dominated insured losses (78.0%), reflecting their substantially higher insurance density and stricter safety regulations. Aggregated indicators and frequency-consequence (F-N) curves showed that energy-related accident risks in non-OECD countries are distinctly higher than in OECD countries. Hydropower in non-OECD countries and upstream stages within fossil energy chains are most accident-prone. Expected fatality rates are lowest for Western hydropower and nuclear power plants; however, the maximum credible consequences can be very large. Total economic damages due to severe accidents are substantial, but small when compared with natural disasters. Similarly, external costs associated with severe accidents are generally much smaller than monetized damages caused by air pollution.

  6. Weighted Markov chains for forecasting and analysis in Incidence of infectious diseases in jiangsu Province, China☆

    PubMed Central

    Peng, Zhihang; Bao, Changjun; Zhao, Yang; Yi, Honggang; Xia, Letian; Yu, Hao; Shen, Hongbing; Chen, Feng

    2010-01-01

    This paper first applies the sequential cluster method to set up the classification standard of infectious disease incidence state based on the fact that there are many uncertainty characteristics in the incidence course. Then the paper presents a weighted Markov chain, a method which is used to predict the future incidence state. This method assumes the standardized self-coefficients as weights based on the special characteristics of infectious disease incidence being a dependent stochastic variable. It also analyzes the characteristics of infectious diseases incidence via the Markov chain Monte Carlo method to make the long-term benefit of decision optimal. Our method is successfully validated using existing incidents data of infectious diseases in Jiangsu Province. In summation, this paper proposes ways to improve the accuracy of the weighted Markov chain, specifically in the field of infection epidemiology. PMID:23554632

  7. Analysis of solitary wave impulses in granular chains using ultrasonic excitation

    NASA Astrophysics Data System (ADS)

    Yang, J.; Hutchins, D. A.; Akanji, O.; Thomas, P. J.; Davis, L. A. J.; Harput, S.; Gelat, P.; Freear, S.; Saffari, N.

    2016-06-01

    The propagation of broad bandwidth solitary wave impulses, generated within granular chains by narrow bandwidth ultrasonic excitation, is studied in detail. Theoretical predictions are compared to experimental results. It is demonstrated that the observed effects result from a sum of a solitary wave traveling out from the source with a wave that reflects from the far end of the chain. It is shown that this combination, when used with an excitation in the form of a long-duration tone burst, encourages the generation of multiple impulses with a characteristic periodicity. This study shows that the properties of the chain structure and the excitation can be adjusted so as to generate ultrasonic solitary wave impulses with a high amplitude and known frequency content, which are of interest in applications such as biomedical ultrasound.

  8. Highly sensitive DNA methylation analysis at CpG resolution by surface-enhanced Raman scattering via ligase chain reaction.

    PubMed

    Wang, Yuling; Wee, Eugene J H; Trau, Matt

    2015-07-11

    Sensitive and accurate DNA methylation analysis at CpG resolution was demonstrated using surface-enhanced Raman scattering (SERS) via ligase chain reaction (LCR). The method was sensitive to 10% changes in methylation and the accuracy of methylation estimates in cells and serum DNA validated with sequencing. The LCR/SERS approach may have broad applications as an alternative (epi)genetic detection method. PMID:26063626

  9. Twist-radial normal mode analysis in double-stranded DNA chains

    NASA Astrophysics Data System (ADS)

    Torrellas, Germán; Maciá, Enrique

    2012-10-01

    We study the normal modes of a duplex DNA chain at low temperatures. We consider the coupling between the hydrogen-bond radial oscillations and the twisting motion of each base pair within the Peyrard-Bishop-Dauxois model. The coupling is mediated by the stacking interaction between adjacent base pairs along the helix. We explicitly consider different mass values for different nucleotides, extending previous works. We disclose several resonance conditions of interest, determined by the fine-tuning of certain model parameters. The role of these dynamical effects on the DNA chain charge transport properties is discussed.

  10. Techno-economic analysis of an improved process for producing saturated branched-chain fatty acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vegetable oils provide a source of environmentally desirable lubricants, but they are not widely utilized because of their poor oxidative stability. Branched-chain fatty acid isomers are desirable products because they have excellent thermostabilities and lubricities when compared to the parent veg...

  11. Molecular cloning and characterization analysis of immunoglobulin M heavy chain gene in European eel (Anguilla anguilla).

    PubMed

    Feng, Jianjun; Guan, Ruizhang; Lin, Peng; Guo, Songlin

    2009-01-15

    In this study, the immunoglobulin M heavy chain gene of European eel (Anguilla anguilla) was cloned and analyzed. The full-length cDNA of the IgM heavy chain gene (GenBank accession no. EF062515) has 2089 nucleotides encoding a putative protein of 581 amino acids. The IgM heavy chain was composed of leader peptide (L), variable domain (VH), CH1, CH2, Hinge, CH3, CH4, and C-terminus and two novel continuous putative N-glycosylation sites were found close to the second cysteine of CH3 in A. anguilla-H1 and A. anguilla-H2. The deduced amino acid sequence of the European eel IgM heavy chain constant region shared similarities to that of the Ladyfish (Elops saurus), Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), Grass carp (Ctenopharingodon idella), Common carp (Cyprinus carpio), Channel catfish (Ictalurus punctatus), and the orange-spotted grouper (Epinephelus coioides) with the identity of 46.1%, 39.7%, 38.9%, 32.4%, 32.3%, 31.7%, and 30.7%, respectively. The highest level of IgM gene expression was observed in the kidney, followed by the spleen, gills, liver, muscle and heart in the apparently healthy European eels. PMID:19013650

  12. Purification, Characterization and Analysis of the Allergenic Properties of Myosin Light Chain in Procambarus clarkia.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Myosin light chain (MLC) plays a vital role in cell and muscle functions and has been identified as an allergen in close species. In this study, MLC with the molecular mass of 18kDa was purified from crayfish (Procambarus clarkii) muscle fibrils. Its physicochemical characterization showed that the...

  13. Understanding Latina and Latino College Choice: A Social Capital and Chain Migration Analysis

    ERIC Educational Resources Information Center

    Perez, Patricia A.; McDonough, Patricia M.

    2008-01-01

    Through interviews and focus groups with 106 high school juniors and seniors, this research examined the college choice process for Latina and Latino students in the greater Los Angeles basin. Using chain migration theory within a social capital framework, the results indicated that as primarily first-generation college students, the students in…

  14. An integrated one-chip-sensor system for microRNA quantitative analysis based on digital droplet polymerase chain reaction

    NASA Astrophysics Data System (ADS)

    Tsukuda, Masahiko; Wiederkehr, Rodrigo Sergio; Cai, Qing; Majeed, Bivragh; Fiorini, Paolo; Stakenborg, Tim; Matsuno, Toshinobu

    2016-04-01

    A silicon microfluidic chip was developed for microRNA (miRNA) quantitative analysis. It performs sequentially reverse transcription and polymerase chain reaction in a digital droplet format. Individual processes take place on different cavities, and reagent and sample mixing is carried out on a chip, prior to entering each compartment. The droplets are generated on a T-junction channel before the polymerase chain reaction step. Also, a miniaturized fluorescence detector was developed, based on an optical pick-up head of digital versatile disc (DVD) and a micro-photomultiplier tube. The chip integrated in the detection system was tested using synthetic miRNA with known concentrations, ranging from 300 to 3,000 templates/µL. Results proved the functionality of the system.

  15. Purification, crystallization and preliminary X-ray crystallographic analysis of branched-chain aminotransferase from Deinococcus radiodurans

    SciTech Connect

    Chen, Chung-Der; Huang, Tien-Feng; Lin, Chih-Hao; Guan, Hong-Hsiang; Hsieh, Yin-Cheng; Lin, Yi-Hung; Huang, Yen-Chieh; Liu, Ming-Yih; Chang, Wen-Chang; Chen, Chun-Jung

    2007-06-01

    The crystallization of branched-chain aminotransferase from D. radiodurans is described. The branched-chain amino-acid aminotransferase (BCAT), which requires pyridoxal 5′-phosphate (PLP) as a cofactor, is a key enzyme in the biosynthetic pathway of the hydrophobic amino acids leucine, isoleucine and valine. DrBCAT from Deinococcus radiodurans, which has a molecular weight of 40.9 kDa, was crystallized using the hanging-drop vapour-diffusion method. According to X-ray diffraction data to 2.50 Å resolution from a DrBCAT crystal, the crystal belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 56.37, b = 90.70, c = 155.47 Å. Preliminary analysis indicates the presence of two DrBCAT molecules in the asymmetric unit, with a solvent content of 47.52%.

  16. Bioaccumulation and food-chain analysis for evaluating ecological risks in terrestrial and wetland habitats: Availability-transfer factors (ATFs) in soil {r_arrow} soil macroinvertebrate {r_arrow} amphibian food chains

    SciTech Connect

    Linder, G.; Bollman, M.; Callahan, C.; Gillette, C.; Nebeker, A.; Wilborn, D.

    1998-12-31

    As part of the ecological risk assessment process for terrestrial and wetland habitats, the evaluation of bioaccumulative chemicals of concern (BCCs) is frequently pursued through food-chain analysis with a subsequent comparison of daily doses to benchmark toxicity reference values, when available. Food-chain analysis has frequently been applied to the analysis of exposure to BCCs identified as chemicals of potential ecological concern (COPECs) in the ecological risk assessment process. Here, designed studies focused on wetland food-chains such as hydric soil {r_arrow} soil macroinvertebrate {r_arrow} amphibian and terrestrial food-chains such as soil {r_arrow} plant {r_arrow} small mammal illustrate an approach for the derivation and validation of trophic transfer factors for metals considered as COPECs such as cadmium, chromium, copper, lead, and zinc. The results clearly indicate that the transfer of chemicals between trophic levels is critical in the bioaccumulation process in wetland and terrestrial food-chains and is influenced by numerous interacting abiotic and biotic factors, including physicochemical properties of soil, and the role, if any, that the metal has in the receptor as a required trace element.

  17. From Puffins to Plankton: A DNA-Based Analysis of a Seabird Food Chain in the Northern Gulf of Maine

    PubMed Central

    Bowser, A. Kirsten; Diamond, Antony W.; Addison, Jason A.

    2013-01-01

    The predator-prey interactions within food chains are used to both characterize and understand ecosystems. Conventional methods of constructing food chains from visual identification of prey in predator diet can suffer from poor taxonomic resolution, misidentification, and bias against small or completely digestible prey. Next-generation sequencing (NGS) technology has become a powerful tool for diet reconstruction through barcoding of DNA in stomach content or fecal samples. Here we use multi-locus (16S and CO1) next-generation sequencing of DNA barcodes on the feces of Atlantic puffin (Fratercula arctica) chicks (n=65) and adults (n=64) and the stomach contents of their main prey, Atlantic herring (Clupea harengus, n=44) to investigate a previously studied food chain. We compared conventional and molecular-derived chick diet, tested the similarity between the diets of puffin adults and chicks, and determined whether herring prey can be detected in puffin diet samples. There was high variability in the coverage of prey groups between 16S and CO1 markers. We identified more unique prey with our 16S compared to CO1 barcoding markers (51 and 39 taxa respectively) with only 12 taxa identified by both genes. We found no significant difference between the 16S-identified diets of puffin adults (n=17) and chicks (n=41). Our molecular method is more taxonomically resolved and detected chick prey at higher frequencies than conventional field observations. Many likely planktonic prey of herring were detected in feces from puffin adults and chicks, highlighting the impact secondary consumption may have on the interpretation of molecular dietary analysis. This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain and highlights the utility of a multi-locus approach to diet reconstruction that is broadly applicable to food web analysis. PMID:24358258

  18. From puffins to plankton: a DNA-based analysis of a seabird food chain in the northern Gulf of Maine.

    PubMed

    Bowser, A Kirsten; Diamond, Antony W; Addison, Jason A

    2013-01-01

    The predator-prey interactions within food chains are used to both characterize and understand ecosystems. Conventional methods of constructing food chains from visual identification of prey in predator diet can suffer from poor taxonomic resolution, misidentification, and bias against small or completely digestible prey. Next-generation sequencing (NGS) technology has become a powerful tool for diet reconstruction through barcoding of DNA in stomach content or fecal samples. Here we use multi-locus (16S and CO1) next-generation sequencing of DNA barcodes on the feces of Atlantic puffin (Fratercula arctica) chicks (n=65) and adults (n=64) and the stomach contents of their main prey, Atlantic herring (Clupea harengus, n=44) to investigate a previously studied food chain. We compared conventional and molecular-derived chick diet, tested the similarity between the diets of puffin adults and chicks, and determined whether herring prey can be detected in puffin diet samples. There was high variability in the coverage of prey groups between 16S and CO1 markers. We identified more unique prey with our 16S compared to CO1 barcoding markers (51 and 39 taxa respectively) with only 12 taxa identified by both genes. We found no significant difference between the 16S-identified diets of puffin adults (n=17) and chicks (n=41). Our molecular method is more taxonomically resolved and detected chick prey at higher frequencies than conventional field observations. Many likely planktonic prey of herring were detected in feces from puffin adults and chicks, highlighting the impact secondary consumption may have on the interpretation of molecular dietary analysis. This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain and highlights the utility of a multi-locus approach to diet reconstruction that is broadly applicable to food web analysis. PMID:24358258

  19. Adaptive relaxation for the steady-state analysis of Markov chains

    NASA Technical Reports Server (NTRS)

    Horton, Graham

    1994-01-01

    We consider a variant of the well-known Gauss-Seidel method for the solution of Markov chains in steady state. Whereas the standard algorithm visits each state exactly once per iteration in a predetermined order, the alternative approach uses a dynamic strategy. A set of states to be visited is maintained which can grow and shrink as the computation progresses. In this manner, we hope to concentrate the computational work in those areas of the chain in which maximum improvement in the solution can be achieved. We consider the adaptive approach both as a solver in its own right and as a relaxation method within the multi-level algorithm. Experimental results show significant computational savings in both cases.

  20. Adaptive Markov chain Monte Carlo forward projection for statistical analysis in epidemic modelling of human papillomavirus.

    PubMed

    Korostil, Igor A; Peters, Gareth W; Cornebise, Julien; Regan, David G

    2013-05-20

    A Bayesian statistical model and estimation methodology based on forward projection adaptive Markov chain Monte Carlo is developed in order to perform the calibration of a high-dimensional nonlinear system of ordinary differential equations representing an epidemic model for human papillomavirus types 6 and 11 (HPV-6, HPV-11). The model is compartmental and involves stratification by age, gender and sexual-activity group. Developing this model and a means to calibrate it efficiently is relevant because HPV is a very multi-typed and common sexually transmitted infection with more than 100 types currently known. The two types studied in this paper, types 6 and 11, are causing about 90% of anogenital warts. We extend the development of a sexual mixing matrix on the basis of a formulation first suggested by Garnett and Anderson, frequently used to model sexually transmitted infections. In particular, we consider a stochastic mixing matrix framework that allows us to jointly estimate unknown attributes and parameters of the mixing matrix along with the parameters involved in the calibration of the HPV epidemic model. This matrix describes the sexual interactions between members of the population under study and relies on several quantities that are a priori unknown. The Bayesian model developed allows one to estimate jointly the HPV-6 and HPV-11 epidemic model parameters as well as unknown sexual mixing matrix parameters related to assortativity. Finally, we explore the ability of an extension to the class of adaptive Markov chain Monte Carlo algorithms to incorporate a forward projection strategy for the ordinary differential equation state trajectories. Efficient exploration of the Bayesian posterior distribution developed for the ordinary differential equation parameters provides a challenge for any Markov chain sampling methodology, hence the interest in adaptive Markov chain methods. We conclude with simulation studies on synthetic and recent actual data. PMID

  1. Probabilistic accident consequence uncertainty analysis: Food chain uncertainty assessment. Volume 2: Appendices

    SciTech Connect

    Brown, J.; Goossens, L.H.J.; Kraan, B.C.P.

    1997-06-01

    This volume is the second of a two-volume document that summarizes a joint project by the US Nuclear Regulatory and the Commission of European Communities to assess uncertainties in the MACCS and COSYMA probabilistic accident consequence codes. These codes were developed primarily for estimating the risks presented by nuclear reactors based on postulated frequencies and magnitudes of potential accidents. This two-volume report, which examines mechanisms and uncertainties of transfer through the food chain, is the first in a series of five such reports. A panel of sixteen experts was formed to compile credible and traceable uncertainty distributions for food chain transfer that affect calculations of offsite radiological consequences. Seven of the experts reported on transfer into the food chain through soil and plants, nine reported on transfer via food products from animals, and two reported on both. The expert judgment elicitation procedure and its outcomes are described in these volumes. This volume contains seven appendices. Appendix A presents a brief discussion of the MAACS and COSYMA model codes. Appendix B is the structure document and elicitation questionnaire for the expert panel on soils and plants. Appendix C presents the rationales and responses of each of the members of the soils and plants expert panel. Appendix D is the structure document and elicitation questionnaire for the expert panel on animal transfer. The rationales and responses of each of the experts on animal transfer are given in Appendix E. Brief biographies of the food chain expert panel members are provided in Appendix F. Aggregated results of expert responses are presented in graph format in Appendix G.

  2. Sequence analysis of the 3' non-coding region of mouse immunoglobulin light chain messenger RNA.

    PubMed Central

    Hamlyn, P H; Gillam, S; Smith, M; Milstein, C

    1977-01-01

    Using an oligonucleotide d(pT10-C-A) as primer, cDNA has been transcribed from the 3' non-coding region of mouse immunoglobulin light chain mRNA and sequenced by a modification1 of the 'plus-minus' gel method2. The sequence obtained has partially corrected and extended a previously obtained sequence3. The new data contains an unusual sequence in which a trinucleotide is repeated seven times. Images PMID:405661

  3. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies

    PubMed Central

    Nyuzuki, Hiromi; Moriyama, Yohsuke; Mizuno, Yosuke; Hirata, Tomoko; Yatsuka, Yukiko; Yamashita-Sugahara, Yzumi; Nakachi, Yutaka; Kato, Hidemasa; Okuda, Akihiko; Tamaru, Shunsuke; Borna, Nurun Nahar; Banshoya, Kengo; Aigaki, Toshiro; Sato-Miyata, Yukiko; Ohnuma, Kohei; Suzuki, Tsutomu; Nagao, Asuteka; Maehata, Hazuki; Matsuda, Fumihiko; Higasa, Koichiro; Nagasaki, Masao; Yasuda, Jun; Yamamoto, Masayuki; Fushimi, Takuya; Shimura, Masaru; Kaiho-Ichimoto, Keiko; Harashima, Hiroko; Yamazaki, Taro; Mori, Masato; Murayama, Kei; Ohtake, Akira; Okazaki, Yasushi

    2016-01-01

    Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4) as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3) and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21) as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder. PMID:26741492

  4. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies.

    PubMed

    Kohda, Masakazu; Tokuzawa, Yoshimi; Kishita, Yoshihito; Nyuzuki, Hiromi; Moriyama, Yohsuke; Mizuno, Yosuke; Hirata, Tomoko; Yatsuka, Yukiko; Yamashita-Sugahara, Yzumi; Nakachi, Yutaka; Kato, Hidemasa; Okuda, Akihiko; Tamaru, Shunsuke; Borna, Nurun Nahar; Banshoya, Kengo; Aigaki, Toshiro; Sato-Miyata, Yukiko; Ohnuma, Kohei; Suzuki, Tsutomu; Nagao, Asuteka; Maehata, Hazuki; Matsuda, Fumihiko; Higasa, Koichiro; Nagasaki, Masao; Yasuda, Jun; Yamamoto, Masayuki; Fushimi, Takuya; Shimura, Masaru; Kaiho-Ichimoto, Keiko; Harashima, Hiroko; Yamazaki, Taro; Mori, Masato; Murayama, Kei; Ohtake, Akira; Okazaki, Yasushi

    2016-01-01

    Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4) as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3) and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21) as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder. PMID:26741492

  5. Applying commodity chain analysis to changing modes of alcohol supply in a developing country.

    PubMed

    Jernigan, D H

    2000-12-01

    Development sociology has used global commodity chains as one way of analyzing the dynamics of power and profit-taking in globalized production networks made up of multiple firms and occurring in multiple national settings. A substantial portion of the alcohol supply in developing countries is now produced through such production networks. Particularly in the beer and spirits trade, a small number of transnational firms control networks of local producers, importers, advertisers and distributors. These networks serve to embed transnational or transnationally backed brands in the local culture, using the tools of market research, product design and marketing to influence local drinking practices. Case materials from Malaysia's beer industry help to illustrate how the transnational firms dominate in those links of the commodity chain in which monopoly or oligopoly control is most likely to be found: the design/recipe and marketing/advertising nodes. Their control of the commodity chains and extraction of monopoly or oligopoly profits from them places substantial resources and influence over drinking settings and practices in foreign hands. The impact of this influence on state efficacy and autonomy in setting alcohol policy is an important subject for future research on the creation and implementation of effective alcohol policies in developing societies. PMID:11218345

  6. Designing Performance Measurement For Supply Chain's Actors And Regulator Using Scale Balanced Scorecard And Data Envelopment Analysis

    NASA Astrophysics Data System (ADS)

    Kusrini, Elisa; Subagyo; Aini Masruroh, Nur

    2016-01-01

    This research is a sequel of the author's earlier conducted researches in the fields of designing of integrated performance measurement between supply chain's actors and regulator. In the previous paper, the design of performance measurement is done by combining Balanced Scorecard - Supply Chain Operation Reference - Regulator Contribution model and Data Envelopment Analysis. This model referred as B-S-Rc-DEA model. The combination has the disadvantage that all the performance variables have the same weight. This paper investigates whether by giving weight to performance variables will produce more sensitive performance measurement in detecting performance improvement. Therefore, this paper discusses the development of the model B-S-Rc-DEA by giving weight to its performance'variables. This model referred as Scale B-S-Rc-DEA model. To illustrate the model of development, some samples from small medium enterprises of leather craft industry supply chain in province of Yogyakarta, Indonesia are used in this research. It is found that Scale B-S-Rc-DEA model is more sensitive to detecting performance improvement than B-S- Rc-DEA model.

  7. Alternative method for gas chromatography-mass spectrometry analysis of short-chain fatty acids in faecal samples.

    PubMed

    García-Villalba, Rocio; Giménez-Bastida, Juan A; García-Conesa, Maria T; Tomás-Barberán, Francisco A; Carlos Espín, Juan; Larrosa, Mar

    2012-08-01

    Short-chain fatty acids are the major end products of bacterial metabolism in the large bowel. They derive mostly from the bacterial breakdown of carbohydrates and are known to have positive health benefits. Due to the biological relevance of these compounds it is important to develop efficient, cheap, fast, and sensitive analytical methods that enable the identification and quantification of the short-chain fatty acids in a large number of biological samples. In this study, a gas chromatography-mass spectrometry method was developed and validated for the analysis of short-chain fatty acids in faecal samples. These volatile compounds were extracted with ethyl acetate and 4-methyl valeric acid was used as an internal standard. No further cleanup, concentration, and derivatization steps were needed and the extract was directly injected onto the column. Recoveries ranged between 65 and 105%, and no matrix effects were observed. The proposed method has wide linear ranges, good inter- and intraday variability values (below 2.6 and 5.6%, respectively) and limits of detection between 0.49 μM (0.29 μg/g) and 4.31 μM (3.8 μg/g). The applicability of this analytical method was successfully tested in faecal samples from rats and humans. PMID:22865755

  8. Alternative method for gas chromatography-mass spectrometry analysis of short-chain fatty acids in faecal samples.

    PubMed

    García-Villalba, Rocio; Giménez-Bastida, Juan A; García-Conesa, Maria T; Tomás-Barberán, Francisco A; Espín, Juan Carlos; Larrosa, Mar

    2012-06-01

    Short-chain fatty acids are the major end products of bacterial metabolism in the large bowel. They derive mostly from the bacterial breakdown of carbohydrates and are known to have positive health benefits. Due to the biological relevance of these compounds it is important to develop efficient, cheap, fast, and sensitive analytical methods that enable the identification and quantification of the short-chain fatty acids in a large number of biological samples. In this study, a gas chromatography-mass spectrometry method was developed and validated for the analysis of short-chain fatty acids in faecal samples. These volatile compounds were extracted with ethyl acetate and 4-methyl valeric acid was used as an internal standard. No further cleanup, concentration, and derivatization steps were needed and the extract was directly injected onto the column. Recoveries ranged between 65 and 105%, and no matrix effects were observed. The proposed method has wide linear ranges, good inter- and intraday variability values (below 2.6 and 5.6%, respectively) and limits of detection between 0.49 μM (0.29 μg/g) and 4.31 μM (3.8 μg/g). The applicability of this analytical method was successfully tested in faecal samples from rats and humans. PMID:22674825

  9. Mitigation of ammonia, nitrous oxide and methane emissions from manure management chains: a meta-analysis and integrated assessment.

    PubMed

    Hou, Yong; Velthof, Gerard L; Oenema, Oene

    2015-03-01

    Livestock manure contributes considerably to global emissions of ammonia (NH3 ) and greenhouse gases (GHG), especially methane (CH4 ) and nitrous oxide (N2 O). Various measures have been developed to mitigate these emissions, but most of these focus on one specific gas and/or emission source. Here, we present a meta-analysis and integrated assessment of the effects of mitigation measures on NH3 , CH4 and (direct and indirect) N2 O emissions from the whole manure management chain. We analysed the effects of mitigation technologies on NH3 , CH4 and N2 O emissions from individual sources statistically using results of 126 published studies. Whole-chain effects on NH3 and GHG emissions were assessed through scenario analysis. Significant NH3 reduction efficiencies were observed for (i) housing via lowering the dietary crude protein (CP) content (24-65%, compared to the reference situation), for (ii) external slurry storages via acidification (83%) and covers of straw (78%) or artificial films (98%), for (iii) solid manure storages via compaction and covering (61%, compared to composting), and for (iv) manure application through band spreading (55%, compared to surface application), incorporation (70%) and injection (80%). Acidification decreased CH4 emissions from stored slurry by 87%. Significant increases in N2 O emissions were found for straw-covered slurry storages (by two orders of magnitude) and manure injection (by 26-199%). These side-effects of straw covers and slurry injection on N2 O emission were relatively small when considering the total GHG emissions from the manure chain. Lowering the CP content of feed and acidifying slurry are strategies that consistently reduce NH3 and GHG emissions in the whole chain. Other strategies may reduce emissions of a specific gas or emissions source, by which there is a risk of unwanted trade-offs in the manure management chain. Proper farm-scale combinations of mitigation measures are important to minimize impacts of

  10. Markov chain Monte Carlo methods for statistical analysis of RF photonic devices.

    PubMed

    Piels, Molly; Zibar, Darko

    2016-02-01

    The microwave reflection coefficient is commonly used to characterize the impedance of high-speed optoelectronic devices. Error and uncertainty in equivalent circuit parameters measured using this data are systematically evaluated. The commonly used nonlinear least-squares method for estimating uncertainty is shown to give unsatisfactory and incorrect results due to the nonlinear relationship between the circuit parameters and the measured data. Markov chain Monte Carlo methods are shown to provide superior results, both for individual devices and for assessing within-die variation. PMID:26906783

  11. FE analysis of stress and displacements occurring in the bony chain of leg

    PubMed Central

    Filardi, Vincenzo

    2014-01-01

    Aims The aim of this study was to assess how the stress shielding can influence the integrity and resistance of bones. Methods With this purpose a complete FE model of the human leg was realised. A load of 700 N has been applied at the top of pelvis and the feet, at the tip, was rigidly fixed. Results Obtained results reveal interesting consequences deriving by taking into account the complete bony chain. Conclusion A comparison among the literature data and our models can furnish a complete vision of the global spreading of the forces along the various bony components. PMID:25561749

  12. Anaerobic Fe(III) reduction by Shewanella putrefaciens: Analysis of the electron transport chain

    SciTech Connect

    Daad Saffarini

    2004-01-20

    The goals of the project were to isolate mutants that are deficient in metal reduction, identify components of the electron transport chain that are involved in this process, and purify some of these proteins for biochemical analyses. In the 3-year period since the start of the project, we have accomplished many of these goals. We have isolated several new S. oneidensis mutants that are deficient in metal reduction, and have initiated the development of vectors for the overexpression of cytochromes and other proteins in S. oneidensis. We have also overexpressed CymA, one of the c cytochromes that are involved in metal reduction.

  13. Polymerase chain reaction-denaturing gradient gel electrophoresis analysis of microbial community structure in landfill leachate.

    PubMed

    Uchida, Miho; Hatayoshi, Haruna; Syuku-nobe, Aoi; Shimoyama, Takefumi; Nakayama, Toru; Okuwaki, Akitsugu; Nishino, Tokuzo; Hemmi, Hisashi

    2009-05-30

    The structures of microbial communities in water samples obtained from a landfill site that had been a source of environmental pollution by emitting hydrogen sulfide were elucidated using polymerase chain reaction-denaturing gradient gel electrophoresis. The microbial communities, which consisted of a limited number of major microorganisms, were stable for several months. Microorganisms capable of degrading such chemical compounds as 2-hydroxybenzothiazole and bisphenol A were observed in landfill leachate. Microorganisms responsible for the production of hydrogen sulfide were not the primary microbes detected, even in water samples obtained from the site of gas emission. PMID:18977596

  14. Stability and bifurcation analysis on a three-species food chain system with two delays

    NASA Astrophysics Data System (ADS)

    Cui, Guo-Hu; Yan, Xiang-Ping

    2011-09-01

    The present paper deals with a three-species Lotka-Volterra food chain system with two discrete delays. By linearizing the system at the positive equilibrium and analyzing the associated characteristic equation, the asymptotic stability of the positive equilibrium and existence of local Hopf bifurcations are investigated. Furthermore, by using the normal form theory and the center manifold reduction, explicit formulae are derived to determine the direction of bifurcations and the stability of bifurcating periodic solutions. Finally, to verify our theoretical predictions, some numerical simulations are also included at the end of this paper.

  15. Quantitative analysis of MDR1 (multidrug resistance) gene expression in human tumors by polymerase chain reaction

    SciTech Connect

    Noonan, K.E.; Beck, C.; Holzmayer, T.A.; Chin, J.E.; Roninson, I.B. ); Wunder, J.S.; Andrulis, I.L. ); Gazdar, A.F. ); Willman, C.L.; Griffith, B. ); Von Hoff, D.D. )

    1990-09-01

    The resistance of tumor cells ot chemotheraprutic drugs is a major obstacle to successful cancer chemotherapy. In human cells, expression of the MDR1 gene, encoding a transmembrane efflux pump (P-glycoprotein), leads to decreased intracellular accumulation and resistance to a variety of lipophilic drugs (multidrug resistance; MDR). The levels of MDR in cell lines selected in bitro have been shown to correlate with the steady-state levels of MDR1 mRNA and P-glycoprotein. In cells with a severalfold increase in cellular drug resistance, MDR1 expression levels are close to the limits of detection by conventional assays. MDR1 expression has been frequently observed in human tumors after chemotherapy and in some but not all types of clinically refactory tumors untreated with chemotherapeutic drugs. The authors have devised a highly sensitive, specific, and quantitative protocol for measuring the levels of MDR1 mRNA in clincal samples, based on the polymerase chain reaction. They have used this assay to measure MDR1 gene expression in MDR cell lines and >300 normal tissues, tumor-derived cell lines, and clinical specimens of untreated tumors of the types in which MDR1 expression was rarely observed by standard assays. Low levels of MDR1 expression were found by polymerase chain reaction in most solid tumors and leukemias tested. The frequency of samples without detectable MDR1 expression varied among different types of tumors; MDR1-negative samples were ost common among tumor types known to be relatively responsive to chemotherapy.

  16. Ionic polymer cluster energetics: Computational analysis of pendant chain stiffness and charge imbalance

    NASA Astrophysics Data System (ADS)

    Weiland, Lisa Mauck; Leo, Donald J.

    2005-06-01

    In recent years there has been considerable study of the potential mechanisms underlying the electromechanical response of ionic-polymer-metal composites. The most recent models have been based on the response of the ion-containing clusters that are formed when the material is synthesized. Most of these efforts have employed assumptions of uniform ion distribution within spherical cluster shapes. This work investigates the impact of dispensing with these assumptions in order to better understand the parameters that impact cluster shape, size, and ion transport potential. A computational micromechanics model applying Monte Carlo methodology is employed to predict the equilibrium state of a single cluster of a solvated ionomeric polymer. For a constant solvated state, the model tracks the position of individual ions within a given cluster in response to ion-ion interaction, mechanical stiffness of the pendant chain, cluster surface energy, and external electric-field loading. Results suggest that cluster surface effects play a significant role in the equilibrium cluster state, including ion distribution; pendant chain stiffness also plays a role in ion distribution but to a lesser extent. Moreover, ion pairing is rarely complete even in cation-rich clusters; this in turn supports the supposition of the formation of anode and cathode boundary layers.

  17. Mechanical analysis and force chain determination in granular materials using digital image correlation.

    PubMed

    Chen, Fanxiu; Zhuang, Qi; Zhang, Huixin

    2016-06-20

    The mechanical behaviors of granular materials are governed by the grain properties and microstructure of the materials. We conducted experiments to study the force transmission in granular materials using plane strain tests. The large amount of nearly continuous displacement data provided by the advanced noncontact experimental technique of digital image correlation (DIC) has provided a means to quantify local displacements and strains at the particle level. The average strain of each particle could be calculated based on the DIC method, and the average stress could be obtained using Hooke's law. The relationship between the stress and particle force could be obtained based on basic Newtonian mechanics and the balance of linear momentum at the particle level. This methodology is introduced and validated. In the testing procedure, the system is tested in real 2D particle cases, and the contact forces and force chain are obtained and analyzed. The system has great potential for analyzing a real granular system and measuring the contact forces and force chain. PMID:27409099

  18. Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.

    PubMed

    Kung, Camy C-H; Naik, Mandar T; Wang, Szu-Huan; Shih, Hsiu-Ming; Chang, Che-Chang; Lin, Li-Ying; Chen, Chia-Lin; Ma, Che; Chang, Chi-Fon; Huang, Tai-Huang

    2014-08-15

    The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the β2-strand and the α1-helix parallel to the β2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule. PMID:24844634

  19. Molecular analysis of the effect of short-chain fatty acids on intestinal cell proliferation.

    PubMed

    Blottière, Hervé M; Buecher, Bruno; Galmiche, Jean-Paul; Cherbut, Christine

    2003-02-01

    Short-chain fatty acids (SCFA), particularly butyrate, were shown to regulate cell proliferation in vitro and in vivo. Indeed, butyrate is the major fuel for colonic epithelial cells, and it can influence cell proliferation through the release of growth factors or gastrointestinal peptides such as gastrin, or through modulation of mucosal blood flow. Lastly, SCFA can act directly on genes regulating cell proliferation, and butyrate is the main SCFA to display such an effect. Butyrate inhibits histone deacetylase, which will allow histone hyperacetylation. Such hyperacetylation leads to transcription of several genes, including p21/Cip1. Moreover, it will allow cyclin D3 hyper-expression by inhibiting its degradation. The induction of the cyclin-dependent kinase inhibitory protein p21/Cip1 accounts for cell arrest in the G1 phase of the cell cycle. However, in the absence of p21 other mechanisms are initiated, leading to inhibition of cell proliferation. PMID:12740064

  20. Supply Chain Vulnerability Analysis Using Scenario-Based Input-Output Modeling: Application to Port Operations.

    PubMed

    Thekdi, Shital A; Santos, Joost R

    2016-05-01

    Disruptive events such as natural disasters, loss or reduction of resources, work stoppages, and emergent conditions have potential to propagate economic losses across trade networks. In particular, disruptions to the operation of container port activity can be detrimental for international trade and commerce. Risk assessment should anticipate the impact of port operation disruptions with consideration of how priorities change due to uncertain scenarios and guide investments that are effective and feasible for implementation. Priorities for protective measures and continuity of operations planning must consider the economic impact of such disruptions across a variety of scenarios. This article introduces new performance metrics to characterize resiliency in interdependency modeling and also integrates scenario-based methods to measure economic sensitivity to sudden-onset disruptions. The methods will be demonstrated on a U.S. port responsible for handling $36.1 billion of cargo annually. The methods will be useful to port management, private industry supply chain planning, and transportation infrastructure management. PMID:26271771

  1. Analysis of a stochastic tri-trophic food-chain model with harvesting.

    PubMed

    Liu, Meng; Bai, Chuanzhi

    2016-09-01

    We consider a tri-trophic stochastic food-chain model with harvesting. We first establish critical values between persistence in mean and extinction for each species. The results show that persistence and extinction of a species only depends on the demographic impacts of environmental stochasticity on the species and species at lower tropic levels; however, the mean abundance of a species depends on the impacts of environmental stochasticity at all trophic levels. Then we consider stability in distribution of the model. Finally, we provide a necessary and sufficient condition for existence of optimal harvesting strategy and give the optimal harvesting effort and maximum of sustainable yield. The results show that the optimal harvesting strategy is closely related to the stochastic noises in the model. PMID:26846770

  2. 'Chain pooling' model selection as developed for the statistical analysis of a rotor burst protection experiment

    NASA Technical Reports Server (NTRS)

    Holms, A. G.

    1977-01-01

    A statistical decision procedure called chain pooling had been developed for model selection in fitting the results of a two-level fixed-effects full or fractional factorial experiment not having replication. The basic strategy included the use of one nominal level of significance for a preliminary test and a second nominal level of significance for the final test. The subject has been reexamined from the point of view of using as many as three successive statistical model deletion procedures in fitting the results of a single experiment. The investigation consisted of random number studies intended to simulate the results of a proposed aircraft turbine-engine rotor-burst-protection experiment. As a conservative approach, population model coefficients were chosen to represent a saturated 2 to the 4th power experiment with a distribution of parameter values unfavorable to the decision procedures. Three model selection strategies were developed.

  3. A methodology for stochastic analysis of share prices as Markov chains with finite states.

    PubMed

    Mettle, Felix Okoe; Quaye, Enoch Nii Boi; Laryea, Ravenhill Adjetey

    2014-01-01

    Price volatilities make stock investments risky, leaving investors in critical position when uncertain decision is made. To improve investor evaluation confidence on exchange markets, while not using time series methodology, we specify equity price change as a stochastic process assumed to possess Markov dependency with respective state transition probabilities matrices following the identified state pace (i.e. decrease, stable or increase). We established that identified states communicate, and that the chains are aperiodic and ergodic thus possessing limiting distributions. We developed a methodology for determining expected mean return time for stock price increases and also establish criteria for improving investment decision based on highest transition probabilities, lowest mean return time and highest limiting distributions. We further developed an R algorithm for running the methodology introduced. The established methodology is applied to selected equities from Ghana Stock Exchange weekly trading data. PMID:25520904

  4. Analysis of infectious laryngotracheitis virus isolates from Ontario and New Brunswick by the polymerase chain reaction.

    PubMed Central

    Alexander, H S; Key, D W; Nagy, E

    1998-01-01

    The polymerase chain reaction (PCR) was used to amplify DNA of infectious laryngotracheitis virus (ILTV) isolates obtained from field specimens. The examined 47 samples included 37 isolates representing 35 cases of infectious laryngotracheitis from Ontario and 10 isolates originating from 10 field cases in New Brunswick. The viruses were grown in either embryonated chicken eggs or cell culture, the DNA extracted and amplified using primers designed from the sequence information of a 1.1 kb BamHI fragment of the Ontario 1598 ILTV strain. Thirty-four of the Ontario isolates and all of the New Brunswick isolates were amplified successfully. This suggests that the selected primers would be useful for the majority of the isolates encountered in outbreaks of ILTV. Images Figure 1. Figure 2. PMID:9442943

  5. Analysis of aerial survey data on Florida manatee using Markov chain Monte Carlo.

    PubMed

    Craig, B A; Newton, M A; Garrott, R A; Reynolds, J E; Wilcox, J R

    1997-06-01

    We assess population trends of the Atlantic coast population of Florida manatee, Trichechus manatus latirostris, by reanalyzing aerial survey data collected between 1982 and 1992. To do so, we develop an explicit biological model that accounts for the method by which the manatees are counted, the mammals' movement between surveys, and the behavior of the population total over time. Bayesian inference, enabled by Markov chain Monte Carlo, is used to combine the survey data with the biological model. We compute marginal posterior distributions for all model parameters and predictive distributions for future counts. Several conclusions, such as a decreasing population growth rate and low sighting probabilities, are consistent across different prior specifications. PMID:9192449

  6. Genomic Analysis of Genes Involved in the Biosynthesis of Very Long Chain Polyunsaturated Fatty Acids in Thraustochytrium sp. 26185.

    PubMed

    Zhao, Xianming; Dauenpen, Meesapyodsuk; Qu, Cunmin; Qiu, Xiao

    2016-09-01

    Thraustochytrium sp. 26185 is a marine protist that can produce a large amount of docosahexaenoic acid (DHA, 22:6n-3), an ω3 very long chain polyunsaturated fatty acid (VLCPUFA) of nutritional importance. However, the mechanism of how this fatty acid is synthesized and assembled into the storage lipid triacylglycerol is unclear. Here we report sequencing of the whole genome and genomic analysis of genes involved in the biosynthesis and assembly of the fatty acids in this species. Genome sequencing produced a total of 2,418,734,139 bp clean sequences with about 62 fold genome coverage. Annotation of the genome sequences revealed 10,797 coding genes. Among them, 10,216 genes could be assigned into 25 KOG classes where 451 genes were specifically assigned to the group of lipid transport and metabolism. Detailed analysis of these genes revealed co-existence of both aerobic pathway and anaerobic pathways for the biosynthesis of DHA in this species. However, in the aerobic pathway, a key gene encoding stearate Δ9 desaturase introducing the first double bond to long chain saturated fatty acid 18:0 was missing from the genome. Genomic survey of genes involved in the acyl trafficking among glycerolipids showed that, unlike plants, this protist did not possess phosphatidylcholine:diacylglycerol cholinephosphotransferase, an important enzyme in bridging two types of glycerolipids, diacylglycerols (DAG) and phosphatidylcholines (PtdCho). These results shed new insight on the biosynthesis and assembly of VLCPUFA in the Thraustochytrium. PMID:27514858

  7. Binary 3-D Markov Chain Random Fields: Finite-size Scaling Analysis of Percolation Properties

    NASA Astrophysics Data System (ADS)

    Harter, T.

    2004-12-01

    Percolation phenomena in random media have been extensively studied in a wide variety of fields in physics, chemistry, engineering, bio-, earth-, and environmental sciences. Most work has focused on uncorrelated random fields. The critical behavior in media with short-range correlations is thought to be identical to that in uncorrelated systems. However, the percolation threshold, pc, which is 0.3116 in uncorrelated media, has been observed to vary with the correlation scale and also with the random field type. Here, we present percolation properties and finite-size scaling effects in three-dimensional binary cubic lattices represented by correlated Markov-chain random fields and compare them to those in sequential Gaussian and sequential indicator random fields. We find that the computed percolation threshold in correlated random fields is significantly lower than in the uncorrelated lattice and decreases with increasing correlation scale. The rate of decrease rapidly flattens out for correlation lengths larger than 2-3 grid-blocks. At correlation scales of 5-6 grid blocks, pc is found to be 0.126 for the Markov chain random fields and slightly higher for sequential Gaussian and indicator random fields. The universal scaling constants for mean cluster size, backbone fraction, and connectivity are found to be consistent with results on uncorrelated lattices. For numerical studies, it is critical to understand finite-size effects on the percolation and associated phase connectivity properties of lattices. We present detailed statistical results on the percolation properties in finite sized lattice and their dependence on correlation scale. We show that appropriate grid resolution and choice of simulation boundaries is critical to properly simulate correlated natural geologic systems, which may display significant finite-size effects.

  8. Ethanol distribution, dispensing, and use: analysis of a portion of the biomass-to-biofuels supply chain using system dynamics.

    PubMed

    Vimmerstedt, Laura J; Bush, Brian; Peterson, Steve

    2012-01-01

    The Energy Independence and Security Act of 2007 targets use of 36 billion gallons of biofuels per year by 2022. Achieving this may require substantial changes to current transportation fuel systems for distribution, dispensing, and use in vehicles. The U.S. Department of Energy and the National Renewable Energy Laboratory designed a system dynamics approach to help focus government action by determining what supply chain changes would have the greatest potential to accelerate biofuels deployment. The National Renewable Energy Laboratory developed the Biomass Scenario Model, a system dynamics model which represents the primary system effects and dependencies in the biomass-to-biofuels supply chain. The model provides a framework for developing scenarios and conducting biofuels policy analysis. This paper focuses on the downstream portion of the supply chain-represented in the distribution logistics, dispensing station, and fuel utilization, and vehicle modules of the Biomass Scenario Model. This model initially focused on ethanol, but has since been expanded to include other biofuels. Some portions of this system are represented dynamically with major interactions and feedbacks, especially those related to a dispensing station owner's decision whether to offer ethanol fuel and a consumer's choice whether to purchase that fuel. Other portions of the system are modeled with little or no dynamics; the vehicle choices of consumers are represented as discrete scenarios. This paper explores conditions needed to sustain an ethanol fuel market and identifies implications of these findings for program and policy goals. A large, economically sustainable ethanol fuel market (or other biofuel market) requires low end-user fuel price relative to gasoline and sufficient producer payment, which are difficult to achieve simultaneously. Other requirements (different for ethanol vs. other biofuel markets) include the need for infrastructure for distribution and dispensing and

  9. Markov chains and entropy tests in genetic-based lithofacies analysis of deep-water clastic depositional systems

    NASA Astrophysics Data System (ADS)

    Borka, Szabolcs

    2016-01-01

    The aim of this study was to examine the relationship between structural elements and the so-called genetic lithofacies in a clastic deep-water depositional system. Process-sedimentology has recently been gaining importance in the characterization of these systems. This way the recognized facies attributes can be associated with the depositional processes establishing the genetic lithofacies. In this paper this approach was presented through a case study of a Tertiary deep-water sequence of the Pannonian-basin. Of course it was necessary to interpret the stratigraphy of the sequences in terms of "general" sedimentology, focusing on the structural elements. For this purpose, well-logs and standard deep-water models were applied. The cyclicity of sedimentary sequences can be easily revealed by using Markov chains. Though Markov chain analysis has broad application in mainly fluvial depositional environments, its utilization is uncommon in deep-water systems. In this context genetic lithofacies was determined and analysed by embedded Markov chains. The randomness in the presence of a lithofacies within a cycle was estimated by entropy tests (entropy after depositional, before depositional, for the whole system). Subsequently the relationships between lithofacies were revealed and a depositional model (i.e. modal cycle) was produced with 90% confidence level of stationarity. The non-randomness of the latter was tested by chi-square test. The consequences coming from the comparison of "general" sequences (composed of architectural elements), the genetic-based sequences (showing the distributions of the genetic lithofacies) and the lithofacies relationships were discussed in details. This way main depositional channel has the best, channelized lobes have good potential hydrocarbon reservoir attributes, with symmetric alternation of persistent fine-grained sandstone (Facies D) and muddy fine-grained sandstone with traction structures (Facies F)

  10. Ethanol Distribution, Dispensing, and Use: Analysis of a Portion of the Biomass-to-Biofuels Supply Chain Using System Dynamics

    SciTech Connect

    Vimmerstedt, L. J.; Bush, B.; Peterson, S.

    2012-05-01

    The Energy Independence and Security Act of 2007 targets use of 36 billion gallons of biofuels per year by 2022. Achieving this may require substantial changes to current transportation fuel systems for distribution, dispensing, and use in vehicles. The U.S. Department of Energy and the National Renewable Energy Laboratory designed a system dynamics approach to help focus government action by determining what supply chain changes would have the greatest potential to accelerate biofuels deployment. The National Renewable Energy Laboratory developed the Biomass Scenario Model, a system dynamics model which represents the primary system effects and dependencies in the biomass-to-biofuels supply chain. The model provides a framework for developing scenarios and conducting biofuels policy analysis. This paper focuses on the downstream portion of the supply chain-represented in the distribution logistics, dispensing station, and fuel utilization, and vehicle modules of the Biomass Scenario Model. This model initially focused on ethanol, but has since been expanded to include other biofuels. Some portions of this system are represented dynamically with major interactions and feedbacks, especially those related to a dispensing station owner's decision whether to offer ethanol fuel and a consumer's choice whether to purchase that fuel. Other portions of the system are modeled with little or no dynamics; the vehicle choices of consumers are represented as discrete scenarios. This paper explores conditions needed to sustain an ethanol fuel market and identifies implications of these findings for program and policy goals. A large, economically sustainable ethanol fuel market (or other biofuel market) requires low end-user fuel price relative to gasoline and sufficient producer payment, which are difficult to achieve simultaneously. Other requirements (different for ethanol vs. other biofuel markets) include the need for infrastructure for distribution and dispensing and

  11. Markov chain Monte Carlo based analysis of post-translationally modified VDAC gating kinetics

    PubMed Central

    Tewari, Shivendra G.; Zhou, Yifan; Otto, Bradley J.; Dash, Ranjan K.; Kwok, Wai-Meng; Beard, Daniel A.

    2015-01-01

    The voltage-dependent anion channel (VDAC) is the main conduit for permeation of solutes (including nucleotides and metabolites) of up to 5 kDa across the mitochondrial outer membrane (MOM). Recent studies suggest that VDAC activity is regulated via post-translational modifications (PTMs). Yet the nature and effect of these modifications is not understood. Herein, single channel currents of wild-type, nitrosated, and phosphorylated VDAC are analyzed using a generalized continuous-time Markov chain Monte Carlo (MCMC) method. This developed method describes three distinct conducting states (open, half-open, and closed) of VDAC activity. Lipid bilayer experiments are also performed to record single VDAC activity under un-phosphorylated and phosphorylated conditions, and are analyzed using the developed stochastic search method. Experimental data show significant alteration in VDAC gating kinetics and conductance as a result of PTMs. The effect of PTMs on VDAC kinetics is captured in the parameters associated with the identified Markov model. Stationary distributions of the Markov model suggest that nitrosation of VDAC not only decreased its conductance but also significantly locked VDAC in a closed state. On the other hand, stationary distributions of the model associated with un-phosphorylated and phosphorylated VDAC suggest a reversal in channel conformation from relatively closed state to an open state. Model analyses of the nitrosated data suggest that faster reaction of nitric oxide with Cys-127 thiol group might be responsible for the biphasic effect of nitric oxide on basal VDAC conductance. PMID:25628567

  12. Sequence analysis of the myosin regulatory light chain gene of the vestimentiferan Riftia pachyptila.

    PubMed

    Ravaux, J; Hassanin, A; Deutsch, J; Gaill, F; Markmann-Mulisch, U

    2001-01-24

    We have isolated and characterized a cDNA (DNA complementary to RNA) clone (Rf69) from the vestimentiferan Riftia pachyptila. The cDNA insert consists of 1169 base pairs. The aminoacid sequence deduced from the longest reading frame is 193 residues in length, and clearly characterized it as a myosin regulatory light chain (RLC). The RLC primary structure is described in relation to its function in muscle contraction. The comparison with other RLCs suggested that Riftia myosin is probably regulated through its RLC either by phosphorylation like the vertebrate smooth muscle myosins, and/or by Ca2+-binding like the mollusk myosins. Riftia RLC possesses a N-terminal extension lacking in all other species besides the earthworm Lumbricus terrestris. Aminoacid sequence comparisons with a number of RLCs from vertebrates and invertebrates revealed a relatively high identity score (64%) between Riftia RLC and the homologous gene from Lumbricus. The relationships between the members of the myosin RLCs were examined by two phylogenetic methods, i.e. distance matrix and maximum parsimony. The resulting trees depict the grouping of the RLCs according to their role in myosin activity regulation. In all trees, Riftia RLC groups with RLCs that depend on Ca2+-binding for myosin activity regulation. PMID:11223252

  13. Probabilistic accident consequence uncertainty analysis: Food chain uncertainty assessment. Volume 1: Main report

    SciTech Connect

    Brown, J.; Goossens, L.H.J.; Kraan, B.C.P.

    1997-06-01

    This volume is the first of a two-volume document that summarizes a joint project conducted by the US Nuclear Regulatory Commission and the European Commission to assess uncertainties in the MACCS and COSYMA probabilistic accident consequence codes. These codes were developed primarily for estimating the risks presented by nuclear reactors based on postulated frequencies and magnitudes of potential accidents. This document reports on an ongoing project to assess uncertainty in the MACCS and COSYMA calculations for the offsite consequences of radionuclide releases by hypothetical nuclear power plant accidents. A panel of sixteen experts was formed to compile credible and traceable uncertainty distributions for food chain variables that affect calculations of offsite consequences. The expert judgment elicitation procedure and its outcomes are described in these volumes. Other panels were formed to consider uncertainty in other aspects of the codes. Their results are described in companion reports. Volume 1 contains background information and a complete description of the joint consequence uncertainty study. Volume 2 contains appendices that include (1) a summary of the MACCS and COSYMA consequence codes, (2) the elicitation questionnaires and case structures for both panels, (3) the rationales and results for the panels on soil and plant transfer and animal transfer, (4) short biographies of the experts, and (5) the aggregated results of their responses.

  14. Capillary electrophoresis for the analysis of short-chain organic acids in coffee.

    PubMed

    Galli, Verónica; Barbas, Coral

    2004-04-01

    A simple and rapid capillary electrophoresis method for low-molecular mass carboxylic acids measurement in coffee has been optimised and validated. Regarding separation conditions, phosphate concentration in the background electrolyte, surfactant type [cetyltrimethylammonium bromide (CTAB), tetradecyltri methylammonium bromide (TTAB) and hexadimethrine bromide (HDB)], percentages of organic modifier and pH were assayed. The best conditions were: 500 mM phosphate buffer at pH 6.25 with CTAB 0.5 mM. The separation was carried out with an uncoated fused-silica capillary (57 cm x 50 microm i.d.) which was operated at -10 kV potential. Detection was performed at 200 nm. In such conditions 17 short-chain organic acids: oxalic, formic, fumaric, mesaconic, succinic, maleic, malic, isocitric, citric, acetic, citraconic, glycolic, propionic, lactic, furanoic, pyroglutamic, quinic acids plus nitrate were separated, identified and measured. Validation parameters of the method allow us to consider it lineal, accurate and precise and, therefore, reliable for its employment in food composition studies or for quality control. Results in coffees with different industrial treatment allow the detection of important differences in the organic acid profile. PMID:15065808

  15. Maple syrup urine disease: analysis of branched chain ketoacid decarboxylation in cultured fibroblasts.

    PubMed

    Wendel, U; Wentrup, H; Rüdiger, H W

    1975-09-01

    Kinetic data are presented for the decarboxylation of branched chain alpha-ketoacids (BCKA) by intact human fibroblasts. Cultured cells of normal individuals and nine patients with different clinical pictures of maple syrup urine disease (MSUD) are studied with both alpha-ketoisocaproic acid (2-oxo-4-methylpentanoic acid (KIC)) and alpha-ketoisovaleric acid (2-oxo-3-methylbutanoic acid (KIVA)) as substrates. One normal cell strain and one patient cell strain is analyzed with alpha-keto-beta-methyl-n-valeric acid (2-oxo-3-methylpentanoic acid (MEVA)) as a substrate. A biphasic degradation kinetic for each BCKA is obtained for normal control subjects. The component with higher substrate affinity is affected in MSUD: for KIC the normally hyperbolic substrate curve is changed to sigmoid shape, for KIVA and MEVA as substrates this component is not detectable at all. Considering qualitative aspects of the BCKA decarboxylation kinetics intact fibroblasts yield the same results as our recent studies with the decarboxylase moieties of partially purified kidney BCKA dehydrogenase of normal individuals and one patient with classic MSUD (27). The decarboxylation velocities for normal and patient fibroblasts with one exception differ widely at low but not at high substrate concentrations of BCKA. To get meaningful data on the residual substrate degradation activities with intact fibroblasts of different phenotypes of MSUD physiologically low substrate concentrations are required in the assay. PMID:1202420

  16. Genetic analysis of pathway regulation for enhancing branched-chain amino acid biosynthesis in plants.

    PubMed

    Chen, Hao; Saksa, Kristen; Zhao, Feiyi; Qiu, Joyce; Xiong, Liming

    2010-08-01

    The branched-chain amino acids (BCAAs) valine, leucine and isoleucine are essential amino acids that play critical roles in animal growth and development. Animals cannot synthesize these amino acids and must obtain them from their diet. Plants are the ultimate source of these essential nutrients, and they synthesize BCAAs through a conserved pathway that is inhibited by its end products. This feedback inhibition has prevented scientists from engineering plants that accumulate high levels of BCAAs by simply over-expressing the respective biosynthetic genes. To identify components critical for this feedback regulation, we performed a genetic screen for Arabidopsis mutants that exhibit enhanced resistance to BCAAs. Multiple dominant allelic mutations in the VALINE-TOLERANT 1 (VAT1) gene were identified that conferred plant resistance to valine inhibition. Map-based cloning revealed that VAT1 encodes a regulatory subunit of acetohydroxy acid synthase (AHAS), the first committed enzyme in the BCAA biosynthesis pathway. The VAT1 gene is highly expressed in young, rapidly growing tissues. When reconstituted with the catalytic subunit in vitro, the vat1 mutant-containing AHAS holoenzyme exhibits increased resistance to valine. Importantly, transgenic plants expressing the mutated vat1 gene exhibit valine tolerance and accumulate higher levels of BCAAs. Our studies not only uncovered regulatory characteristics of plant AHAS, but also identified a method to enhance BCAA accumulation in crop plants that will significantly enhance the nutritional value of food and feed. PMID:20497381

  17. Polymerase chain reaction-based analysis to detect terrestrial animal protein in fish meal.

    PubMed

    Bellagamba, Federica; Valfrè, Franco; Panseri, Sara; Moretti, Vittorio M

    2003-04-01

    The recent European bovine spongiform encephalopathy crisis has focused attention on the importance of adopting stringent control measures to avoid the risk of the diffusion of mad cow disease through meat meal-based animal feedstuffs. Potential adulteration of such feedstuffs with bone particles from terrestrial animals is determined by microscopic examination by law before the release of these feedstuffs for free circulation in the European Community. This study describes a DNA monitoring method to examine fish meal for contamination with mammalian and poultry products. A polymerase chain reaction (PCR) method based on the nucleotide sequence variation in the 12S ribosomal RNA gene of mitochondrial DNA was developed and evaluated. Three species-specific primer pairs were designed for the identification of ruminant, pig, and poultry DNA. The specificity of the primers used in the PCR was tested by comparison with DNA samples for several vertebrate species and confirmed. The PCR specifically detected mammalian and poultry adulteration in fish meals containing 0.125% beef, 0.125% sheep, 0.125% pig, 0.125% chicken, and 0.5% goat. A multiplex PCR assay for ruminant and pig adulteration was optimized and had a detection limit of 0.25%. PMID:12696697

  18. Characteristics analysis of the one-dimensional pulsating dynamics of chain-branching detonations

    NASA Astrophysics Data System (ADS)

    Leung, C.; Radulescu, M. I.; Sharpe, G. J.

    2010-12-01

    The nonlinear pulsating mechanism of one-dimensional detonations was studied numerically using a simple two-step chain-branching model with separate induction and reaction zones. Numerical simulations were performed for a wide range of parameters, which revealed four distinct pulsating regimes classified according to the mechanism controlling the frequency of the pulsations. The dynamics of these regimes were clarified by reconstructing the characteristics, representing the trajectory of pressure waves and particle paths. The high and low frequency regimes of oscillation previously observed in one-step and realistic chemistry simulations were clarified. Under some parameter range, simultaneous low and high frequency pulsations were observed. A novel regime was also found with a pulsation period smaller than the induction time. It involves coupling between the acoustic and the reactivity disturbances propagating, respectively, along the C- and C0 characteristics. These are generated at successive lead shock pulsations and arrive at the reaction zone simultaneously. For all regimes, the dominating mechanism of the pulsating instability was found to be in good qualitative agreement with Toong's phenomenological model based on the wave dynamics in a square wave reaction zone structure.

  19. Trends and advances in food analysis by real-time polymerase chain reaction.

    PubMed

    Salihah, Nur Thaqifah; Hossain, Mohammad Mosharraf; Lubis, Hamadah; Ahmed, Minhaz Uddin

    2016-05-01

    Analyses to ensure food safety and quality are more relevant now because of rapid changes in the quantity, diversity and mobility of food. Food-contamination must be determined to maintain health and up-hold laws, as well as for ethical and cultural concerns. Real-time polymerase chain reaction (RT-PCR), a rapid and inexpensive quantitative method to detect the presence of targeted DNA-segments in samples, helps in determining both accidental and intentional adulterations of foods by biological contaminants. This review presents recent developments in theory, techniques, and applications of RT-PCR in food analyses, RT-PCR addresses the limitations of traditional food analyses in terms of sensitivity, range of analytes, multiplexing ability, cost, time, and point-of-care applications. A range of targets, including species of plants or animals which are used as food ingredients, food-borne bacteria or viruses, genetically modified organisms, and allergens, even in highly processed foods can be identified by RT-PCR, even at very low concentrations. Microfluidic RT-PCR eliminates the separate sample-processing step to create opportunities for point-of-care analyses. We also cover the challenges related to using RT-PCR for food analyses, such as the need to further improve sample handling. PMID:27407185

  20. Branched-chain amino acid biosynthesis in Salmonella typhimurium: a quantitative analysis.

    PubMed

    Epelbaum, S; LaRossa, R A; VanDyk, T K; Elkayam, T; Chipman, D M; Barak, Z

    1998-08-01

    We report here the first quantitative study of the branched-chain amino acid biosynthetic pathway in Salmonella typhimurium LT2. The intracellular levels of the enzymes of the pathway and of the 2-keto acid intermediates were determined under various physiological conditions and used for estimation of several of the fluxes in the cells. The results led to a revision of previous ideas concerning the way in which multiple acetohydroxy acid synthase (AHAS) isozymes contribute to the fitness of enterobacteria. In wild-type LT2, AHAS isozyme I provides most of the flux to valine, leucine, and pantothenate, while isozyme II provides most of the flux to isoleucine. With acetate as a carbon source, a strain expressing AHAS II only is limited in growth because of the low enzyme activity in the presence of elevated levels of the inhibitor glyoxylate. A strain with AHAS I only is limited during growth on glucose by the low tendency of this enzyme to utilize 2-ketobutyrate as a substrate; isoleucine limitation then leads to elevated threonine deaminase activity and an increased 2-ketobutyrate/2-ketoisovalerate ratio, which in turn interferes with the synthesis of coenzyme A and methionine. The regulation of threonine deaminase is also crucial in this regard. It is conceivable that, because of fundamental limitations on the specificity of enzymes, no single AHAS could possibly be adequate for the varied conditions that enterobacteria successfully encounter. PMID:9696751

  1. Lipidomic analysis and electron transport chain activities in C57BL/6J mouse brain mitochondria

    PubMed Central

    Kiebish, Michael A.; Han, Xianlin; Cheng, Hua; Lunceford, Adam; Clarke, Catherine F.; Moon, Hwi; Chuang, Jeffrey H.; Seyfried, Thomas N.

    2011-01-01

    The objective of this study was to characterize the lipidome and electron transport chain activities in purified non-synaptic (NS) and synaptic (Syn) mitochondria from C57BL/6J mouse cerebral cortex. Contamination from subcellular membranes, especially myelin, has hindered past attempts to accurately characterize the lipid composition of brain mitochondria. An improved Ficoll and sucrose discontinuous gradient method was employed that yielded highly enriched mitochondrial populations free of myelin contamination. The activities of Complexes I, II, III, and II/III were lower in Syn than in NS mitochondria, while Complexes I/III and IV activities were similar in both populations. Shotgun lipidomics showed that levels of cardiolipin (Ptd2Gro) were lower, whereas levels of ceramide and phosphatidylserine were higher in Syn than in NS mitochondria. Coenzyme Q9 and Q10 was also lower in Syn than in NS mitochondria. Gangliosides, phosphatidic acid, sulfatides, and cerebrosides were undetectable in brain mitochondria. The distribution of Ptd2Gro molecular species was similar in both populations and formed a unique pattern, consisting of seven major molecular species groups, when arranged according to mass to charge ratios. Remodeling involving choline and ethanolamine phosphoglycerides could explain Ptd2Gro heterogeneity. NS and Syn mitochondrial lipidomic heterogeneity could influence energy metabolism, which may contribute to metabolic compartmentation of the brain. PMID:18373617

  2. Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences.

    PubMed

    Schbath, S; Prum, B; de Turckheim, E

    1995-01-01

    Identifying exceptional motifs is often used for extracting information from long DNA sequences. The two difficulties of the method are the choice of the model that defines the expected frequencies of words and the approximation of the variance of the difference T(W) between the number of occurrences of a word W and its estimation. We consider here different Markov chain models, either with stationary or periodic transition probabilities. We estimate the variance of the difference T(W) by the conditional variance of the number of occurrences of W given the oligonucleotides counts that define the model. Two applications show how to use asymptotically standard normal statistics associated with the counts to describe a given sequence in terms of its outlying words. Sequences of Escherichia coli and of Bacillus subtilis are compared with respect to their exceptional tri- and tetranucleotides. For both bacteria, exceptional 3-words are mainly found in the coding frame. E. coli palindrome counts are analyzed in different models, showing that many overabundant words are one-letter mutations of avoided palindromes. PMID:8521272

  3. Vibrational nonequilibrium in chain branching reactions of hydrogen combustion using quasi-classical trajectory analysis

    NASA Astrophysics Data System (ADS)

    Voelkel, Stephen; Raman, Venkat; Varghese, Philip

    2015-11-01

    In high-speed reactive flows in scramjets, thermal nonequilibrium is introduced in the flow via shock waves. Though rotational and translational energy modes relax back to equilibrium quickly, vibrational relaxation is comparable to the bulk mixing and reaction timescales. The discrepancy between vibration and rotation/translation energy distributions can dramatically alter on the initiation of the fuel oxidation process. For continuum-scale applications, thermal nonequilibrium effects are derived from the rovibrational state-specific reaction and scattering rates associated with the chemical mechanism. In this work, the state-specific reaction rates are calculated for the chain branching reactions in the hydrogen combustion mechanism using a quasi-classical trajectory (QCT) framework. The state-specific rates are incorporated into a multiple temperature continuum-scale model whereby each species is characterized by a Boltzmann distribution parametrized by its own vibrational temperature. The flame ignition rates are implemented in a CFD code to simulate a reactive coflow. Funded by AFOSR FA9550-12-1-0460.

  4. Concordant clonal delineation of methicillin-resistant Staphylococcus aureus by macrorestriction analysis and polymerase chain reaction genome fingerprinting.

    PubMed Central

    Struelens, M J; Bax, R; Deplano, A; Quint, W G; Van Belkum, A

    1993-01-01

    Pulsed-field gel electrophoresis of DNA macrorestriction fragments (macrorestriction analysis) allows epidemiologic typing and delineation of genetic relatedness of methicillin-resistant Staphylococcus aureus (MRSA) by indexing variations in the global chromosome architecture. Polymerase chain reaction (PCR)-mediated genome fingerprinting can also discriminate MRSA strains by detecting locally variable DNA motifs. To assess the correlation between these methods, 48 epidemic MRSA strains collected from 20 hospitals over a 10-year period were tested in a blind comparison by (i) macrorestriction analysis with SstII or SmaI endonuclease and (ii) PCR fingerprinting with four primer sets aimed at the mecA gene, enterobacterial repetitive intergenic consensus sequences, and arbitrary sequences. Isolates were discriminated into 22 macrorestriction patterns and 15 PCR fingerprints. MRSA strains belonging to 12 distinct clones by macrorestriction analysis showed 11 distinct PCR genotypes distinguished by multiple band differences. In contrast, 34 of 37 MRSA strains found to be clonally related by macrorestriction analysis clustered in two highly related PCR genotypes that differed by a single DNA fragment (P < 0.0001). These data demonstrate concordant clonal delineation of epidemic MRSA by macrorestriction analysis and PCR fingerprinting and thereby indicate that the rapid PCR assay may be an efficient epidemiologic typing system. Images PMID:8370721

  5. An input-output procedure for calculating economy-wide economic impacts in supply chains using homeland security consequence analysis tools.

    SciTech Connect

    Smith, Braeton J.; Vugrin, Eric D.; Loose, Verne W.; Warren, Drake E.; Vargas, Vanessa N.

    2010-10-01

    Sandia National Laboratories has developed several models to analyze potential consequences of homeland security incidents. Two of these models (the National Infrastructure Simulation and Analysis Center Agent-Based Laboratory for Economics, N-ABLE{trademark}, and Loki) simulate detailed facility- and product-level consequences of simulated disruptions to supply chains. Disruptions in supply chains are likely to reduce production of some commodities, which may reduce economic activity across many other types of supply chains throughout the national economy. The detailed nature of Sandia's models means that simulations are limited to specific supply chains in which detailed facility-level data has been collected, but policymakers are often concerned with the national-level economic impacts of supply-chain disruptions. A preliminary input-output methodology has been developed to estimate national-level economic impacts based upon the results of supply-chain-level simulations. This methodology overcomes two primary challenges. First, the methodology must be relatively simple to integrate successfully with existing models; it must be easily understood, easily applied to the supply-chain models without user intervention, and run quickly. The second challenge is more fundamental: the methodology must account for both upstream and downstream impacts that result from supply-chain disruptions. Input-output modeling typically estimates only upstream impacts, but shortages resulting from disruptions in many supply chains (for example, energy, communications, and chemicals) are likely to have large downstream impacts. In overcoming these challenges, the input-output methodology makes strong assumptions about technology and substitution. This paper concludes by applying the methodology to chemical supply chains.

  6. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis.

    PubMed

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela; Pongolini, Stefano

    2016-02-01

    The quantitative and qualitative patterns of environmental contamination by Listeria monocytogenes were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for L. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of L. monocytogenes within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of L. monocytogenes within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments. PMID:26590278

  7. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis

    PubMed Central

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela

    2015-01-01

    The quantitative and qualitative patterns of environmental contamination by Listeria monocytogenes were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for L. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of L. monocytogenes within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of L. monocytogenes within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments. PMID:26590278

  8. An efficient method for isolating individual long-chain alkenones for compound-specific hydrogen isotope analysis.

    PubMed

    D'Andrea, William J; Liu, Zhonghui; Da Rosa Alexandre, Marcelo; Wattley, Sarah; Herbert, Timothy D; Huang, Yongsong

    2007-05-01

    Hydrogen isotope ratios (2H/H or D/H) of long-chain unsaturated ketones (alkenones) preserved in lake and marine sediments hold great promise for paleoclimate studies. However, compound-specific hydrogen isotope analysis of individual alkenones has not been possible due to chromatographic coelution of alkenones with the same carbon chain length but different numbers of double bonds. Published studies have only reported the deltaD values of the mixture of coeluting alkenones. We developed an efficient procedure to isolate individual alkenones based on double-bond numbers using silica gel impregnated with silver nitrate. The chromatographic procedure is simple, inexpensive, and highly reproducible, offers 87-100% sample recovery, and allows for the first time hydrogen isotopic measurement on individual alkenones. deltaD values of specific di-, tri- and tetraunsaturated C37 alkenones produced by an Emiliania huxleyi culture, as well as those isolated from Greenland lake sediments, differ consecutively by 43-65 per thousand. These findings suggest that alkenones with different numbers of carbon-carbon double bonds express significantly different deltaD values and that coelution of different alkenones may lead to erroneous source water deltaD reconstructions. Our alkenone isolation approach opens a new avenue for paleoclimate reconstructions using hydrogen isotope ratios of individual alkenones. PMID:17391004

  9. Neutralization Analysis of a Chicken Single-Chain Variable Fragment Derived from an Immune Antibody Library Against Infectious Bronchitis Virus.

    PubMed

    Lin, Yuan; Li, Benqiang; Ye, Jiaxin; Wang, Man; Wang, Jianhua; Zhang, Ying; Zhu, Jianguo

    2015-09-01

    Avian infectious bronchitis virus (IBV), which is prevalent in many countries causing severe economic loss to the poultry industry, causes infectious bronchitis (IB) in birds. Recombinant single-chain variable fragments (scFvs) have been proven to effectively inhibit many viruses, both in vitro and in vivo, and they could be a potential diagnostic and therapeutic reagent to control IB. In this study, six anti-IBV chicken scFvs, ZL.10, ZL.64, ZL.78, ZL.80, ZL.138, and ZL.256, were obtained by screening random clones from an immune antibody library. An analysis of nucleotide sequences revealed that they represented distinctive genetic sequences and greatly varied in complementarity-determining region three of the heavy chain. Neutralization tests showed that ZL.10, which bound the S1 protein in western blots, inhibited the formation of syncytia in Vero cells 48 h post IBV infection and decreased the transcriptional level of nucleoprotein mRNA to 17.2%, while the other five scFvs, including ZL.78 and ZL.256, that bound the N protein did not. In conclusion, the results suggested that specific and neutralizing chicken scFvs against IBV, which can be safe and economical antibody reagents, can be produced in vitro through prokaryotic expression. PMID:26090700

  10. Biosynthesis and genomic analysis of medium-chain hydrocarbon production by the endophytic fungal isolate Nigrograna mackinonnii E5202H

    PubMed Central

    Shaw, Jeffery J; Spakowicz, Daniel J; Dalal, Rahul S; Davis, Jared H; Lehr, Nina A; Dunican, Brian F; Orellana, Esteban A; Narváez-Trujillo, Alexandra; Strobel, Scott A

    2015-01-01

    An endophytic fungus was isolated that produces a series of volatile natural products, including terpenes and odd chain polyenes. Phylogenetic analysis of the isolate using five loci suggests that it is closely related to Nigrograna mackinnonii CBS 674.75. The main component of the polyene series was purified and identified as (3E,5E,7E)-nona-1,3,5,7-tetraene (NTE), a novel natural product. Non-oxygenated hydrocarbons of this chain length are uncommon and desirable as gasoline-surrogate biofuels. The biosynthetic pathway for NTE production was explored using metabolic labeling and GCMS. Two-carbon incorporation 13C acetate suggests that it is derived from a polyketide synthase (PKS) followed by decarboxylation. There are several known mechanisms for such decarboxylation, though none have been discovered in fungi. Towards identifying the PKS responsible for the production of NTE, the genome of N. mackinnonii E5202H (ATCC SD-6839) was sequenced and assembled. Of the 32 PKSs present in the genome, 17 are predicted to contain sufficient domains for the production of NTE. These results exemplify the capacity of endophytic fungi to produce novel natural products that may have many uses, such as biologically derived fuels and commodity chemicals. PMID:25672844

  11. Biosynthesis and genomic analysis of medium-chain hydrocarbon production by the endophytic fungal isolate Nigrograna mackinnonii E5202H.

    PubMed

    Shaw, Jeffery J; Spakowicz, Daniel J; Dalal, Rahul S; Davis, Jared H; Lehr, Nina A; Dunican, Brian F; Orellana, Esteban A; Narváez-Trujillo, Alexandra; Strobel, Scott A

    2015-04-01

    An endophytic fungus was isolated that produces a series of volatile natural products, including terpenes and odd chain polyenes. Phylogenetic analysis of the isolate using five loci suggests that it is closely related to Nigrograna mackinnonii CBS 674.75. The main component of the polyene series was purified and identified as (3E,5E,7E)-nona-1,3,5,7-tetraene (NTE), a novel natural product. Non-oxygenated hydrocarbons of this chain length are uncommon and desirable as gasoline-surrogate biofuels. The biosynthetic pathway for NTE production was explored using metabolic labeling and gas chromatography time of flight mass spectometer (GCMS). Two-carbon incorporation (13)C acetate suggests that it is derived from a polyketide synthase (PKS) followed by decarboxylation. There are several known mechanisms for such decarboxylation, though none have been discovered in fungi. Towards identifying the PKS responsible for the production of NTE, the genome of N. mackinnonii E5202H (ATCC SD-6839) was sequenced and assembled. Of the 32 PKSs present in the genome, 17 are predicted to contain sufficient domains for the production of NTE. These results exemplify the capacity of endophytic fungi to produce novel natural products that may have many uses, such as biologically derived fuels and commodity chemicals. PMID:25672844

  12. The Belgian PCB/dioxin incident: analysis of the food chain contamination and health risk evaluation.

    PubMed

    Bernard, Alfred; Broeckaert, Fabrice; De Poorter, Geert; De Cock, Ann; Hermans, Cédric; Saegerman, Claude; Houins, Gilbert

    2002-01-01

    The Belgian PCB incident occurred at the end of January 1999 when a mixture of polychlorinated biphenyls (PCBs) contaminated with dioxins was accidentally added to a stock of recycled fat used in the production of animal feeds. Although signs of poultry poisoning were noticed by February, 1999, the source and the extent of the contamination were discovered only in May 1999, when it appeared that more than 2500 farms could have been supplied with contaminated feeds. This resulted in a major food crisis, which rapidly extended to the whole country and could be resolved only by the implementation of a large PCB/dioxin food monitoring program. Screening for PCB contamination was based on the determination of the seven PCB markers. When PCB concentrations exceeded the tolerance levels of 0.1 (milk), 0.2 (poultry, bovine, and pig meat), or 1 (animal feed) microg/g fat, dioxins (17 PCDD/Fs congeners) were also determined. At the end of December 1999, the database contained the results of more than 55,000 PCB and 500 dioxin analyses. The study of PCB levels and profiles in contaminated feeds delivered to poultry or pig farms confirmed that the Belgian PCB incident was due to a single source of PCB oil introduced into the food chain at the end of January 1999. This PCB oil had a congeners pattern closely matched to a mixture of Aroclor 1260/1254 in the proportion 75/25. The total amount of PCBs added to recycled fats was estimated at 50 kg (sum of the seven markers) or approximately 150 kg total PCBs, which corresponds to about 100 liters of PCB oil. This PCB mixture contained about 1g TEQ dioxins (more than 90- contributed by PCDFs) and about 2g TEQ dioxin-like PCBs. The proportions of PCB 52 and 101 congeners were fairly constant in animal feeds, excluding the possibility of secondary contamination due to fat recycling from contaminated animals. The highest concentrations of PCBs and dioxins were found in poultry and especially in the reproduction animals (hens and chicks

  13. Analysis of Heavy-Chain Antibody Responses and Resistance to Parelaphostrongylus tenuis in Experimentally Infected Alpacas

    PubMed Central

    Purdy, S. R.; Gagliardo, L. F.; Lefman, S.; Hamel, P. J. S.; Ku, S.; Mainini, T.; Hoyt, G.; Justus, K.; Daley-Bauer, L. P.; Duffy, M. S.

    2012-01-01

    The parasitic nematode Parelaphostrongylus tenuis is an important cause of neurologic disease of camelids in central and eastern North America. The aim of this study was to determine whether alpacas develop resistance to disease caused by P. tenuis in response to a previous infection or a combination of controlled infection and immunization. Alpacas were immunized with a homogenate of third-stage larvae (L3) and simultaneously implanted subcutaneously with diffusion chambers containing 20 live L3. Sham-treated animals received adjuvant alone and empty chambers. The protocol was not effective in inducing resistance to oral challenge with 10 L3, and disease developed between 60 and 71 days following infection. Immediately following the onset of neurologic disease, affected animals were treated with a regimen of anthelmintic and anti-inflammatory drugs, and all recovered. One year later, a subset of alpacas from this experiment was challenged with 20 L3 and the results showed that prior infection induced resistance to disease. Primary and secondary infections induced production of conventional and heavy-chain IgGs that reacted with soluble antigens in L3 homogenates but did not consistently recognize a recombinant form of a parasite-derived aspartyl protease inhibitor. Thus, the latter antigen may not be a good candidate for serology-based diagnostic tests. Antibody responses to parasite antigens occurred in the absence of overt disease, demonstrating that P. tenuis infection can be subclinical in a host that has been considered to be highly susceptible to disease. The potential for immunoprophylaxis to be effective in preventing disease caused by P. tenuis was supported by evidence of resistance to reinfection. PMID:22593238

  14. Recovering the inflationary potential: An analysis using flow methods and Markov chain Monte Carlo

    NASA Astrophysics Data System (ADS)

    Powell, Brian A.

    Since its inception in 1980 by Guth [1], inflation has emerged as the dominant paradigm for describing the physics of the early universe. While inflation has matured theoretically over two decades, it has only recently begun to be rigorously tested observationally. Measurements of the cosmic microwave background (CMB) and large-scale structure surveys (LSS) have begun to unravel the mysteries of the inflationary epoch with exquisite and unprecedented accuracy. This thesis is a contribution to the effort of reconstructing the physics of inflation. This information is largely encoded in the potential energy function of the inflaton, the field that drives the inflationary expansion. With little theoretical guidance as to the probable form of this potential, reconstruction is a predominantly data-driven endeavor. This thesis presents an investigation of the constrainability of the inflaton potential given current CMB and LSS data. We develop a methodology based on the inflationary flow formalism that provides an assessment of our current ability to resolve the form of the inflaton potential in the face of experimental and statistical error. We find that there is uncertainty regarding the initial dynamics of the inflaton field, related to the poor constraints that can be drawn on the primordial power spectrum on large scales. We also investigate the future prospects of potential reconstruction, as might be expected when data from ESA's Planck Surveyor becomes available. We develop an approach that utilizes Markov chain Monte Carlo to analyze the statistical properties of the inflaton potential. Besides providing constraints on the parameters of the potential, this method makes it possible to perform model selection on the inflationary model space. While future data will likely determine the general features of the inflaton, there will likely be many different models that remain good fits to the data. Bayesian model selection will then be needed to draw comparisons

  15. Phase analysis in single-chain variable fragment production by recombinant Pichia pastoris based on proteomics combined with multivariate statistics.

    PubMed

    Fujiki, Yuya; Kumada, Yoichi; Kishimoto, Michimasa

    2015-08-01

    The proteomics technique, which consists of two-dimensional gel electrophoresis (2-DE), peptide mass fingerprinting (PMF), gel image analysis, and multivariate statistics, was applied to the phase analysis of a fed-batch culture for the production of a single-chain variable fragment (scFv) of an anti-C-reactive protein (CRP) antibody by Pichia pastoris. The time courses of the fed-batch culture were separated into three distinct phases: the growth phase of the batch process, the growth phase of the fed-batch process, and the production phase of the fed-batch process. Multivariate statistical analysis using 2-DE gel image analysis data clearly showed the change in the culture phase and provided information concerning the protein expression, which suggested a metabolic change related to cell growth and production during the fed-batch culture. Furthermore, specific proteins, such as alcohol oxidase, which is strongly related to scFv expression, and proteinase A, which could biodegrade scFv in the latter phases of production, were identified via the PMF method. The proteomics technique provided valuable information about the effect of the methanol concentration on scFv production. PMID:25636980

  16. Detection of Mycobacterium tuberculosis with nested polymerase chain reaction analysis in enucleated eye ball in Eales' disease.

    PubMed

    Verma, Aditya; Biswas, Jyotirmay; Dhanurekha, L; Gayathri, R; Lily Therese, K

    2016-06-01

    Nested polymerase chain reaction (nPCR) was performed on enucleated eyeball for detection of Mycobacterium tuberculosis (M. tb) genome in a patient with Eales' disease. PCR analysis in all previous studies has been done mainly using aqueous, vitreous and epiretinal membranes from these patients. Paraffin wax embedded tissue section of the enucleated eyeball was analyzed by histopathology and nPCR targeting MPB64 gene and IS6110 region of M. tb genome. Lymphocytic infiltration was seen in the vitreous, iris and the retinal tissue. Ziehl Neelsen stain was negative for acid fast bacilli. Caseation necrosis was not seen in any section. Agarose gel electrophoretogram showed positive results with 200 bp specific amplified product targeting MPB64 gene, whereas nPCR targeting IS6110 region was negative. Since biopsy proven M. tb is extremely difficult in ocular tissues due to extensive necrosis, the nPCR technique aided in the diagnosis. PMID:26499903

  17. Identification of marker genes for lipid-lowering effect of a short-chain fructooligosaccharide by DNA microarray analysis.

    PubMed

    Fukasawa, Tomoyuki; Murashima, Koichiro; Nemoto, Tomoko; Matsumoto, Ichiro; Koga, Jinichiro; Kubota, Hidetoshi; Kanegae, Minoru

    2009-01-01

    Administration of short-chain fructooligosaccharide (scFOS) is known to lower serum triglyceride levels in rats fed a high-fat diet, but the molecular mechanisms remain unclear. This study aimed to identify marker genes for lipid-lowering effect of scFOS administration. The changes in hepatic gene expressions in rats fed scFOS were investigated using DNA microarray and quantitative RT-PCR analysis. The DNA microarray showed that phytanoyl-CoA 2-hydroxylase 2 (Phyh2), lipoprotein lipase (Lpl) and tyrosine aminotransferase (Tat) were significantly affected by scFOS administration (p < .05). Since Lpl is involved in lipid metabolism, the up-regulation of Lpl in the liver can be a potential marker of the lipid-lowering effect of scFOS. PMID:22435477

  18. Epistasis Test in Meta-Analysis: A Multi-Parameter Markov Chain Monte Carlo Model for Consistency of Evidence.

    PubMed

    Lin, Chin; Chu, Chi-Ming; Su, Sui-Lung

    2016-01-01

    Conventional genome-wide association studies (GWAS) have been proven to be a successful strategy for identifying genetic variants associated with complex human traits. However, there is still a large heritability gap between GWAS and transitional family studies. The "missing heritability" has been suggested to be due to lack of studies focused on epistasis, also called gene-gene interactions, because individual trials have often had insufficient sample size. Meta-analysis is a common method for increasing statistical power. However, sufficient detailed information is difficult to obtain. A previous study employed a meta-regression-based method to detect epistasis, but it faced the challenge of inconsistent estimates. Here, we describe a Markov chain Monte Carlo-based method, called "Epistasis Test in Meta-Analysis" (ETMA), which uses genotype summary data to obtain consistent estimates of epistasis effects in meta-analysis. We defined a series of conditions to generate simulation data and tested the power and type I error rates in ETMA, individual data analysis and conventional meta-regression-based method. ETMA not only successfully facilitated consistency of evidence but also yielded acceptable type I error and higher power than conventional meta-regression. We applied ETMA to three real meta-analysis data sets. We found significant gene-gene interactions in the renin-angiotensin system and the polycyclic aromatic hydrocarbon metabolism pathway, with strong supporting evidence. In addition, glutathione S-transferase (GST) mu 1 and theta 1 were confirmed to exert independent effects on cancer. We concluded that the application of ETMA to real meta-analysis data was successful. Finally, we developed an R package, etma, for the detection of epistasis in meta-analysis [etma is available via the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/etma/index.html]. PMID:27045371

  19. Analysis of Chain Branch of Polyolefins by a New Proton NMR Approach.

    PubMed

    Jung, Minhwan; Lee, Yura; Kwak, Sooyoung; Park, Heeyong; Kim, Byoungsoo; Kim, Sulhee; Lee, Kwang Hwan; Cho, Hye Sung; Hwang, Kwang Yeon

    2016-02-01

    The crystallinity of polyethylene, which significantly affects the properties of the polymer, is quite sensitive to the concentration of its branches. Thus, it is necessary to estimate branch concentration with reasonable accuracy. Currently, (13)C NMR and gel permeation chromatography-Fourier transform infrared spectroscopy are widely-used analysis methods for the analysis of branch concentration. Despite several advantages, these methods sometimes have limitations. For instance, the preparation of samples for (13)C- NMR is tedious because high-concentration samples are required and the time for analysis is greater than 12 h. To more efficiently estimate the branch concentration of polyethylene, we developed a new high-field (1)H NMR method with an improved peak resolution by employing (1) homonuclear decoupling and (2) 2D heteronuclear correlation. The new method was observed to significantly reduce the experimental time to ∼ 30 min; furthermore, sample preparation was relatively simple because the method did not require high-concentration samples. PMID:26713895

  20. Assessment of parameter uncertainty in hydrological model using a Markov-Chain-Monte-Carlo-based multilevel-factorial-analysis method

    NASA Astrophysics Data System (ADS)

    Zhang, Junlong; Li, Yongping; Huang, Guohe; Chen, Xi; Bao, Anming

    2016-07-01

    Without a realistic assessment of parameter uncertainty, decision makers may encounter difficulties in accurately describing hydrologic processes and assessing relationships between model parameters and watershed characteristics. In this study, a Markov-Chain-Monte-Carlo-based multilevel-factorial-analysis (MCMC-MFA) method is developed, which can not only generate samples of parameters from a well constructed Markov chain and assess parameter uncertainties with straightforward Bayesian inference, but also investigate the individual and interactive effects of multiple parameters on model output through measuring the specific variations of hydrological responses. A case study is conducted for addressing parameter uncertainties in the Kaidu watershed of northwest China. Effects of multiple parameters and their interactions are quantitatively investigated using the MCMC-MFA with a three-level factorial experiment (totally 81 runs). A variance-based sensitivity analysis method is used to validate the results of parameters' effects. Results disclose that (i) soil conservation service runoff curve number for moisture condition II (CN2) and fraction of snow volume corresponding to 50% snow cover (SNO50COV) are the most significant factors to hydrological responses, implying that infiltration-excess overland flow and snow water equivalent represent important water input to the hydrological system of the Kaidu watershed; (ii) saturate hydraulic conductivity (SOL_K) and soil evaporation compensation factor (ESCO) have obvious effects on hydrological responses; this implies that the processes of percolation and evaporation would impact hydrological process in this watershed; (iii) the interactions of ESCO and SNO50COV as well as CN2 and SNO50COV have an obvious effect, implying that snow cover can impact the generation of runoff on land surface and the extraction of soil evaporative demand in lower soil layers. These findings can help enhance the hydrological model

  1. Epistasis Test in Meta-Analysis: A Multi-Parameter Markov Chain Monte Carlo Model for Consistency of Evidence

    PubMed Central

    Lin, Chin; Chu, Chi-Ming; Su, Sui-Lung

    2016-01-01

    Conventional genome-wide association studies (GWAS) have been proven to be a successful strategy for identifying genetic variants associated with complex human traits. However, there is still a large heritability gap between GWAS and transitional family studies. The “missing heritability” has been suggested to be due to lack of studies focused on epistasis, also called gene–gene interactions, because individual trials have often had insufficient sample size. Meta-analysis is a common method for increasing statistical power. However, sufficient detailed information is difficult to obtain. A previous study employed a meta-regression-based method to detect epistasis, but it faced the challenge of inconsistent estimates. Here, we describe a Markov chain Monte Carlo-based method, called “Epistasis Test in Meta-Analysis” (ETMA), which uses genotype summary data to obtain consistent estimates of epistasis effects in meta-analysis. We defined a series of conditions to generate simulation data and tested the power and type I error rates in ETMA, individual data analysis and conventional meta-regression-based method. ETMA not only successfully facilitated consistency of evidence but also yielded acceptable type I error and higher power than conventional meta-regression. We applied ETMA to three real meta-analysis data sets. We found significant gene–gene interactions in the renin–angiotensin system and the polycyclic aromatic hydrocarbon metabolism pathway, with strong supporting evidence. In addition, glutathione S-transferase (GST) mu 1 and theta 1 were confirmed to exert independent effects on cancer. We concluded that the application of ETMA to real meta-analysis data was successful. Finally, we developed an R package, etma, for the detection of epistasis in meta-analysis [etma is available via the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/etma/index.html]. PMID:27045371

  2. Capillary-based fully integrated and automated system for nanoliter polymerase chain reaction analysis directly from cheek cells.

    PubMed

    He, Y; Zhang, Y H; Yeung, E S

    2001-07-27

    A miniaturized, integrated and automated system based on capillary fluidics has been developed for nanoliter DNA analysis directly from cheek cells. All steps for DNA analysis, including injecting aqueous reagents and DNA samples, mixing the solutions together, thermal cell lysis, polymerase chain reaction (PCR), transfer and injection of PCR product, separation, sizing and detection of those products are performed in a capillary-based integrated system. A small amount of cheek cells collected by a plastic toothpick is directly dissolved in the PCR cocktail in a plastic vial or mixed on-line with a small volume of PCR cocktail (125 nl) in the capillary. After thermal cell lysis and PCR in a microthermal cycler, the DNA fragments are mixed with DNA size standards and transferred to a micro-cross for injection and separation by capillary gel electrophoresis. Programmable syringe pumps, switching valves, multiposition and freeze-thaw valves are used for microfluidic control in the entire system. This work establishes the feasibility of performing all the steps of DNA analysis from real samples in a capillary-based nanoliter integrated system. PMID:11521874

  3. Meta-Analysis of Long-Chain Omega-3 Polyunsaturated Fatty Acids (LCω-3PUFA) and Prostate Cancer

    PubMed Central

    Alexander, Dominik D.; Bassett, Julie K.; Weed, Douglas L.; Barrett, Erin Cernkovich; Watson, Heather; Harris, William

    2015-01-01

    We conducted a systematic review and meta-analysis to estimate the potential association between LCω-3PUFAs and prostate cancer (PC). A comprehensive literature search was performed through 2013 to identify prospective studies that examined dietary intakes of long-chain omega-3 polyunsaturated fatty acids (LCω-3PUFA) or blood biomarkers of LCω-3PUFA status and risk of PC. Random-effects meta-analyses were conducted to generate summary relative risk estimates (SRREs) for LCω-3PUFAs and total PC, and by stage and grade. Subgroup analyses were also conducted for specific fatty acids and other study characteristics. Twelve self-reported dietary intake and 9 biomarker studies from independent study populations were included in the analysis, with 446,243 and 14,897 total participants, respectively. No association between LCω-3PUFAs and total PC was observed (SRRE = 1.00, 95% CI: 0.93–1.09) for the dietary intake studies (high vs. low LCω-3PUFAs category comparison) or for the biomarker studies (SRRE of 1.07, 95% CI: 0.94–1.20). In general, most summary associations for the dietary intake studies were in the inverse direction, whereas the majority of summary associations for the biomarker studies were in the positive direction, but all were weak in magnitude. The results from this meta-analysis do not support an association between LCω-3PUFAs and PC. PMID:25826711

  4. Analysis of Myosin Heavy Chain Isoforms from Longissimus Thoracis Muscle of Hanwoo Steer by Electrophoresis and LC-MS/MS

    PubMed Central

    2014-01-01

    The purpose of this study was to analyze myosin heavy chain (MHC) isoforms in bovine longissimus thoracis (LT) muscle by liquid chromatography (LC) and mass spectrometry (MS). LT muscles taken from Hanwoo (Korean native cattle) steer (n=3) used to separate myosin bands by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The peptide queries were obtained from the myosin bands by LC-MS/MS analysis following in-gel digestion with trypsin. A total of 33 and 43 queries were identified as common and unique peptides, respectively, of MHC isoforms (individual ions scores >43 indicate identity or extensive homology, p<0.05). MHC-1 (IIx), -2 (IIa), -4 (IIb), and -7 (slow/I) were identified based on the Mowse score (5118, 3951, 2526, and 2541 for MHC-1, -2, -4, and -7, respectively). However, more analysis is needed to confirm the expression of MHC-4 in bovine LT muscle because any query identified as a unique peptide of MHC-4 was not found. The queries that were identified as unique peptides could be used as peptide markers to confirm MHC-1 (14 queries), -2 (8 queries), and -7 (21 queries) in bovine LT muscle; no query identified as a unique peptide of MHC-4 was found. LC-MS/MS analysis is a useful approach to study MHC isoforms at the protein level. PMID:26761500

  5. Statistical Models for the Analysis and Design of Digital Polymerase Chain Reaction (dPCR) Experiments.

    PubMed

    Dorazio, Robert M; Hunter, Margaret E

    2015-11-01

    Statistical methods for the analysis and design of experiments using digital PCR (dPCR) have received only limited attention and have been misused in many instances. To address this issue and to provide a more general approach to the analysis of dPCR data, we describe a class of statistical models for the analysis and design of experiments that require quantification of nucleic acids. These models are mathematically equivalent to generalized linear models of binomial responses that include a complementary, log-log link function and an offset that is dependent on the dPCR partition volume. These models are both versatile and easy to fit using conventional statistical software. Covariates can be used to specify different sources of variation in nucleic acid concentration, and a model's parameters can be used to quantify the effects of these covariates. For purposes of illustration, we analyzed dPCR data from different types of experiments, including serial dilution, evaluation of copy number variation, and quantification of gene expression. We also showed how these models can be used to help design dPCR experiments, as in selection of sample sizes needed to achieve desired levels of precision in estimates of nucleic acid concentration or to detect differences in concentration among treatments with prescribed levels of statistical power. PMID:26436653

  6. Statistical models for the analysis and design of digital polymerase chain (dPCR) experiments

    USGS Publications Warehouse

    Dorazio, Robert; Hunter, Margaret

    2015-01-01

    Statistical methods for the analysis and design of experiments using digital PCR (dPCR) have received only limited attention and have been misused in many instances. To address this issue and to provide a more general approach to the analysis of dPCR data, we describe a class of statistical models for the analysis and design of experiments that require quantification of nucleic acids. These models are mathematically equivalent to generalized linear models of binomial responses that include a complementary, log–log link function and an offset that is dependent on the dPCR partition volume. These models are both versatile and easy to fit using conventional statistical software. Covariates can be used to specify different sources of variation in nucleic acid concentration, and a model’s parameters can be used to quantify the effects of these covariates. For purposes of illustration, we analyzed dPCR data from different types of experiments, including serial dilution, evaluation of copy number variation, and quantification of gene expression. We also showed how these models can be used to help design dPCR experiments, as in selection of sample sizes needed to achieve desired levels of precision in estimates of nucleic acid concentration or to detect differences in concentration among treatments with prescribed levels of statistical power.

  7. Role of the Escherichia coli O157:H7 O side chain in adherence and analysis of an rfb locus.

    PubMed Central

    Bilge, S S; Vary, J C; Dowell, S F; Tarr, P I

    1996-01-01

    Shiga-toxigenic Escherichia coli strains belonging to serotype O157 are important human pathogens, but the genetic basis of expression of the O157 antigen and the role played by the lipopolysaccharide O side chain in the adherence of this organism to epithelial cells are not understood. We performed TnphoA mutagenesis on E. coli O157:H7 strain 86-24 to identify a mutant (strain F12) deficient in O-antigen expression. Nucleotide sequence analysis demonstrated that the transposon inserted within an open reading frame with significant homology to rfbE of Vibrio cholerae O1 (U. H. Stroeher, L. E. Karageorgos, R. Morona, and P. A. Manning, Proc. Natl. Acad. Sci. USA 89:2566-2570, 1992), which is postulated to encode perosamine synthetase. This open reading frame was designated rfbE(EcO157:H7). The guanine-plus-cytosine fraction (0.35) suggests that rfbE(EcO157:H7) may have originated in a species other than E. coli. rfbE(EcO157:H7) is conserved in nontoxigenic E. coli O157 strains expressing a variety of other flagellar antigens but is not found in E. coli O55:H7 strains, which are more closely related to E. coli O157:H7. Strain F12 was significantly more adherent to HeLa cells in a quantitative adherence assay than was its E. coli O157:H7 parent, but they did not differ in other phenotypes. Restoration of the expression of the O side chain by complementation of the TnphoA mutation in strain F12 by a plasmid expressing intact rfbE(EcO157:H7) reduced the adherence of the hyperadherent strain F12. We conclude that rfbE(EcO157:H7) is necessary for the expression of the O157 antigen, that acquisition of E. coli rfb genes occurred independently in E. coli O157:H7 and unrelated O157 strains, and that the O side chain of E. coli O157:H7 lipopolysaccharide interferes with the adherence of E. coli O157:H7 to epithelial cells. PMID:8890241

  8. Immunoglobulin heavy/light chain analysis enhances the detection of residual disease and monitoring of multiple myeloma patients

    PubMed Central

    Batinić, Josip; Perić, Zinaida; Šegulja, Dragana; Last, James; Prijić, Sanja; Dubravčić, Klara; Volarić, Lidija; Sertić, Dubravka; Radman, Ivo; Bašić-Kinda, Sandra; Matišić, Danica; Batinić, Drago; Labar, Boris; Nemet, Damir

    2015-01-01

    Aim To evaluate the clinical utility of incorporating a novel heavy/light chain immunoassay (HLC) into the existing methods for the assessment of multiple myeloma (MM) patients. Methods Convenience sera samples from 90 previously treated IgG and IgA MM patients in different disease stages were analyzed. The study was conducted in Clinical Hospital Center Zagreb between 2011 and 2013. The collected sera were analyzed by standard laboratory techniques (serum protein electrophoresis, quantification of total immunoglobulins, serum immunofixation, serum free light chain [FLC] assay) and HLC assay. Results HLC ratios outside the normal range were found in 58 of 90 patients, including 28 out of 61 patients with total immunoglobulin measurements within the normal range and 5 out of 23 patients in complete response. Both elevated HLC isotype level and abnormal HLC ratio correlated with the parameters of tumor burden, including percentage of plasma cells in the bone marrow (P < 0.001 and P = 0.002, respectively) and an abnormal serum FLC ratio (for both P < 0.001). In addition, abnormal HLC isotype level correlated with serum beta-2-microglobulin level (P = 0.038). In terms of prognosis, abnormal HLC isotype level and abnormal HLC ratio were significantly associated with shorter overall survival (P < 0.001 and P = 0.002, respectively). Interestingly, suppression of the uninvolved (polyclonal) isotype pair, but not other non-myeloma immunoglobulin isotypes, was also associated with a shorter overall survival (P = 0.021). In a multivariate analysis, an abnormal HLC ratio and β2-microglobulin level >3.5mg/L were independent risk factors for survival. Conclusion The new HLC assay has greater sensitivity in detecting monoclonal protein, correlates with tumor burden markers, and affects patients' outcome. PMID:26088851

  9. Ethanol Distribution, Dispensing, and Use: Analysis of a Portion of the Biomass-to-Biofuels Supply Chain Using System Dynamics

    PubMed Central

    Vimmerstedt, Laura J.; Bush, Brian; Peterson, Steve

    2012-01-01

    The Energy Independence and Security Act of 2007 targets use of 36 billion gallons of biofuels per year by 2022. Achieving this may require substantial changes to current transportation fuel systems for distribution, dispensing, and use in vehicles. The U.S. Department of Energy and the National Renewable Energy Laboratory designed a system dynamics approach to help focus government action by determining what supply chain changes would have the greatest potential to accelerate biofuels deployment. The National Renewable Energy Laboratory developed the Biomass Scenario Model, a system dynamics model which represents the primary system effects and dependencies in the biomass-to-biofuels supply chain. The model provides a framework for developing scenarios and conducting biofuels policy analysis. This paper focuses on the downstream portion of the supply chain–represented in the distribution logistics, dispensing station, and fuel utilization, and vehicle modules of the Biomass Scenario Model. This model initially focused on ethanol, but has since been expanded to include other biofuels. Some portions of this system are represented dynamically with major interactions and feedbacks, especially those related to a dispensing station owner’s decision whether to offer ethanol fuel and a consumer’s choice whether to purchase that fuel. Other portions of the system are modeled with little or no dynamics; the vehicle choices of consumers are represented as discrete scenarios. This paper explores conditions needed to sustain an ethanol fuel market and identifies implications of these findings for program and policy goals. A large, economically sustainable ethanol fuel market (or other biofuel market) requires low end-user fuel price relative to gasoline and sufficient producer payment, which are difficult to achieve simultaneously. Other requirements (different for ethanol vs. other biofuel markets) include the need for infrastructure for distribution and dispensing and

  10. The influence of surface and tectonic processes on landscape evolution of the Iberian Chain (Spain): Quantitative geomorphological analysis and geochronology

    NASA Astrophysics Data System (ADS)

    Scotti, V. N.; Molin, P.; Faccenna, C.; Soligo, M.; Casas-Sainz, A.

    2014-02-01

    In tectonically active areas, the landscape response to tectonic forcing is described and possibly quantified by regional topographic and hydrographic features as well as by spatial variation in rates of surface processes. We investigated the recent landscape evolution of the Iberian Chain (NE Spain), an intraplate thrust-belt formed in Cenozoic times and characterized by a dome-shaped topography. In its central sector the landscape is dominated by low relief surfaces, Late Neogene (?) in age, presently standing at an average altitude of 1300 m. A recent regional uplift controlled the organization of the present fluvial network and dissection of the landscape. In this framework we investigated the geomorphic responses to tectonic forcing by the calculation of morphometric parameters, focusing on topography (map of local relief, swath profiles) and hydrography (basin hypsometric curve and integral, basin asymmetry factor, river longitudinal profiles and relative indices), and using SRTM DEM. The results of morphometric analysis have been coupled with radiometric uranium-series dating of calcareous tufas lying on fluvial strath terraces. The obtained ages allow the estimation of incision rate along the High Tajo and Martín rivers. Our results indicate that uplift and rock-type erodibility are the main factors influencing landscape evolution of the study area. The incision rates are very similar throughout the central sector of the range, indicating that, despite subtle local variation, the rivers are responding to a main tectonic input: the regional uplift. In conclusion, the Iberian Chain landscape is in a transient state in response to a recent dome-like uplift. Indeed, the fluvial processes that weakly incised this landscape at a rate of ~ 0.6 mm/yr are approaching a radial pattern. On the basis of geological and geomorphic constraints, we hypothesize that the uplift started around or after 3 Ma.

  11. Radionuclide migration through fractured rock for arbitrary-length decay chain: Analytical solution and global sensitivity analysis

    NASA Astrophysics Data System (ADS)

    Shahkarami, Pirouz; Liu, Longcheng; Moreno, Luis; Neretnieks, Ivars

    2015-01-01

    This study presents an analytical approach to simulate nuclide migration through a channel in a fracture accounting for an arbitrary-length decay chain. The nuclides are retarded as they diffuse in the porous rock matrix and stagnant zones in the fracture. The Laplace transform and similarity transform techniques are applied to solve the model. The analytical solution to the nuclide concentrations at the fracture outlet is governed by nine parameters representing different mechanisms acting on nuclide transport through a fracture, including diffusion into the rock matrices, diffusion into the stagnant water zone, chain decay and hydrodynamic dispersion. Furthermore, to assess how sensitive the results are to parameter uncertainties, the Sobol method is applied in variance-based global sensitivity analyses of the model output. The Sobol indices show how uncertainty in the model output is apportioned to the uncertainty in the model input. This method takes into account both direct effects and interaction effects between input parameters. The simulation results suggest that in the case of pulse injections, ignoring the effect of a stagnant water zone can lead to significant errors in the time of first arrival and the peak value of the nuclides. Likewise, neglecting the parent and modeling its daughter as a single stable species can result in a significant overestimation of the peak value of the daughter nuclide. It is also found that as the dispersion increases, the early arrival time and the peak time of the daughter decrease while the peak value increases. More importantly, the global sensitivity analysis reveals that for time periods greater than a few thousand years, the uncertainty of the model output is more sensitive to the values of the individual parameters than to the interaction between them. Moreover, if one tries to evaluate the true values of the input parameters at the same cost and effort, the determination of priorities should follow a certain

  12. Chain Confinement in Electrospun Nanocomposites: using Thermal Analysis to Investigate Polymer-Filler Interactions

    SciTech Connect

    Q Ma; B Mao; P Cebe

    2011-12-31

    We investigate the interaction of the polymer matrix and filler in electrospun nanofibers using advanced thermal analysis methods. In particular, we study the ability of silicon dioxide nanoparticles to affect the phase structure of poly(ethylene terephthalate), PET. SiO{sub 2} nanoparticles (either unmodified or modified with silane) ranging from 0 to 2.0 wt% in PET were electrospun from hexafluoro-2-propanol solutions. The morphologies of both the electrospun (ES) nanofibers and the SiO{sub 2} powders were observed by scanning and transmission electron microscopy, while the amorphous or crystalline nature of the fibers was determined by real-time wide-angle X-ray scattering. The fractions of the crystal, mobile amorphous, and rigid amorphous phases of the non-woven, nanofibrous composite mats were quantified by using heat capacity measurements. The amount of the immobilized polymer layer, the rigid amorphous fraction, was obtained from the specific reversing heat capacity for both as-spun amorphous fibers and isothermally crystallized fibers. Existence of the rigid amorphous phase in the absence of crystallinity was verified in nanocomposite fibers, and two origins for confinement of the rigid amorphous fraction are proposed. Thermal analysis of electrospun fibers, including quasi-isothermal methods, provides new insights to quantitatively characterize the polymer matrix phase structure and thermal transitions, such as devitrification of the rigid amorphous fraction.

  13. Value-Chain Dynamics of the West Point Foundry, 1817-1911: A Historical Case Analysis in Marketing

    ERIC Educational Resources Information Center

    Petkus, Ed, Jr.

    2013-01-01

    This case provides the opportunity for students to explore marketing and value/supply-chain dynamics in a unique historical context. The West Point Foundry (WPF), located in Cold Spring, New York, was one of the most important manufacturing ventures in the United States from 1817 to 1911. The case outlines the supply-chain details of the WPF as…

  14. Assessment of hybridization among wild and cultivated Vigna unguiculata subspecies revealed by arbitrarily primed polymerase chain reaction analysis

    PubMed Central

    Vijaykumar, Archana; Saini, Ajay; Jawali, Narendra

    2012-01-01

    Background and aims Intra-species hybridization and incompletely homogenized ribosomal RNA repeat units have earlier been reported in 21 accessions of Vigna unguiculata from six subspecies using internal transcribed spacer (ITS) and 5S intergenic spacer (IGS) analyses. However, the relationships among these accessions were not clear from these analyses. We therefore assessed intra-species hybridization in the same set of accessions. Methodology Arbitrarily primed polymerase chain reaction (AP-PCR) analysis was carried out using 12 primers. The PCR products were resolved on agarose gels and the DNA fragments were scored manually. Genetic relationships were inferred by TREECON software using unweighted paired group method with arithmetic averages (UPGMA) cluster analysis evaluated by bootstrapping and compared with previous analyses based on ITS and 5S IGS. Principal results A total of 202 (86 %) fragments were found to be polymorphic and used for generating a genetic distance matrix. Twenty-one V. unguiculata accessions were grouped into three main clusters. The cultivated subspecies (var. unguiculata) and most of its wild progenitors (var. spontanea) were placed in cluster I along with ssp. pubescens and ssp. stenophylla. Whereas var. spontanea were grouped with ssp. alba and ssp. tenuis accessions in cluster II, ssp. alba and ssp. baoulensis were included in cluster III. Close affinities of ssp. unguiculata, ssp. alba and ssp. tenuis suggested inter-subspecies hybridization. Conclusions Multi-locus AP-PCR analysis reveals that intra-species hybridization is prevalent among V. unguiculata subspecies and suggests that grouping of accessions from two different subspecies is not solely due to the similarity in the ITS and 5S IGS regions but also due to other regions of the genome. PMID:22619698

  15. Unsupervised DInSAR processing chain for multi-scale displacement analysis

    NASA Astrophysics Data System (ADS)

    Casu, Francesco; Manunta, Michele

    2016-04-01

    , thus leading to the generation of Interferometric products for both global and local scale displacement analysis. Among several examples, we will show a wide displacement SBAS processing, carried out over the southern California, during which the whole ascending ENVISAT data set of more than 740 images has been fully processed on a Cloud Computing environment in less than 9 hours, leading to the generation of a displacement map of about 150,000 square kilometres. The P-SBAS characteristics allowed also us to integrate the algorithm within the ESA Geohazard Exploitation Platform (GEP), which is based on the use of GRID and Cloud Computing facilities, thus making freely available to the EO community a web tool for massive and systematic interferometric displacement time series generation. This work has been partially supported by: the Italian MIUR under the RITMARE project; the CNR-DPC agreement and the ESA GEP project.

  16. Topological analysis of polymeric melts: Chain-length effects and fast-converging estimators for entanglement length

    NASA Astrophysics Data System (ADS)

    Hoy, Robert S.; Foteinopoulou, Katerina; Kröger, Martin

    2009-09-01

    Primitive path analyses of entanglements are performed over a wide range of chain lengths for both bead spring and atomistic polyethylene polymer melts. Estimators for the entanglement length Ne which operate on results for a single chain length N are shown to produce systematic O(1/N) errors. The mathematical roots of these errors are identified as (a) treating chain ends as entanglements and (b) neglecting non-Gaussian corrections to chain and primitive path dimensions. The prefactors for the O(1/N) errors may be large; in general their magnitude depends both on the polymer model and the method used to obtain primitive paths. We propose, derive, and test new estimators which eliminate these systematic errors using information obtainable from the variation in entanglement characteristics with chain length. The new estimators produce accurate results for Ne from marginally entangled systems. Formulas based on direct enumeration of entanglements appear to converge faster and are simpler to apply.

  17. Restricted access chiral stationary phase synthesized via reversible addition-fragmentation chain-transfer polymerization for direct analysis of biological samples by high performance liquid chromatography.

    PubMed

    Song, Wen-Jun; Wei, Ji-Ping; Wang, Su-Ying; Wang, Huai-Song

    2014-06-17

    Novel hydrophilic microparticles containing β-cyclodextrin (β-CD) were prepared via one-pot synthesis using reversible addition-fragmentation chain-transfer (RAFT) precipitation polymerization, a "controlled/living" radical polymerization technique. The polymerization was initiated by hydrophilic macromolecular chain-transfer agent [poly(2-hydroxyethyl methacrylate), PHEMA]. The hydrophilic PHEMA on the surface of microparticles can well improve their surface hydrophilicity and lead to their biological compatibility. As chiral restricted access material (RAM), the hydrophilic microparticles can be used for determination of enantiomers in biological samples with direct injection via HPLC analysis. PMID:24890695

  18. Rapid detection of HLA-B*51 by real-time polymerase chain reaction and high-resolution melting analysis.

    PubMed

    Imperiali, C; Alía-Ramos, P; Padró-Miquel, A

    2015-08-01

    HLA-B*51, a class I human leukocyte antigen (HLA) molecule, is the strongest known genetic risk factor for Behçet disease. However, there are only few articles reporting methods to determine the presence or absence of HLA-B51. For this reason, we designed and developed an easy, fast, and inexpensive real-time high-resolution melting (HRM) assay to detect HLA-B*51. We genotyped 61 samples by our HRM assay and by conventional polymerase chain reaction, and no discrepancies were found between results. Besides, a subgroup of 25 samples was also genotyped in a different laboratory, and another subgroup of 16 samples was obtained from the International Histocompatibility Working Group DNA Bank, and a full concordance of results was observed with those obtained by HRM. Regarding the identifying system evaluated, we obtained 100% of specificity, sensibility, and repeatability, and 0% of false positive and false negative rates. Therefore, this HRM analysis is easily applicable to the rapid detection of HLA-B*51, exhibits a high speed, and requires a very low budget. PMID:26176813

  19. A MARKOV CHAIN MONTE CARLO ALGORITHM FOR ANALYSIS OF LOW SIGNAL-TO-NOISE COSMIC MICROWAVE BACKGROUND DATA

    SciTech Connect

    Jewell, J. B.; O'Dwyer, I. J.; Huey, Greg; Gorski, K. M.; Eriksen, H. K.; Wandelt, B. D. E-mail: h.k.k.eriksen@astro.uio.no

    2009-05-20

    We present a new Markov Chain Monte Carlo (MCMC) algorithm for cosmic microwave background (CMB) analysis in the low signal-to-noise regime. This method builds on and complements the previously described CMB Gibbs sampler, and effectively solves the low signal-to-noise inefficiency problem of the direct Gibbs sampler. The new algorithm is a simple Metropolis-Hastings sampler with a general proposal rule for the power spectrum, C {sub l}, followed by a particular deterministic rescaling operation of the sky signal, s. The acceptance probability for this joint move depends on the sky map only through the difference of {chi}{sup 2} between the original and proposed sky sample, which is close to unity in the low signal-to-noise regime. The algorithm is completed by alternating this move with a standard Gibbs move. Together, these two proposals constitute a computationally efficient algorithm for mapping out the full joint CMB posterior, both in the high and low signal-to-noise regimes.

  20. Markov Chain Monte Carlo Joint Analysis of Chandra X-Ray Imaging Spectroscopy and Sunyaev-Zel'dovich Effect Data

    NASA Technical Reports Server (NTRS)

    Bonamente, Massimillano; Joy, Marshall K.; Carlstrom, John E.; Reese, Erik D.; LaRoque, Samuel J.

    2004-01-01

    X-ray and Sunyaev-Zel'dovich effect data can be combined to determine the distance to galaxy clusters. High-resolution X-ray data are now available from Chandra, which provides both spatial and spectral information, and Sunyaev-Zel'dovich effect data were obtained from the BIMA and Owens Valley Radio Observatory (OVRO) arrays. We introduce a Markov Chain Monte Carlo procedure for the joint analysis of X-ray and Sunyaev- Zel'dovich effect data. The advantages of this method are the high computational efficiency and the ability to measure simultaneously the probability distribution of all parameters of interest, such as the spatial and spectral properties of the cluster gas and also for derivative quantities such as the distance to the cluster. We demonstrate this technique by applying it to the Chandra X-ray data and the OVRO radio data for the galaxy cluster A611. Comparisons with traditional likelihood ratio methods reveal the robustness of the method. This method will be used in follow-up paper to determine the distances to a large sample of galaxy cluster.

  1. Application of Markov chain Monte Carlo analysis to biomathematical modeling of respirable dust in US and UK coal miners

    PubMed Central

    Sweeney, Lisa M.; Parker, Ann; Haber, Lynne T.; Tran, C. Lang; Kuempel, Eileen D.

    2015-01-01

    A biomathematical model was previously developed to describe the long-term clearance and retention of particles in the lungs of coal miners. The model structure was evaluated and parameters were estimated in two data sets, one from the United States and one from the United Kingdom. The three-compartment model structure consists of deposition of inhaled particles in the alveolar region, competing processes of either clearance from the alveolar region or translocation to the lung interstitial region, and very slow, irreversible sequestration of interstitialized material in the lung-associated lymph nodes. Point estimates of model parameter values were estimated separately for the two data sets. In the current effort, Bayesian population analysis using Markov chain Monte Carlo simulation was used to recalibrate the model while improving assessments of parameter variability and uncertainty. When model parameters were calibrated simultaneously to the two data sets, agreement between the derived parameters for the two groups was very good, and the central tendency values were similar to those derived from the deterministic approach. These findings are relevant to the proposed update of the ICRP human respiratory tract model with revisions to the alveolar-interstitial region based on this long-term particle clearance and retention model. PMID:23454101

  2. Determination of locust bean gum and guar gum by polymerase chain reaction and restriction fragment length polymorphism analysis.

    PubMed

    Meyer, K; Rosa, C; Hischenhuber, C; Meyer, R

    2001-01-01

    A polymerase chain reaction (PCR) was developed to differentiate the thickening agents locust bean gum (LBG) and the cheaper guar gum in finished food products. Universal primers for amplification of the intergenic spacer region between trnL 3' (UAA) exon and trnF (GAA) gene in the chloroplast (cp) genome and subsequent restriction analysis were applied to differentiate guar gum and LBG. The presence of <5% (w/w) guar gum powder added to LBG powder was detectable. Based on data obtained from sequencing this intergenic spacer region, a second PCR method for the specific detection of guar gum DNA was also developed. This assay detected guar gum powder in LBG in amounts as low as 1% (w/w). Both methods successfully detected guar gum and/or LBG in ice cream stabilizers and in foodstuffs, such as dairy products, ice cream, dry seasoning mixes, a finished roasting sauce, and a fruit jelly product, but not in products with highly degraded DNA, such as tomato ketchup and sterilized chocolate cream. Both methods detected guar gum and LBG in ice cream and fresh cheese at levels <0.1%. PMID:11234856

  3. Molecular characterization and mutational analysis of the human B17 subunit of the mitochondrial respiratory chain complex I.

    PubMed

    Smeitink, J; Loeffen, J; Smeets, R; Triepels, R; Ruitenbeek, W; Trijbels, F; van den Heuvel, L

    1998-08-01

    Bovine NADH:ubiquinone oxidoreductase (complex 1) of the mitochondrial respiratory chain consists of about 36 nuclear-encoded subunits. We review the current knowledge of the 15 human complex I subunits cloned so far, and report the 598-bp cDNA sequence, the chromosomal localization and the tissue expression of an additional subunit, the B17 subunit. The cDNA open reading frame of B17 comprises 387 bp and encodes a protein of 128 amino acids (calculated Mr 15.5 kDa). There is 82.7% and 78.1% homology, respectively, at the cDNA and amino acid level with the bovine counterpart. The gene of the B17 subunit has been mapped to chromosome 2. Multiple-tissue dot-blots showed ubiquitous expression of the mRNA with relatively higher expression in tissues known for their high energy demand. Of these, kidney showed the highest expression. Mutational analysis of the subunit revealed no mutations or polymorphisms in 20 patients with isolated enzymatic complex I deficiency in cultured skin fibroblasts. PMID:9760212

  4. Molecular cloning and comparative analysis of immunoglobulin heavy chain genes from Phasianus colchicus, Meleagris gallopavo, and Coturnix japonica.

    PubMed

    Choi, Jin Won; Kim, Jin-Kyoo; Seo, Hee Won; Cho, Byung Wook; Song, Gwonhwa; Han, Jae Yong

    2010-08-15

    To date, immunoglobulin (Ig) genes have only been fully characterized in a small number of aves, which pose a major obstacle to understanding Ig evolution. Thus, we cloned the cDNAs of three immunoglobulin classes, IgA, IgM, and IgY, from Phasianus colchicus, Coturnix japonica, and Meleagris gallopavo. Multiple sequence alignments revealed that the highest degree of sequence homology in all Ig classes was observed between pheasant and turkey whereas the degree of homology between the galliforms and non-galliforms was relatively low compared to that among the galliforms. When the constant region domains of the four human Ig classes were compared with the corresponding regions in aves, the average percent homology between human CH2 and avian CH3, and between human CH3 and avian CH4, was greater than between identical domains in IgA and IgY, which are in partial agreement with the hypothesis that the avian CH2 domain evolved to form the mammalian hinge via domain condensation. Phylogenetic analysis showed that the galliform Ig heavy chain constant regions were divided into quail and the common ancestor of chicken, turkey, and pheasant, and that chicken was separated from turkey and pheasant, which were grouped together. These results add to our knowledge of galliform Igs and the diversification of these genes. PMID:20398946

  5. Evaluating environmental impacts of alternative construction waste management approaches using supply-chain-linked life-cycle analysis.

    PubMed

    Kucukvar, Murat; Egilmez, Gokhan; Tatari, Omer

    2014-05-22

    Waste management in construction is critical for the sustainable treatment of building-related construction and demolition (C&D) waste materials, and recycling of these wastes has been considered as one of the best strategies in minimization of C&D debris. However, recycling of C&D materials may not always be a feasible strategy for every waste type and therefore recycling and other waste treatment strategies should be supported by robust decision-making models. With the aim of assessing the net carbon, energy, and water footprints of C&D recycling and other waste management alternatives, a comprehensive economic input-output-based hybrid life-cycle assessment model is developed by tracing all of the economy-wide supply-chain impacts of three waste management strategies: recycling, landfilling, and incineration. Analysis results showed that only the recycling of construction materials provided positive environmental footprint savings in terms of carbon, energy, and water footprints. Incineration is a better option as a secondary strategy after recycling for water and energy footprint categories, whereas landfilling is found to be as slightly better strategy when carbon footprint is considered as the main focus of comparison. In terms of construction materials' environmental footprint, nonferrous metals are found to have a significant environmental footprint reduction potential if recycled. PMID:24855225

  6. Morphological and Morphometrical Study of the Human Ossicular Chain: A Review of the Literature and a Meta-Analysis of Experience Over 50 Years

    PubMed Central

    Noussios, George; Chouridis, Pantelis; Kostretzis, Lazaros; Natsis, Konstantinos

    2016-01-01

    The ossicular chain has been known for 500 years and yet there are a small number of morphometrical studies. We reviewed the whole literature that is available online regarding the human ossicular chain from an anatomist perspective and correlated the data from all the papers that showed any relevance. Inclusion and exclusion criteria were developed a priori. A thorough description of all ossicular differences has been made and we present their variations in dimensions trying to associate measurements obtained with race. This research included papers spreading on a horizon of over 50 years of worldwide experience. Statistical analysis revealed that there is a great difference in measurements and the results cannot be sufficiently associated. The explanation of this variation in the measurements obtained might be due to errors in the procedure. We conclude that ossicular chain reveals a great variety, and propose that a measurement protocol for auditory ossicles must be widely performed. PMID:26767074

  7. The Inference of Phased Haplotypes for the Immunoglobulin H Chain V Region Gene Loci by Analysis of VDJ Gene Rearrangements

    PubMed Central

    Kidd, Marie J.; Chen, Zhiliang; Wang, Yan; Jackson, Katherine J.; Zhang, Lyndon; Boyd, Scott D.; Fire, Andrew Z.; Tanaka, Mark M.; Gaëta, Bruno A.; Collins, Andrew M.

    2014-01-01

    The existence of many highly similar genes in the lymphocyte receptor gene loci makes them difficult to investigate, and the determination of phased “haplotypes” has been particularly problematic. However, V(D)J gene rearrangements provide an opportunity to infer the association of Ig genes along the chromosomes. The chromosomal distribution of H chain genes in an Ig genotype can be inferred through analysis of VDJ rearrangements in individuals who are heterozygous at points within the IGH locus. We analyzed VDJ rearrangements from 44 individuals for whom sufficient unique rearrangements were available to allow comprehensive genotyping. Nine individuals were identified who were heterozygous at the IGHJ6 locus and for whom sufficient suitable VDJ rearrangements were available to allow comprehensive haplotyping. Each of the 18 resulting IGHV|IGHD|IGHJ haplotypes was unique. Apparent deletion polymorphisms were seen that involved as many as four contiguous, functional IGHV genes. Two deletion polymorphisms involving multiple contiguous IGHD genes were also inferred. Three previously unidentified gene duplications were detected, where two sequences recognized as allelic variants of a single gene were both inferred to be on a single chromosome. Phased genomic data brings clarity to the study of the contribution of each gene to the available repertoire of rearranged VDJ genes. Analysis of rearrangement frequencies suggests that particular genes may have substantially different yet predictable propensities for rearrangement within different haplotypes. Together with data highlighting the extent of haplotypic variation within the population, this suggests that there may be substantial variability in the available Ab repertoires of different individuals. PMID:22205028

  8. 1H NMR sequential assignments and secondary structure analysis of human fibrinogen gamma-chain C-terminal residues 385-411

    SciTech Connect

    Mayo, K.H.; Burke, C.; Lindon, J.N.; Kloczewiak, M. )

    1990-04-03

    The human fibrinogen gamma-chain, C-terminal fragment, residues 385-411, i.e., KIIPFNRLTIGEGQQHHLGGAKQAGDV, contains two biologically important functional domains: (1) fibrinogen gamma-chain polymerization center and (2) platelet receptor recognition domain. This peptide was isolated from cyanogen bromide degraded human fibrinogen and was investigated by 1H NMR (500 MHz) spectroscopy. Sequence-specific assignments of NMR resonances were obtained for backbone and side-chain protons via analysis of 2D NMR COSY, double quantum filtered COSY, HOHAHA, and NOESY spectra. The N-terminal segment from residues 385-403 seems to adopt a relatively fixed solution conformation. Strong sequential alpha CH-NH NOESY connectivities and a continuous run of NH-NH NOESY connectivities and several long-lived backbone NH protons strongly suggest the presence of multiple-turn or helix-like structure for residues 390 to about 402. The conformation of residues 403-411 seems to be much less constrained as evidenced by the presence of weaker and sequential alpha CH-NH NOEs, the absence of sequential NH-NH NOEs, and the lack of longer lived amides. Chemical shifts of resonances from backbone and side-chain protons of the C-terminal dodecapeptide, residues 400-411, differ significantly from those of the parent chain, suggesting that some preferred C-terminal conformation does exist.

  9. Distribution and primary source analysis of per- and poly-fluoroalkyl substances with different chain lengths in surface and groundwater in two cities, North China.

    PubMed

    Yao, Yiming; Zhu, Hongkai; Li, Bing; Hu, Hongwei; Zhang, Tao; Yamazaki, Eriko; Taniyasu, Sachi; Yamashita, Nobuyoshi; Sun, Hongwen

    2014-10-01

    Per- and poly-fluoroalkyl substances (PFASs) have been widely detected in the hydrosphere. The knowledge on the distribution and composition patterns of PFAS analogues with different chain length significantly contribute to their source analysis. In the present study, a regional scale investigation of PFASs in surface river waters and adjacent ground waters was carried out in two cities of China with potential contamination, Tianjin and Weifang. A total of 31 water samples were collected, and 20 PFASs therein were measured by a high-performance liquid chromatograph-tandem mass spectrometer (HPLC-MS/MS). The possible sources of PFASs in the aquatic environment were assessed primarily by concentration patterns as well as hierarchical cluster analysis. In all 4 rivers investigated in the two cities, perfluoroalkyl carboxylic acids (PFCAs) were the dominant compounds contributing over 70% of the PFASs detected. Perfluorooctanoic acid (PFOA) was the dominant PFCA with a concentration range of 8.58-20.3ng/L in Tianjin and 6.37-25.9ng/L in Weifang, respectively. On the average, the highest concentration was observed in samples from Dagu Drainage Canal (Dagu) in Tianjin and those short-chain PFASs (C4-C6) was detected with a comparable level of the longer-chain PFASs (>C6). Specifically, perfluorobutanoic acid (PFBA) was dominant in the short-chain analogues. This indicates that a remarkably increasing input of short-chain PFASs might be related to wastewater treatment plant effluent or industrial discharges, which could be possibly due to the switch of manufacturing to short-chain products. In Weifang, precipitation and subsequent surface runoff as non-point sources could be significant inputs of PFASs into surface water while groundwater was possibly subjected to severe point sources with ∑PFASs concentration up to ~100ng/L. The inconsistent distribution patterns in groundwater suggest complicated pathways of contamination. PMID:25108512

  10. Facile analysis of contents and compositions of the chondroitin sulfate/dermatan sulfate hybrid chain in shark and ray tissues.

    PubMed

    Takeda, Naoko; Horai, Sawako; Tamura, Jun-ichi

    2016-04-01

    The chondroitin sulfate (CS)/dermatan sulfate (DS) hybrid chain was extracted from specific tissues of several kinds of sharks and rays. The contents and sulfation patterns of the CS/DS hybrid chain were precisely analyzed by digestion with chondroitinases ABC and AC. All samples predominantly contained the A- and C-units. Furthermore, all samples characteristically contained the D-unit. Species-specific differences were observed in the contents of the CS/DS hybrid chain, which were the highest in Mako and Blue sharks and Sharpspine skates, but were lower in Hammerhead sharks. Marked differences were observed in the ratio of the C-unit/A-unit between sharks and rays. The contents of the CS/DS hybrid chain and the ratio of the C-unit/A-unit may be related to an oxidative stress-decreasing ability. PMID:26986023

  11. Multiple qualitative and quantitative methods for free light chain analysis are necessary as first line tests for AL amyloidosis.

    PubMed

    Sečník, Peter; Honsová, Eva; Jabor, Antonín; Lavríková, Petra; Franeková, Janka

    2016-06-01

    The objective of this study was to demonstrate the necessity of using different methods for amyloidogenic light chain detection. Serum and urine agarose gel electrophoresis and immunofixation, as well as serum free light chain (FLC) immunoassay measurements, were evaluated in a patient with verified multiple myeloma and consequent AL amyloidosis confirmed by Congo red staining and immunofluorescence techniques. Conventional chemistry tests [serum and urine electrophoresis (SPE and UPE); serum and urine immunofixation (SIFE and UIFE)] were inconclusive. Only quantitative FLC immunoassay (serum free light chain immunoanalysis, SFLC) provided correct diagnostic information. A combination of gel-based SIFE and UIFE with more novel quantitative FLC immunoassays appears necessary when searching for monoclonal immunoglobulin light chain-related diseases. PMID:26760309

  12. Quantitative analysis of site-specific N-glycans on sera haptoglobin β chain in liver diseases.

    PubMed

    Zhang, Shu; Jiang, Kai; Sun, Chun; Lu, Haojie; Liu, Yinkun

    2013-12-01

    The site-specific characterization of N-glycans in glycoproteins with the potential of clinical application is important. In our previous report, the overall N-glycans of sera haptoglobin (Hp) β chain were found to be different in liver diseases. Hp β chain contains four potential sites of N-glycosylation. In this study, we investigated the potential change of N-glycans on Hp β chain in a site-specific fashion. Sera Hp β chain in healthy individuals as well as patients with hepatitis B virus (HBV), liver cirrhosis (LC) and hepatocellular carcinoma (HCC) were purified, digested and subjected to liquid chromatography-electrospray ionization-higher energy collision dissociation mass spectrometry, which allowed identification and structure determination of the glycopeptide, as well as the relative quantification of glycans present on each glycopeptide. The quantitative results revealed that the sialylation of NLFLN(207)HSEN(211)ATAK and the fucosylated structure at all glycopeptides increased significantly in LC and HCC patients compared with those in HBV patients and healthy individuals. A set of different N-glycan patterns of Hp β chain in various liver diseases has been determined. Thus, the sialylated and fucosylated glycoforms of Hp β chain might be related to early hepatocarcinogenesis and also might be useful as novel differential markers for LC and HCC patients. PMID:24103369

  13. When Phase Contrast Fails: ChainTracer and NucTracer, Two ImageJ Methods for Semi-Automated Single Cell Analysis Using Membrane or DNA Staining

    PubMed Central

    Syvertsson, Simon; Vischer, Norbert O. E.; Gao, Yongqiang; Hamoen, Leendert W.

    2016-01-01

    Within bacterial populations, genetically identical cells often behave differently. Single-cell measurement methods are required to observe this heterogeneity. Flow cytometry and fluorescence light microscopy are the primary methods to do this. However, flow cytometry requires reasonably strong fluorescence signals and is impractical when bacteria grow in cell chains. Therefore fluorescence light microscopy is often used to measure population heterogeneity in bacteria. Automatic microscopy image analysis programs typically use phase contrast images to identify cells. However, many bacteria divide by forming a cross-wall that is not detectable by phase contrast. We have developed ‘ChainTracer’, a method based on the ImageJ plugin ObjectJ. It can automatically identify individual cells stained by fluorescent membrane dyes, and measure fluorescence intensity, chain length, cell length, and cell diameter. As a complementary analysis method we developed 'NucTracer', which uses DAPI stained nucleoids as a proxy for single cells. The latter method is especially useful when dealing with crowded images. The methods were tested with Bacillus subtilis and Lactococcus lactis cells expressing a GFP-reporter. In conclusion, ChainTracer and NucTracer are useful single cell measurement methods when bacterial cells are difficult to distinguish with phase contrast. PMID:27008090

  14. Analysis of fluorotelomer alcohols, fluorotelomer acids, and short- and long-chain perfluorinated acids in water and biota.

    PubMed

    Taniyasu, Sachi; Kannan, Kurunthachalam; So, Man Ka; Gulkowska, Anna; Sinclair, Ewan; Okazawa, Tsuyoshi; Yamashita, Nobuyoshi

    2005-11-01

    Fluorotelomer alcohols and fluorotelomer acids have been proposed as a source of the perfluorinated carboxylic acids found in remote marine locations. To examine the sources and fate of perfluorinated acids in the environment, a method to determine a wide range of poly- and perfluorinated acids in environmental and biological matrices is needed. In this study, a method has been developed to measure a suite of neutral and acidic fluorochemicals including, fluorotelomer alcohols, fluorotelomer acids, and short- and long-chain perfluorinated acids, in water and biological samples. The method involves solid-phase extraction with weak anion exchange (WAX) cartridges, followed by sequential elution with sodium acetate buffer, methanol, and 0.1% NH4OH in methanol. For biological samples, prior to solid-phase extraction, tissues are digested in 0.5N potassium hydroxide/methanol, diluted in water, and passed through the WAX cartridge. Neutral compounds and telomer alcohols are separated from other poly- and perfluorinated acids. The method is robust (i.e., capable of measuring neutral and acidic compounds), and can be applied for the analysis of a range of poly- and perfluorinated acids, including telomer alcohols, telomer acids, perfluoroalkylcarboxylates, and perfluoroalkylsulfonates in water and biota. With the use of high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), a method detection limit in the range of several tens to hundreds of parts-per-quadrillion (pg/L) in water and at a few tens to hundreds of parts-per-trillion (pg/g) levels in biological matrices can be achieved. PMID:16233874

  15. Markov Chain Modelling Analysis of HIV/AIDS Progression: A Race-based Forecast in the United States

    PubMed Central

    Lee, S.; Ko, J.; Tan, Xi; Patel, Isha; Balkrishnan, R.; Chang, J.

    2014-01-01

    HIV/AIDS has reached a pandemic level across the world with more than 33 million people who are living with HIV. In the United States, more than half a million people have been victims of AIDS. This study investigates the most vulnerable racial minority population (the African Americans) in the United States and the second least affected (the Caucasians) in order to predict the trends of the epidemic. A Markov chain analysis was used to model the progression of the disease among vulnerable people, infective people and AIDS cases for the two races separately, based on the 2009 Centers of Disease Control and Prevention HIV/AIDS Surveillance Report. Based on the Markov model, our study predicts that the number of African American people living with AIDS diagnosis and HIV infection and dead due to HIV/AIDS will be 662.2, 1225.3 and 62.9 in 2015 and 794.9, 1566.5 and 79.2 in 2030, respectively. The number of Caucasian people living with AIDS diagnosis and HIV infection and dead due to HIV/AIDS will be 96.4, 160 and 6.5 in 2015 and 118.6, 206.9 and 8.3 in 2030, respectively. The numbers of deaths due to HIV/AIDS are quite stable over the years in both the races. There is an increasing trend in the number of people living with HIV infection and AIDS diagnosis in Caucasians compared with African Americans. The absolute number of Caucasians living with AIDS diagnosis and HIV infection is quite smaller compared with African Americans. The results reveal discrepancy in HIV infection, AIDS diagnosis and deaths due to HIV/AIDS among the African Americans and the Caucasians races. There is a need for interventions focusing on HIV/AIDS prevention and management, optimum resource allocation and development of antiAIDS campaigns to reduce the infection rate. PMID:24843183

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

    PubMed

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

    2016-01-01

    Molecular methods are powerful tools in characterizing and determining relationships between plants. The aim of this study was to study genetic divergence between 103 accessions of Mexican Opuntia. To accomplish this, polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of three chloroplast intergenic spacers (atpB-rbcL, trnL-trnF, and psbA-trnH), one chloroplast gene (ycf1), two nuclear genes (ppc and PhyC), and one mitochondrial gene (cox3) was conducted. The amplified products from all the samples had very similar molecular sizes, and there were only very small differences between the undigested PCR amplicons for all regions, with the exception of ppc. We obtained 5850 bp from the seven regions, and 136 fragments were detected with eight enzymes, 37 of which (27.2%) were polymorphic. We found that 40% of the fragments from the chloroplast regions were polymorphic, 9.8% of the bands detected in the nuclear genes were polymorphic, and 20% of the bands in the mitochondrial locus were polymorphic. trnL-trnF and psbA-trnH were the most variable regions. The Nei and Li/Dice distance was very short, and ranged from 0 to 0.12; indeed, 77 of the 103 genotypes had the same genetic profile. All the xoconostle accessions (acidic fruits) were grouped together without being separated from three genotypes of prickly pear (sweet fruits). We assume that the genetic divergence between prickly pears and xoconostles is very low, and question the number of Opuntia species currently considered in Mexico. PMID:27323120

  17. Kinematic and kinetic analysis of maximal velocity deadlifts performed with and without the inclusion of chain resistance.

    PubMed

    Swinton, Paul A; Stewart, Arthur D; Keogh, Justin W L; Agouris, Ioannis; Lloyd, Ray

    2011-11-01

    The purpose of this study was to investigate whether the deadlift could be effectively incorporated with explosive resistance training (ERT) and to investigate whether the inclusion of chains enhanced the suitability of the deadlift for ERT. Twenty-three resistance trained athletes performed the deadlift with 30, 50, and 70% 1-repetition maximum (1RM) loads at submaximal velocity, maximal velocity (MAX), and MAX with the inclusion of 2 chain loads equal to 20 or 40% of the subjects' 1RM. All trials were performed on force platforms with markers attached to the barbell to calculate velocity and acceleration using a motion capture system. Significant increases in force, velocity, power, rate of force development, and length of the acceleration phase (p < 0.05) were obtained when repetition velocity increased from submaximal to maximal. During MAX repetitions with a constant resistance, the mean length of the acceleration phase ranged from 73.2 (±7.2%) to 84.9 (±12.2%) of the overall movement. Compared to using a constant resistance, the inclusion of chains enabled greater force to be maintained to the end of the concentric action and significantly increased peak force and impulse (p < 0.05), while concurrently decreasing velocity, power, and rate of force development (p < 0.05). The effects of chains were influenced by the magnitude of the chain and barbell resistance, with greater increases and decreases in mechanical variables obtained when heavier chain and barbell loads were used. The results of the investigation suggest that the deadlift can be incorporated effectively in ERT programs. Coaches and athletes should be aware that the inclusion of heavy chains may have both positive and negative effects on kinematics and kinetics of an exercise. PMID:21993040

  18. Behavioral Analysis of Visitors to a Medical Institution’s Website Using Markov Chain Monte Carlo Methods

    PubMed Central

    Tani, Yuji

    2016-01-01

    Background Consistent with the “attention, interest, desire, memory, action” (AIDMA) model of consumer behavior, patients collect information about available medical institutions using the Internet to select information for their particular needs. Studies of consumer behavior may be found in areas other than medical institution websites. Such research uses Web access logs for visitor search behavior. At this time, research applying the patient searching behavior model to medical institution website visitors is lacking. Objective We have developed a hospital website search behavior model using a Bayesian approach to clarify the behavior of medical institution website visitors and determine the probability of their visits, classified by search keyword. Methods We used the website data access log of a clinic of internal medicine and gastroenterology in the Sapporo suburbs, collecting data from January 1 through June 31, 2011. The contents of the 6 website pages included the following: home, news, content introduction for medical examinations, mammography screening, holiday person-on-duty information, and other. The search keywords we identified as best expressing website visitor needs were listed as the top 4 headings from the access log: clinic name, clinic name + regional name, clinic name + medical examination, and mammography screening. Using the search keywords as the explaining variable, we built a binomial probit model that allows inspection of the contents of each purpose variable. Using this model, we determined a beta value and generated a posterior distribution. We performed the simulation using Markov Chain Monte Carlo methods with a noninformation prior distribution for this model and determined the visit probability classified by keyword for each category. Results In the case of the keyword “clinic name,” the visit probability to the website, repeated visit to the website, and contents page for medical examination was positive. In the case of the

  19. Polymerase chain reaction analysis of hepatitis B virus DNA in formalin-fixed, paraffin-embedded liver biopsies from alcoholics using a simplified and standardized amplification protocol.

    PubMed

    von Weizsäcker, F; Blum, H E; Wands, J R

    1994-05-01

    Sixty-seven formalin-fixed and paraffin-embedded liver biopsies from HBsAg-negative alcoholics without previous blood transfusions or intravenous drug abuse were analyzed for the presence of low-level hepatitis B virus DNA by the polymerase chain reaction. To simplify and standardize the amplification procedure, aliquots of a complete polymerase chain reaction mix were prepared and frozen for storage; random samples were tested prior to analysis of clinical material. Freezing and storage of the aliquots did not affect the activity of Taq polymerase. One large batch of ready-to-use aliquots could thus be used as a standardized polymerase chain reaction kit for all experiments. The suitability of the extracted material for polymerase chain reaction analysis was tested in two ways. First, the absence of nonspecific polymerase chain reaction inhibitors was demonstrated in all samples by amplifying cloned hepatitis B virus DNA in the presence of extracted material. Second, the integrity of the extracted DNA was tested by amplifying a segment of the beta-globin gene. Twenty-three samples were beta-globin DNA positive and thus contained sufficient amounts of nondegraded DNA. These results emphasize the importance of testing both the absence of nonspecific inhibitors and DNA integrity in DNA samples extracted from fixed tissue. Among the 23 beta-globin positive samples, 12 had cirrhosis (52.1%). Two of these samples were hepatitis B virus DNA positive (8.7%); one of these cases had cirrhosis. Thus, even in the absence of common risk factors, the incidence of hepatitis B virus in this alcoholic population was increased compared to the general population. PMID:8071542

  20. The multi-hemoglobin system of the hydrothermal vent tube worm Riftia pachyptila. II. Complete polypeptide chain composition investigated by maximum entropy analysis of mass spectra.

    PubMed

    Zal, F; Lallier, F H; Green, B N; Vinogradov, S N; Toulmond, A

    1996-04-12

    The deep-sea tube worm Riftia pachyptila Jones possesses a complex of three extracellular Hbs: two in the vascular compartment, V1 (approximately 3500 kDa) and V2 (approximately 400 kDa), and one in the coelomic cavity, C1 (approximately 400 kDa). These native Hbs, their dissociation products and derivatives were subjected to electrospray ionization mass spectrometry (ESI-MS). The data were analyzed by the maximum entropy deconvolution system. We identified three groups of peaks for V1 Hb, at approximately 16, 23 27, and 30 kDa, corresponding to (i) two monomeric globin chains, b (Mr 16,133.5) and c (Mr 16,805.9); (ii) four linker subunits, L1 L4 (Mr 23,505.2, 23,851.4, 26,342.4, and 27,425.8, respectively); and (iii) one disulfide-bonded dimer D1 (Mr 31,720.7) composed of globin chains d (Mr 15,578.5) and e (Mr 16, 148.3). V2 and C1 Hbs had no linkers and contained a glycosylated monomeric globin chain, a (Mr 15,933.4) and a second dimer D2 (Mr 32,511.7) composed of chains e and f (Mr 16,368.1). The dimer D1 was absent from C1 Hb, clearly differentiating V2 and C1 Hbs. These Hbs were also subjected to SDS-PAGE analysis for comparative purposes. The following models are proposed ((cD1)(bD1)3) for the one-twelfth protomer of V1 Hb, ((cD)(bD)6(aD)) (D corresponding to either D1 or D2) for V2 and C1 Hbs. HBL V1 Hb would be composed of 180 polypeptide chains with 144 globin chains and 36 linker chains, each twelfth being in contact with three linker subunits, providing a total molecular mass = 3285 kDa. V2 and C1 would be composed of 24 globin chains providing a total molecular mass = 403 kDa and 406 kDa, respectively. These results are in excellent agreement with experimental Mr determined by STEM mass mapping and MALLS. PMID:8621529

  1. Frequent Side Chain Methyl Carbon-Oxygen Hydrogen Bonding in Proteins Revealed by Computational and Stereochemical Analysis of Neutron Structures

    PubMed Central

    Brooks, Charles L.; Trievel, Raymond C.

    2016-01-01

    The propensity of backbone Cα atoms to engage in carbon-oxygen (CH···O) hydrogen bonding is well-appreciated in protein structure, but side chain CH···O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH···O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH···O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH···O hydrogen bonding contributes to the energetics of protein structure and folding. PMID:25401519

  2. Is food allergen analysis flawed? Health and supply chain risks and a proposed framework to address urgent analytical needs.

    PubMed

    Walker, M J; Burns, D T; Elliott, C T; Gowland, M H; Mills, E N Clare

    2016-01-01

    Food allergy is an increasing problem for those affected, their families or carers, the food industry and for regulators. The food supply chain is highly vulnerable to fraud involving food allergens, risking fatalities and severe reputational damage to the food industry. Many facets are being pursued to ameliorate the difficulties including better food labelling and the concept of thresholds of elicitation of allergy symptoms as risk management tools. These efforts depend to a high degree on the ability reliably to detect and quantify food allergens; yet all current analytical approaches exhibit severe deficiencies that jeopardise accurate results being produced particularly in terms of the risks of false positive and false negative reporting. If we fail to realise the promise of current risk assessment and risk management of food allergens through lack of the ability to measure food allergens reproducibly and with traceability to an international unit of measurement, the analytical community will have failed a significant societal challenge. Three distinct but interrelated areas of analytical work are urgently needed to address the substantial gaps identified: (a) a coordinated international programme for the production of properly characterised clinically relevant reference materials and calibrants for food allergen analysis; (b) an international programme to widen the scope of proteomics and genomics bioinformatics for the genera containing the major allergens to address problems in ELISA, MS and DNA methods; (c) the initiation of a coordinated international programme leading to reference methods for allergen proteins that provide results traceable to the SI. This article describes in more detail food allergy, the risks of inapplicable or flawed allergen analyses with examples and a proposed framework, including clinically relevant incurred allergen concentrations, to address the currently unmet and urgently required analytical requirements. Support for the

  3. EFFECTIVE METHOD TO EXTRACT DNA FROM ENVIRONMENTAL SAMPLES FOR POLYMERASE CHAIN REACTION AMPLIFICATION AND DNA FINGERPRINT ANALYSIS

    EPA Science Inventory

    A rapid direct-extraction method was used to obtain DNA from environmental soil samples. eat, enzymes, and guanidine isothiocyanate were utilized to lyse cells. he DNA was purified by agarose gel electrophoresis, amplified with 16S based primers by use of the polymerase chain rea...

  4. Characterization of contact structures for the spread of infectious diseases in a pork supply chain in northern Germany by dynamic network analysis of yearly and monthly networks.

    PubMed

    Büttner, K; Krieter, J; Traulsen, I

    2015-04-01

    A major risk factor in the spread of diseases between holdings is the transport of live animals. This study analysed the animal movements of the pork supply chain of a producer group in Northern Germany. The parameters in-degree and out-degree, ingoing and outgoing infection chain, betweenness and ingoing and outgoing closeness were measured using dynamic network analysis to identify holdings with central positions in the network and to characterize the overall network topology. The potential maximum epidemic size was also estimated. All parameters were calculated for three time periods: the 3-yearly network, the yearly and the monthly networks. The yearly and the monthly networks were more fragmented than the 3-yearly network. On average, one-third of the holdings were isolated in the yearly networks and almost three quarters in the monthly networks. This represented an immense reduction in the number of holdings participating in the trade of the monthly networks. The overall network topology showed right-skewed distributions for all calculated centrality parameters indicating that network resilience was high concerning the random removal of holdings. However, for a targeted removal of holdings according to their centrality, a rapid fragmentation of the trade network could be expected. Furthermore, to capture the real importance of holdings for disease transmission, indirect trade contacts (infection chain) should be considered. In contrast to the parameters regarding direct trade contacts (degree), the infection chain parameter did not underestimate the potential risk of disease transmission. This became more obvious, the longer the observed time period was. For all three time periods, the results for the estimation of the potential maximum epidemic size illustrated that the outgoing infection chain should be chosen. It considers the chronological order and the directed nature of the contacts and has no restrictions such as the strongly connected components of a

  5. Identification of the significant factors in food safety using global sensitivity analysis and the accept-and-reject algorithm: application to the cold chain of ham.

    PubMed

    Duret, Steven; Guillier, Laurent; Hoang, Hong-Minh; Flick, Denis; Laguerre, Onrawee

    2014-06-16

    Deterministic models describing heat transfer and microbial growth in the cold chain are widely studied. However, it is difficult to apply them in practice because of several variable parameters in the logistic supply chain (e.g., ambient temperature varying due to season and product residence time in refrigeration equipment), the product's characteristics (e.g., pH and water activity) and the microbial characteristics (e.g., initial microbial load and lag time). This variability can lead to different bacterial growth rates in food products and has to be considered to properly predict the consumer's exposure and identify the key parameters of the cold chain. This study proposes a new approach that combines deterministic (heat transfer) and stochastic (Monte Carlo) modeling to account for the variability in the logistic supply chain and the product's characteristics. The model generates a realistic time-temperature product history , contrary to existing modeling whose describe time-temperature profile Contrary to existing approaches that use directly a time-temperature profile, the proposed model predicts product temperature evolution from the thermostat setting and the ambient temperature. The developed methodology was applied to the cold chain of cooked ham including, the display cabinet, transport by the consumer and the domestic refrigerator, to predict the evolution of state variables, such as the temperature and the growth of Listeria monocytogenes. The impacts of the input factors were calculated and ranked. It was found that the product's time-temperature history and the initial contamination level are the main causes of consumers' exposure. Then, a refined analysis was applied, revealing the importance of consumer behaviors on Listeria monocytogenes exposure. PMID:24786551

  6. Purification, crystallization, X-ray diffraction analysis and phasing of an engineered single-chain PvuII restriction endonuclease

    SciTech Connect

    Meramveliotaki, Chrysi; Kotsifaki, Dina; Androulaki, Maria; Hountas, Athanasios; Eliopoulos, Elias; Kokkinidis, Michael

    2007-10-01

    PvuII is the first type II restriction endonuclease to be converted from its wild-type homodimeric form into an enzymatically active single-chain variant. The enzyme was crystallized and phasing was successfully performed by molecular replacement. The restriction endonuclease PvuII from Proteus vulgaris has been converted from its wild-type homodimeric form into the enzymatically active single-chain variant scPvuII by tandemly joining the two subunits through the peptide linker Gly-Ser-Gly-Gly. scPvuII, which is suitable for the development of programmed restriction endonucleases for highly specific DNA cleavage, was purified and crystallized. The crystals diffract to a resolution of 2.35 Å and belong to space group P4{sub 2}, with unit-cell parameters a = b = 101.92, c = 100.28 Å and two molecules per asymmetric unit. Phasing was successfully performed by molecular replacement.

  7. Type analysis of the oligosaccharide chains on microheterogeneous components of bovine pancreatic DNAase by the lectin-nitrocellulose sheet method.

    PubMed Central

    Kijimoto-Ochiai, S; Katagiri, Y U; Hatae, T; Okuyama, H

    1989-01-01

    The oligosaccharide chains of microheterogeneous bovine pancreatic DNAases were characterized by the lectin-nitrocellulose sheet method. The active fractions of the DNAases from column chromatography showed four major and several minor spots on a two-dimensional polyacrylamide gel. They were transferred on to nitrocellulose sheets and treated with glycosidases (neuraminidase, endo-beta-N-acetyl glucosaminidase H or F, or peptide N-glycosidase F) and treated with peroxidase-coupled lectins (concanavalin A, Ricinus communis agglutinin or wheat-germ agglutinin). From the results, the most probable oligosaccharide types were proposed to be as follows: the four major spots contained components which had high-mannose type or hybrid-type oligosaccharides, such as those susceptible to endo-beta-N-acetylglucosaminidase H. In addition, spot 1 contained a complex-type biantennary oligosaccharide without sialic acid and spot 3 contained a tri- or tetra-antennary complex-type oligosaccharide with sialic acid. The component corresponding to spot 2 had a hybrid-type oligosaccharide chain with a 'bisecting' acetylglucosamine, linked 1-4 to the beta-mannose residue of the trimannosyl core, and the component corresponding to spot 4 had a high-mannose-type oligosaccharide chain. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. PMID:2920025

  8. The dynamic excitation of a granular chain for biomedical ultrasound applications: contact mechanics finite element analysis and validation

    NASA Astrophysics Data System (ADS)

    Gélat, P.; Yang, J.; Thomas, P. J.; Hutchins, D. A.; Akanji, O.; Davis, L. A. J.; Freear, S.; Harput, S.; Saffari, N.

    2016-01-01

    There has been recent interest in the transmission of acoustic signals along granular chains of spherical beads to produce waveforms of relevance to biomedical ultrasound applications. Hertzian contact between adjacent beads can introduce different harmonic content into the signal as it propagates. This transduction mechanism has the potential to be of use in both diagnostic and therapeutic ultrasound applications, and is the object of the study presented here. Although discrete dynamics models of this behaviour exist, a more comprehensive solution must be sought if changes in shape and deformation of individual beads are to be considered. Thus, the finite element method was used to investigate the dynamics of a granular chain of six, 1 mm diameter chrome steel spherical beads excited at one end using a sinusoidal displacement signal at 73 kHz. Output from this model was compared with the solution provided by the discrete dynamics model, and good overall agreement obtained. In addition, it was able to resolve the complex dynamics of the granular chain, including the multiple collisions which occur. It was demonstrated that under dynamic excitation conditions, the inability of discrete mechanics models to account for elastic deformation of the beads when these lose contact, could lead to discrepancies with experimental observations.

  9. Kinetic analysis of a monoclonal therapeutic antibody and its single-chain homolog by surface plasmon resonance.

    PubMed

    Patel, Rekha; Andrien, Bruce A

    2010-01-01

    Monoclonal antibodies (mAbs) and antibody fragments have become an emerging class of therapeutics since 1986. Their versatility enables them to be engineered for optimal efficiency and decreased immunogenicity, and the path to market has been set by recent regulatory approvals. One of the initial criteria for success of any protein or antibody therapeutic is to understand its binding characteristics to the target antigen. Surface plasmon resonance (SPR) has been widely used and is an important tool for ligand-antigen binding characterization. In this work, the binding kinetics of a recombinant mAb and its single-chain antibody homolog, single-chain variable fragment (scFv), was analyzed by SPR. These two proteins target the same antigen. The binding kinetics of the mAb (bivalent antibody) and scFv (monovalent scFv) for this antigen was analyzed along with an assessment of the thermodynamics of the binding interactions. Alternative binding configurations were investigated to evaluate potential experimental bias because theoretically experimental binding configuration should have no impact on binding kinetics. Self-association binding kinetics in the proteins' respective formulation solutions and antigen epitope mapping were also evaluated. Functional characterization of monoclonal and single-chain antibodies has become just as important as structural characterization in the biotechnology field. PMID:19720041

  10. Human laminin B2 chain

    SciTech Connect

    Pikkarainen, T.; Kallunki, T.; Tryggvason, K.

    1988-05-15

    The complete amino acid sequence of the human laminin B2 chains has been determined by sequencing of cDNA clones. The six overlapping clones studied cover approximately 7.5 kilobases of which 5312 nucleotides were sequenced from the 5' end. The open reading frame codes for a 33-residue signal peptide and a 1576-residue B2 chain proper, which is 189 residues less than in the highly homologous B1 chain. Computer analysis revealed that the B2 chain consists of distinct domains that contain helical structures, cysteine-rich repeats, and globular regions, as does the B1 chain. However, domain ..cap alpha.. and domain ..beta.. of the B1 chain have no counterpart in B2, and the number of cysteine-rich repeats is 12, or 1 less than in the B1 chain. The degree of homology between the two chains is highest in the cysteine repeat-containing domains III and V where 40% of the residues match. However, in helical domains I/II only 16% of residues match. The results demonstrate that the B1 and B2 chains of laminin are highly homologous proteins that are probably the products of related genes.

  11. A Value Chain Analysis of ghost nets in the Arafura Sea: identifying trans-boundary stakeholders, intervention points and livelihood trade-offs.

    PubMed

    Butler, J R A; Gunn, R; Berry, H L; Wagey, G A; Hardesty, B D; Wilcox, C

    2013-07-15

    Lost or discarded fishing nets are a significant component of marine debris which has trans-boundary impacts in large marine ecosystems. Such 'ghost nets' cause the by-catch of marine fauna and require retrieval from coastlines where they wash up. Identifying the causes of discarded nets and feasible intervention points requires analysis of a complex value chain and the stakeholders within it, yet no studies have attempted this. In this paper we combine Value Chain Analysis, commonly applied to understand value-adding for a commodity, with elements of Life Cycle Assessment and social network analysis to examine the drivers, stakeholders, economic, environmental and social costs and benefits in the life of a trawl net. We use the Arafura Sea as a case study, which is shared by Indonesia, Papua New Guinea and Australia, and is the focus of a Trans-boundary Diagnostic Assessment (TDA) within the Arafura-Timor Seas Ecosystem Action program (ATSEA). We follow a trawl net through four sub-systems: manufacture of webbing in South Korea, fishing and loss by an Indonesian vessel, retrieval as ghost net on the northern Australian coastline by Indigenous rangers, and disposal or re-cycling as 'GhostNet Art' by Indigenous artists. Primary stakeholders along the value chain incur economic and social benefits, and economic and environmental costs. There is an anomaly in the chain between Indonesian fishermen and Indigenous rangers, artists and communities due to the lack of market linkages between these primary stakeholders. The first 'nexus of influence' where reductions in net losses and environmental costs can be achieved is through interactions between GhostNets Australia, the World Wide Fund for Nature and the Australian Government, which can influence Indonesian fishery management institutions and fishing crews. The second nexus is via the international art market which by publicising GhostNet Art can raise awareness amongst fish consumers about the impacts of ghost nets

  12. Total Proteome Analysis Identifies Migration Defects as a Major Pathogenetic Factor in Immunoglobulin Heavy Chain Variable Region (IGHV)-unmutated Chronic Lymphocytic Leukemia*

    PubMed Central

    Eagle, Gina L.; Zhuang, Jianguo; Jenkins, Rosalind E.; Till, Kathleen J.; Jithesh, Puthen V.; Lin, Ke; Johnson, Gillian G.; Oates, Melanie; Park, Kevin; Kitteringham, Neil R.; Pettitt, Andrew R.

    2015-01-01

    The mutational status of the immunoglobulin heavy chain variable region defines two clinically distinct forms of chronic lymphocytic leukemia (CLL) known as mutated (M-CLL) and unmutated (UM-CLL). To elucidate the molecular mechanisms underlying the adverse clinical outcome associated with UM-CLL, total proteomes from nine UM-CLL and nine M-CLL samples were analyzed by isobaric tags for relative and absolute quantification (iTRAQ)-based mass spectrometry. Based on the expression of 3521 identified proteins, principal component analysis separated CLL samples into two groups corresponding to immunoglobulin heavy chain variable region mutational status. Computational analysis showed that 43 cell migration/adhesion pathways were significantly enriched by 39 differentially expressed proteins, 35 of which were expressed at significantly lower levels in UM-CLL samples. Furthermore, UM-CLL cells underexpressed proteins associated with cytoskeletal remodeling and overexpressed proteins associated with transcriptional and translational activity. Taken together, our findings indicate that UM-CLL cells are less migratory and more adhesive than M-CLL cells, resulting in their retention in lymph nodes, where they are exposed to proliferative stimuli. In keeping with this hypothesis, analysis of an extended cohort of 120 CLL patients revealed a strong and specific association between UM-CLL and lymphadenopathy. Our study illustrates the potential of total proteome analysis to elucidate pathogenetic mechanisms in cancer. PMID:25645933

  13. Total proteome analysis identifies migration defects as a major pathogenetic factor in immunoglobulin heavy chain variable region (IGHV)-unmutated chronic lymphocytic leukemia.

    PubMed

    Eagle, Gina L; Zhuang, Jianguo; Jenkins, Rosalind E; Till, Kathleen J; Jithesh, Puthen V; Lin, Ke; Johnson, Gillian G; Oates, Melanie; Park, Kevin; Kitteringham, Neil R; Pettitt, Andrew R

    2015-04-01

    The mutational status of the immunoglobulin heavy chain variable region defines two clinically distinct forms of chronic lymphocytic leukemia (CLL) known as mutated (M-CLL) and unmutated (UM-CLL). To elucidate the molecular mechanisms underlying the adverse clinical outcome associated with UM-CLL, total proteomes from nine UM-CLL and nine M-CLL samples were analyzed by isobaric tags for relative and absolute quantification (iTRAQ)-based mass spectrometry. Based on the expression of 3521 identified proteins, principal component analysis separated CLL samples into two groups corresponding to immunoglobulin heavy chain variable region mutational status. Computational analysis showed that 43 cell migration/adhesion pathways were significantly enriched by 39 differentially expressed proteins, 35 of which were expressed at significantly lower levels in UM-CLL samples. Furthermore, UM-CLL cells underexpressed proteins associated with cytoskeletal remodeling and overexpressed proteins associated with transcriptional and translational activity. Taken together, our findings indicate that UM-CLL cells are less migratory and more adhesive than M-CLL cells, resulting in their retention in lymph nodes, where they are exposed to proliferative stimuli. In keeping with this hypothesis, analysis of an extended cohort of 120 CLL patients revealed a strong and specific association between UM-CLL and lymphadenopathy. Our study illustrates the potential of total proteome analysis to elucidate pathogenetic mechanisms in cancer. PMID:25645933

  14. Association between fish consumption, long chain omega 3 fatty acids, and risk of cerebrovascular disease: systematic review and meta-analysis

    PubMed Central

    Chowdhury, Rajiv; Stevens, Sarah; Gorman, Donal; Pan, An; Warnakula, Samantha; Chowdhury, Susmita; Ward, Heather; Johnson, Laura; Crowe, Francesca; Hu, Frank B

    2012-01-01

    Objective To clarify associations of fish consumption and long chain omega 3 fatty acids with risk of cerebrovascular disease for primary and secondary prevention. Design Systematic review and meta-analysis. Data sources Studies published before September 2012 identified through electronic searches using Medline, Embase, BIOSIS, and Science Citation Index databases. Eligibility criteria Prospective cohort studies and randomised controlled trials reporting on associations of fish consumption and long chain omega 3 fatty acids (based on dietary self report), omega 3 fatty acids biomarkers, or supplementations with cerebrovascular disease (defined as any fatal or non-fatal ischaemic stroke, haemorrhagic stroke, cerebrovascular accident, or transient ischaemic attack). Both primary and secondary prevention studies (comprising participants with or without cardiovascular disease at baseline) were eligible. Results 26 prospective cohort studies and 12 randomised controlled trials with aggregate data on 794 000 non-overlapping people and 34 817 cerebrovascular outcomes were included. In cohort studies comparing categories of fish intake the pooled relative risk for cerebrovascular disease for 2-4 servings a week versus ≤1 servings a week was 0.94 (95% confidence intervals 0.90 to 0.98) and for ≥5 servings a week versus 1 serving a week was 0.88 (0.81 to 0.96). The relative risk for cerebrovascular disease comparing the top thirds of baseline long chain omega 3 fatty acids with the bottom thirds for circulating biomarkers was 1.04 (0.90 to 1.20) and for dietary exposures was 0.90 (0.80 to 1.01). In the randomised controlled trials the relative risk for cerebrovascular disease in the long chain omega 3 supplement compared with the control group in primary prevention trials was 0.98 (0.89 to 1.08) and in secondary prevention trials was 1.17 (0.99 to 1.38). For fish or omega 3 fatty acids the estimates for ischaemic and haemorrhagic cerebrovascular events were broadly

  15. Quantitative proteomic analysis reveals metabolic alterations, calcium dysregulation, and increased expression of extracellular matrix proteins in laminin α2 chain-deficient muscle.

    PubMed

    de Oliveira, Bruno Menezes; Matsumura, Cintia Y; Fontes-Oliveira, Cibely C; Gawlik, Kinga I; Acosta, Helena; Wernhoff, Patrik; Durbeej, Madeleine

    2014-11-01

    Congenital muscular dystrophy with laminin α2 chain deficiency (MDC1A) is one of the most severe forms of muscular disease and is characterized by severe muscle weakness and delayed motor milestones. The genetic basis of MDC1A is well known, yet the secondary mechanisms ultimately leading to muscle degeneration and subsequent connective tissue infiltration are not fully understood. In order to obtain new insights into the molecular mechanisms underlying MDC1A, we performed a comparative proteomic analysis of affected muscles (diaphragm and gastrocnemius) from laminin α2 chain-deficient dy(3K)/dy(3K) mice, using multidimensional protein identification technology combined with tandem mass tags. Out of the approximately 700 identified proteins, 113 and 101 proteins, respectively, were differentially expressed in the diseased gastrocnemius and diaphragm muscles compared with normal muscles. A large portion of these proteins are involved in different metabolic processes, bind calcium, or are expressed in the extracellular matrix. Our findings suggest that metabolic alterations and calcium dysregulation could be novel mechanisms that underlie MDC1A and might be targets that should be explored for therapy. Also, detailed knowledge of the composition of fibrotic tissue, rich in extracellular matrix proteins, in laminin α2 chain-deficient muscle might help in the design of future anti-fibrotic treatments. All MS data have been deposited in the ProteomeXchange with identifier PXD000978 (http://proteomecentral.proteomexchange.org/dataset/PXD000978). PMID:24994560

  16. A quantitative analysis of Propionibacterium acnes in lesional and non-lesional skin of patients with progressive macular hypomelanosis by real-time polymerase chain reaction

    PubMed Central

    de Morais Cavalcanti, Silvana Maria; de França, Emmanuel Rodrigues; Magalhães, Marcelo; Lins, Ana Kelly; Brandão, Laura Costa; Magalhães, Vera

    2011-01-01

    Little is known about the etiology of progressive macular hypomelanosis, although it has been suggested that Propionibacterium acnes plays an important role. While microbiological culture is commonly employed to identify Propionibacterium acnes, new identification methods have been under investigation, amongst them polymerase chain reaction. To determine the cut-off point for the number of genome copies of Propionibacterium acnes in the lesional skin of patients with progressive macular hypomelanosis as a positive marker, employing quantitative real-time polymerase chain reaction and anaerobic culture, considered gold standard. An observational study with a comparison group, included 35 patients with dermatosis, attended at the Oswaldo Cruz University Hospital, Pernambuco, Brazil, between March and May 2008. Lesional skin was compared to non-lesional skin through positive testing with real-time polymerase chain reaction and culture. The Statistical Package for Social Sciences, version 12.0, was employed for the association analysis with the McNemar test, and the cut-off point with the ROC curve for maximum values. Propionibacterium acnes was most frequently encountered in lesional areas (p<0,025). The cut-off point of Propionibacterium acnes in lesional skin was 1,333 genome copies, with a sensitivity of 87,9% and a specificity of 100,0%. Since Propionibacterium acnes is a saprophyte, identifying the cut-off point may assist in determining its positivity in lesional skin in patients suffering with this dermatosis. PMID:24031649

  17. Exploration Supply Chain Simulation

    NASA Technical Reports Server (NTRS)

    2008-01-01

    The Exploration Supply Chain Simulation project was chartered by the NASA Exploration Systems Mission Directorate to develop a software tool, with proper data, to quantitatively analyze supply chains for future program planning. This tool is a discrete-event simulation that uses the basic supply chain concepts of planning, sourcing, making, delivering, and returning. This supply chain perspective is combined with other discrete or continuous simulation factors. Discrete resource events (such as launch or delivery reviews) are represented as organizational functional units. Continuous resources (such as civil service or contractor program functions) are defined as enabling functional units. Concepts of fixed and variable costs are included in the model to allow the discrete events to interact with cost calculations. The definition file is intrinsic to the model, but a blank start can be initiated at any time. The current definition file is an Orion Ares I crew launch vehicle. Parameters stretch from Kennedy Space Center across and into other program entities (Michaud Assembly Facility, Aliant Techsystems, Stennis Space Center, Johnson Space Center, etc.) though these will only gain detail as the file continues to evolve. The Orion Ares I file definition in the tool continues to evolve, and analysis from this tool is expected in 2008. This is the first application of such business-driven modeling to a NASA/government-- aerospace contractor endeavor.

  18. Exploratory Analysis of Fast-Food Chain Restaurant Menus Before and After Implementation of Local Calorie-Labeling Policies, 2005–2011

    PubMed Central

    Namba, Alexa; Leonberg, Beth L.; Wootan, Margo G.

    2013-01-01

    Introduction Since 2008, several states and municipalities have implemented regulations requiring provision of nutrition information at chain restaurants to address obesity. Although early research into the effect of such labels on consumer decisions has shown mixed results, little information exists on the restaurant industry’s response to labeling. The objective of this exploratory study was to evaluate the effect of menu labeling on fast-food menu offerings over 7 years, from 2005 through 2011. Methods Menus from 5 fast-food chains that had outlets in jurisdictions subject to menu-labeling laws (cases) were compared with menus from 4 fast-food chains operating in jurisdictions not requiring labeling (controls). A trend analysis assessed whether case restaurants improved the healthfulness of their menus relative to the control restaurants. Results Although the overall prevalence of “healthier” food options remained low, a noteworthy increase was seen after 2008 in locations with menu-labeling laws relative to those without such laws. Healthier food options increased from 13% to 20% at case locations while remaining static at 8% at control locations (test for difference in the trend, P = .02). Since 2005, the average calories for an à la carte entrée remained moderately high (approximately 450 kilocalories), with less than 25% of all entrées and sides qualifying as healthier and no clear systematic differences in the trend between chain restaurants in case versus control areas (P ≥ .50). Conclusion These findings suggest that menu labeling has thus far not affected the average nutritional content of fast-food menu items, but it may motivate restaurants to increase the availability of healthier options. PMID:23786908

  19. A Comparison of Bayesian Monte Carlo Markov Chain and Maximum Likelihood Estimation Methods for the Statistical Analysis of Geodetic Time Series

    NASA Astrophysics Data System (ADS)

    Olivares, G.; Teferle, F. N.

    2013-12-01

    Geodetic time series provide information which helps to constrain theoretical models of geophysical processes. It is well established that such time series, for example from GPS, superconducting gravity or mean sea level (MSL), contain time-correlated noise which is usually assumed to be a combination of a long-term stochastic process (characterized by a power-law spectrum) and random noise. Therefore, when fitting a model to geodetic time series it is essential to also estimate the stochastic parameters beside the deterministic ones. Often the stochastic parameters include the power amplitudes of both time-correlated and random noise, as well as, the spectral index of the power-law process. To date, the most widely used method for obtaining these parameter estimates is based on maximum likelihood estimation (MLE). We present an integration method, the Bayesian Monte Carlo Markov Chain (MCMC) method, which, by using Markov chains, provides a sample of the posteriori distribution of all parameters and, thereby, using Monte Carlo integration, all parameters and their uncertainties are estimated simultaneously. This algorithm automatically optimizes the Markov chain step size and estimates the convergence state by spectral analysis of the chain. We assess the MCMC method through comparison with MLE, using the recently released GPS position time series from JPL and apply it also to the MSL time series from the Revised Local Reference data base of the PSMSL. Although the parameter estimates for both methods are fairly equivalent, they suggest that the MCMC method has some advantages over MLE, for example, without further computations it provides the spectral index uncertainty, is computationally stable and detects multimodality.

  20. Analysis of T cell receptor-gamma gene rearrangements by denaturing gradient gel electrophoresis of GC-clamped polymerase chain reaction products. Correlation with tumor-specific sequences.

    PubMed Central

    Greiner, T. C.; Raffeld, M.; Lutz, C.; Dick, F.; Jaffe, E. S.

    1995-01-01

    We describe a modified denaturing gradient gel electrophoresis (DGGE) procedure with a 40-nucleotide GC clamp in the polymerase chain reaction to improve resolution in amplifying T cell receptor-gamma (TCR-gamma) rearrangements. DNA from 46 cases of lymphoblastic leukemia/lymphoma, 5T cell lines, 2 B cell lines, 7 normal lymphocytes, and 3 cases of Hodgkin's disease was amplified by polymerase chain reaction. In addition, 20 cases of paraffin-embedded T cell lymphomas and 5 cases of reactive hyperplasia were also studied. Clonal TCR-gamma rearrangements were identified on DGGE by the presence of a predominant band. Results obtained from 5 T cell lines and 12 lymphoblastic leukemia/lymphomas containing known TCR-gamma gene rearrangements revealed 100% concordance in detecting clonal rearrangements between DGGE and traditional Southern blot analysis. Of the remaining 34 lymphoblastic leukemia/lymphoma cases studied by DGGE alone, 30 were positive. DGGE analysis of 10 lymphoblastic leukemia/lymphoma cases with known group IV gamma to J gamma 1 or J gamma 2 rearrangement sequences confirmed that the electrophoretic migration was dependent on the tumor-specific rearranged TCR-gamma sequence. In addition, 17 of 20 cases of paraffin-embedded T cell lymphomas were positive by DGGE, 6 of which had the clonal population also identified in fresh tissue DNA. DGGE analysis of GC-clamped polymerase chain reaction products can provide a way to more accurately detect TCR-gamma clonality of lymphoid tumors and can be applied to archival tissues. Images Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 PMID:7856738

  1. Chain networking revealed by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing

    Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)

  2. Crater Chains

    NASA Technical Reports Server (NTRS)

    2003-01-01

    [figure removed for brevity, see original site]

    The large crater at the top of this THEMIS visible image has several other craters inside of it. Most noticeable are the craters that form a 'chain' on the southern wall of the large crater. These craters are a wonderful example of secondary impacts. They were formed when large blocks of ejecta from an impact crashed back down onto the surface of Mars. Secondaries often form radial patterns around the impact crater that generated them, allowing researchers to trace them back to their origin.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

    Image information: VIS instrument. Latitude 19.3, Longitude 347.5 East (12.5 West). 19 meter/pixel resolution.

  3. A Unique Primer with an Inosine Chain at the 5′-Terminus Improves the Reliability of SNP Analysis Using the PCR-Amplified Product Length Polymorphism Method

    PubMed Central

    Shojo, Hideki; Tanaka, Mayumi; Takahashi, Ryohei; Kakuda, Tsuneo; Adachi, Noboru

    2015-01-01

    Polymerase chain reaction-amplified product length polymorphism (PCR-APLP) is one of the most convenient and reliable methods for single nucleotide polymorphism (SNP) analysis. This method is based on PCR, but uses allele-specific primers containing SNP sites at the 3′-terminus of each primer. To use this method at least two allele-specific primers and one “counter-primer”, which serves as a common forward or reverse primer of the allele-specific primers, are required. The allele-specific primers have SNP sites at the 3′-terminus, and another primer should have a few non-complementary flaps at the 5′-terminus to detect SNPs by determining the difference of amplicon length by PCR and subsequent electrophoresis. A major disadvantage of the addition of a non-complementary flap is the non-specific annealing of the primer with non-complementary flaps. However, a design principle for avoiding this undesired annealing has not been fully established, therefore, it is often difficult to design effective APLP primers. Here, we report allele-specific primers with an inosine chain at the 5′-terminus for PCR-APLP analysis. This unique design improves the competitiveness of allele-specific primers and the reliability of SNP analysis when using the PCR-APLP method. PMID:26381262

  4. A facile and fully automated on-fiber derivatization protocol for direct analysis of short-chain aliphatic amines using a matrix compatible solid-phase microextraction coating.

    PubMed

    Gionfriddo, Emanuela; Passarini, Alice; Pawliszyn, Janusz

    2016-07-29

    Solid-phase microextraction (SPME) analysis of short-chain aliphatic amines (C3-C6) in aqueous solutions was investigated using pentafluorobenzaldehyde (PFBAY) as on-fiber derivatization reagent. A standard gas generating vial agent was used for on-fiber loading of the derivatization agent so as to avoid the need for its regeneration at each derivatization cycle. Several parameters such as loading time, reaction temperature, and reaction/extraction time were optimized for headspace and direct sampling in aqueous solutions. Three different coating chemistries were tested and their performances compared in order to achieve the best compromise between sensitivity and analysis throughput. The newly developed PDMS/DVB/PDMS coating showed superior performance in terms of extraction efficiency while the capability to prevent on-fiber degradation of the derivatizing products. The optimized method was used for quantitation of short-chain aliphatic amines in aqueous samples and provided detection limits in the low ppb range for all the amines tested with accuracy values between 79 and 120%. The method was applied towards the analysis of environmental water samples and the accuracy of the results was evaluated by different calibration approaches. PMID:27371022

  5. Insight into earthquake sequencing: analysis and interpretation of time-series constructed from the directed graph of the Markov chain model

    NASA Astrophysics Data System (ADS)

    Cavers, M. S.; Vasudevan, K.

    2015-02-01

    Directed graph representation of a Markov chain model to study global earthquake sequencing leads to a time-series of state-to-state transition probabilities that includes the spatio-temporally linked recurrent events in the record-breaking sense. A state refers to a configuration comprised of zones with either the occurrence or non-occurrence of an earthquake in each zone in a pre-determined time interval. Since the time-series is derived from non-linear and non-stationary earthquake sequencing, we use known analysis methods to glean new information. We apply decomposition procedures such as ensemble empirical mode decomposition (EEMD) to study the state-to-state fluctuations in each of the intrinsic mode functions. We subject the intrinsic mode functions, the orthogonal basis set derived from the time-series using the EEMD, to a detailed analysis to draw information-content of the time-series. Also, we investigate the influence of random-noise on the data-driven state-to-state transition probabilities. We consider a second aspect of earthquake sequencing that is closely tied to its time-correlative behavior. Here, we extend the Fano factor and Allan factor analysis to the time-series of state-to state transition frequencies of a Markov chain. Our results support not only the usefulness the intrinsic mode functions in understanding the time-series but also the presence of power-law behaviour exemplified by the Fano factor and the Allan factor.

  6. Integrated Markov Chain Monte Carlo (MCMC) analysis of primordial non-Gaussianity (f{sub NL}) in the recent CMB data

    SciTech Connect

    Kim, Jaiseung

    2011-04-01

    We have made a Markov Chain Monte Carlo (MCMC) analysis of primordial non-Gaussianity (f{sub NL}) using the WMAP bispectrum and power spectrum. In our analysis, we have simultaneously constrained f{sub NL} and cosmological parameters so that the uncertainties of cosmological parameters can properly propagate into the f{sub NL} estimation. Investigating the parameter likelihoods deduced from MCMC samples, we find slight deviation from Gaussian shape, which makes a Fisher matrix estimation less accurate. Therefore, we have estimated the confidence interval of f{sub NL} by exploring the parameter likelihood without using the Fisher matrix. We find that the best-fit values of our analysis make a good agreement with other results, but the confidence interval is slightly different.

  7. Performance of Polymerase Chain Reaction Analysis of the Amniotic Fluid of Pregnant Women for Diagnosis of Congenital Toxoplasmosis: A Systematic Review and Meta-Analysis

    PubMed Central

    2016-01-01

    Introduction Congenital infection caused by Toxoplasma gondii can cause serious damage that can be diagnosed in utero or at birth, although most infants are asymptomatic at birth. Prenatal diagnosis of congenital toxoplasmosis considerably improves the prognosis and outcome for infected infants. For this reason, an assay for the quick, sensitive, and safe diagnosis of fetal toxoplasmosis is desirable. Goal To systematically review the performance of polymerase chain reaction (PCR) analysis of the amniotic fluid of pregnant women with recent serological toxoplasmosis diagnoses for the diagnosis of fetal toxoplasmosis. Method A systematic literature review was conducted via a search of electronic databases; the literature included primary studies of the diagnostic accuracy of PCR analysis of amniotic fluid from pregnant women who seroconverted during pregnancy. The PCR test was compared to a gold standard for diagnosis. Results A total of 1.269 summaries were obtained from the electronic database and reviewed, and 20 studies, comprising 4.171 samples, met the established inclusion criteria and were included in the review. The following results were obtained: studies about PCR assays for fetal toxoplasmosis are generally susceptible to bias; reports of the tests’ use lack critical information; the protocols varied among studies; the heterogeneity among studies was concentrated in the tests’ sensitivity; there was evidence that the sensitivity of the tests increases with time, as represented by the trimester; and there was more heterogeneity among studies in which there was more time between maternal diagnosis and fetal testing. The sensitivity of the method, if performed up to five weeks after maternal diagnosis, was 87% and specificity was 99%. Conclusion The global sensitivity heterogeneity of the PCR test in this review was 66.5% (I2). The tests show low evidence of heterogeneity with a sensitivity of 87% and specificity of 99% when performed up to five weeks

  8. A novel multiplexing, polymerase chain reaction-based assay for the analysis of chromosome 18q status in colorectal cancer.

    PubMed

    Erill, Nadina; Colomer, Anna; Calvo, Miquel; Vidal, August; Román, Ruth; Verdú, Montse; Cordón-Cardó, Carlos; Puig, Xavier

    2005-10-01

    Chromosome 18q allelic loss has been reported to have prognostic significance in stage II colorectal carcinoma. We have developed a fluorescent multiplex polymerase chain reaction assay to analyze five microsatellite markers (D18S55, D18S58, D18S61, D18S64, and D18S69) for allelic loss at the long arm of chromosome 18. Amplicon detection and evaluation was accomplished by capillary electrophoresis using an ABI 310 genetic analyzer. Robustness of the assay when performed on DNA extracted from formalin-fixed, paraffin-embedded tissue sections was confirmed by analyzing its repeatability and reproducibility. Allelic loss was assessed in 61 stage II colorectal tumors and was detected in 58% (31 of 53) of tumors not showing instability. As part of the study, results of 207 previous polymerase chain reaction/polyacrylamide-based assays were re-evaluated by two independent observers to determine the degree of concordance of visual evaluation. In the case of stage II colorectal tumors, when electropherogram results were compared with those obtained from visual evaluation of the same markers after polyacrylamide gel electrophoresis, discrepancies between observers were detected in 16.4% of determinations. In conclusion, we have developed a robust and reliable assay for multiplexed loss of heterozygosity determination that improves assessment of chromosome 18q allelic loss in colorectal tumors processed as routine formalin-fixed, paraffin-embedded specimens. PMID:16237217

  9. Resonance Assignments and Secondary Structure Analysis of Dynein Light Chain 8 by Magic-angle Spinning NMR Spectroscopy

    SciTech Connect

    Sun, Shangjin; Butterworth, Andrew H.; Paramasivam, Sivakumar; Yan, Si; Lightcap, Christine M.; Williams, John C.; Polenova, Tatyana E.

    2011-08-04

    Dynein light chain LC8 is the smallest subunit of the dynein motor complex and has been shown to play important roles in both dynein-dependent and dynein-independent physiological functions via its interaction with a number of its binding partners. It has also been linked to pathogenesis including roles in viral infections and tumorigenesis. Structural information for LC8-target proteins is critical to understanding the underlying function of LC8 in these complexes. However, some LC8-target interactions are not amenable to structural characterization by conventional structural biology techniques owing to their large size, low solubility, and crystallization difficulties. Here, we report magic-angle spinning (MAS) NMR studies of the homodimeric apo-LC8 protein as a first effort in addressing more complex, multi-partner, LC8-based protein assemblies. We have established site-specific backbone and side-chain resonance assignments for the majority of the residues of LC8, and show TALOS+-predicted torsion angles ø and ψ in close agreement with most residues in the published LC8 crystal structure. Data obtained through these studies will provide the first step toward using MAS NMR to examine the LC8 structure, which will eventually be used to investigate protein–protein interactions in larger systems that cannot be determined by conventional structural studies.

  10. Analysis of chain saw lubricating oils commonly used in Thailand's southern border provinces for forensic science purpose.

    PubMed

    Choodum, Aree; Tripuwanard, Kijja; Daeid, Niamh Nic

    2014-08-01

    In recent years, Thailand's southern border provinces (Malay-Muslim-majority border provinces) have become the scene of violence and insurgency. One of the attack patterns is the blocking of roads with perennial plants followed by planned attacks using improvised explosive devices (IEDs) or weapons on first responders. Containers of viscous dark lubricating oil and traces of lubricants on the felled trees were usually found at the scene. These were suspected to be chain oil lubricant from the chainsaws used to cut down the trees used for the roadblock. This work aimed to differentiate the chromatographic patterns of used lubricating oils available in automobile repair shops from various locations across Thailand's southern border provinces. Lubricating oils were analyzed using gas chromatography/flame ionization detector (GC/FID) every two weeks to study their variation in chemical compositions over time. The results obtained from GC/FID were normalized for differentiation. This included four two-stroke, six four-stroke, and three recycled oils. Two lubricating oils found at an incident scene were also analyzed and the results compared with the chain oil from five seized chainsaws. PMID:24875837

  11. Extensive analysis of D-J-C arrangements allows the identification of different mechanisms enhancing the diversity in sheep T cell receptor β-chain repertoire

    PubMed Central

    2010-01-01

    Background In most species of mammals, the TRB locus has the common feature of a library of TRBV genes positioned at the 5'- end of two in tandem aligned D-J-C gene clusters, each composed of a single TRBD gene, 6-7 TRBJ genes and one TRBC gene. An enhancer located at the 3'end of the last TRBC and a well-defined promoter situated at the 5'end of the TRBD gene and/or a undefined promoter situated at the 5'end of the TRBD2 are sufficient to generate the full recombinase accessibility at the locus. In ruminant species, the 3'end of the TRB locus is characterized by the presence of three D-J-C clusters, each constituted by a single TRBD, 5-7 TRBJ and one TRBC genes with the center cluster showing a structure combined with the clusters upstream and downstream, suggesting that a unequal crossover occurred in the duplication. An enhancer downstream the last TRBC, and a promoter at the 5'-end of each TRBD gene are also present. Results In this paper we focused our attention on the analysis of a large number of sheep TR β-chain transcripts derived from four different lymphoid tissues of three diverse sheep breed animals to certify the use and frequency of the three gene clusters in the β-chain repertoire. As the sheep TRB locus genomic organization is known, the exact interpretation of the V-D-J rearrangements was fully determined. Our results clearly demonstrate that sheep β-chain constitutes a level of variability that is substantially larger than that described in other mammalian species. This is due not only to the increase of the number of D and J genes available to the somatic recombination, but also to the presence of the trans-rearrangement process. Moreover, the functional complexity of β-chain repertoire is resolved by other mechanisms such as alternative cis- and trans-splicing and recombinational diversification that seems to affect the variety of the constant region. Conclusion All together our data demonstrate that a disparate set of molecular mechanisms

  12. Food Chain Security and Vulnerability

    NASA Astrophysics Data System (ADS)

    Brunet, Sébastien; Delvenne, Pierre; Claisse, Frédéric

    In our contemporary societies, the food chain could be defined as a macro-technical system, which depends on a wide variety of actors and risks analysis methods. In this contribution, risks related to the food chain are defined in terms of "modern risks" (Beck 1992). The whole national economic sector of food production/distribution is vulnerable to a local accident, which can affect the functioning of food chain, the export programs and even the political system. Such a complex socio-technical environment is undoubtedly vulnerable to intentional act such as terrorism.

  13. Mitochondrial DNA variation in chinook salmon and chum salmon detected by restriction enzyme analysis of polymerase chain reaction products

    USGS Publications Warehouse

    Cronin, M.; Spearman, R.; Wilmot, R.; Patton, J.; Bickman, J.

    1993-01-01

    We analyze intraspecific mitochondrial DNA variation in chinook salmon from drainages in the Yukon River, the Kenai River, and Oregon and California rivers; and chum salmon from the Yukon River and vancouver Island, and Washington rivers. For each species, three different portions of the mtDNA molecule were amplified seperately using the polymerase chain reaction and then digested with at least 19 restrictions enzymes. Intraspecific sequence divergences between haplotypes were less than 0.01 base subsitution per nucleotide. Nine chum salmon haplotypes were identified. Yukon River chum salmon stocks displayed more haplotypes (8) occurred in all areas. Seven chinook salmon haplotypes were identified. Four haplotypes occurred in the Yukon and Kenai rviers and four occured in the Oregon/California, with only one haplotype shared between the regions. Sample sizes were too small to quantify the degree of stock seperation among drainages, but the patterns of variation that we observed suggest utility of the technique in genetic stock identification.

  14. Analysis of ancient DNA from coprolites: a perspective with random amplified polymorphic DNA-polymerase chain reaction approach.

    PubMed

    Iñiguez, Alena M; Araújo, Adauto; Ferreira, Luiz Fernando; Vicente, Ana Carolina P

    2003-01-01

    The aim of this work was to determine approaches that would improve the quality of ancient DNA (aDNA) present in coprolites to enhance the possibility of success in retrieving specific sequence targets. We worked with coprolites from South American archaeological sites in Brazil and Chile dating up to 7,000 years ago. Using established protocols for aDNA extraction we obtained samples showing high degradation as usually happens with this kind of material. The reconstructive polymerization pretreatment was essential to overcome the DNA degradation and the serial dilutions helped with to prevent polymerase chain reaction (PCR) inhibitors. Moreover, the random amplified polymorphic DNA-PCR has been shown to be a reliable technique for further experiments to recover specific aDNA sequences. PMID:12687765

  15. Genetic analysis of the Pseudomonas aeruginosa PAO high-affinity branched-chain amino acid transport system by use of plasmids carrying the bra genes.

    PubMed Central

    Hoshino, T; Kose, K

    1990-01-01

    About 30 mutants of Pseudomonas aeruginosa PAO defective in the high-affinity branched-chain amino acid transport system (LIV-I) were isolated by the selection for resistance to 4-aza-DL-leucine, a toxic leucine analog for LIV-I. All of the mutants were complemented by plasmid pKTH24, harboring the braC gene, which encodes the branched-chain amino acid-binding protein, and the four open reading frames named braD, braE, braF, and braG (T. Hoshino and K. Kose, J. Bacteriol. 172:5531-5539, 1990). We identified five cistrons corresponding to these bra genes by complementation analysis with various derivatives of pKTH24, confirming that the braD, braE, braF, and braG genes are required for the LIV-I transport system. We also found mutations that seem likely to be mutations in a promoter region for the bra genes and those with polarity in the intercistronic region between braC and braD. Analysis with an omega interposon showed that the bra genes are organized as an operon and are cotranscribed in the order braC-braD-braE-braF-braG from a promoter located in the 5'-flanking region of the braC gene. PMID:2120184

  16. Identification of mycobacteria from animals by restriction enzyme analysis and direct DNA cycle sequencing of polymerase chain reaction-amplified 16S rRNA gene sequences.

    PubMed Central

    Hughes, M S; Skuce, R A; Beck, L A; Neill, S D

    1993-01-01

    Two methods, based on analysis of the polymerase chain reaction-amplified 16S rRNA gene by restriction enzyme analysis (REA) or direct cycle sequencing, were developed for rapid identification of mycobacteria isolated from animals and were compared to traditional phenotypic typing. BACTEC 7H12 cultures of the specimens were examined for "cording," and specific polymerase chain reaction amplification was performed to identify the presence of tubercle complex mycobacteria. Combined results of separate REAs with HhaI, MspI, MboI, and ThaI differentiated 12 of 15 mycobacterial species tested. HhaI, MspI, and ThaI restriction enzyme profiles differentiated Actinobacillus species from mycobacterial species. Mycobacterium bovis could not be differentiated from M. bovis BCG or Mycobacterium tuberculosis. Similarly, Mycobacterium avium and Mycobacterium paratuberculosis could not be distinguished from each other by REA but were differentiated by cycle sequencing. Compared with traditional typing, both methods allowed rapid and more accurate identification of acid-fast organisms recovered from 21 specimens of bovine and badger origin. Two groups of isolates were not typed definitively by either molecular method. One group of four isolates may constitute a new species phylogenetically very closely related to Mycobacterium simiae. The remaining unidentified isolates (three badger and one bovine) had identical restriction enzyme profiles and shared 100% nucleotide identify over the sequenced signature region. This nucleotide sequence most closely resembled the data base sequence of Mycobacterium senegalense. Images PMID:7508456

  17. Application of principal component analysis in the pollution assessment with heavy metals of vegetable food chain in the old mining areas

    PubMed Central

    2012-01-01

    Background The aim of the paper is to assess by the principal components analysis (PCA) the heavy metal contamination of soil and vegetables widely used as food for people who live in areas contaminated by heavy metals (HMs) due to long-lasting mining activities. This chemometric technique allowed us to select the best model for determining the risk of HMs on the food chain as well as on people's health. Results Many PCA models were computed with different variables: heavy metals contents and some agro-chemical parameters which characterize the soil samples from contaminated and uncontaminated areas, HMs contents of different types of vegetables grown and consumed in these areas, and the complex parameter target hazard quotients (THQ). Results were discussed in terms of principal component analysis. Conclusion There were two major benefits in processing the data PCA: firstly, it helped in optimizing the number and type of data that are best in rendering the HMs contamination of the soil and vegetables. Secondly, it was valuable for selecting the vegetable species which present the highest/minimum risk of a negative impact on the food chain and human health. PMID:23234365

  18. AI-based technique for tracking chains of discontinuous symbols and its application to the analysis of topographic maps

    NASA Astrophysics Data System (ADS)

    Mecocci, Alessandro; Lilla, Massimiliano

    1994-12-01

    Automatic digitization of topographic maps is a very important task nowadays. Among the different elements of a topographic map discontinuous lines represent important information. Generally they are difficult to track because they show very large gaps, and abrupt direction changes. In this paper an architecture that automates the digitalization of discontinuous lines (dot-dot lines, dash-dot-dash lines, dash-asterisk lines, etc.) is presented. The tracking process must detect the elementary symbols and then concatenate these symbols into a significant chain that represents the line. The proposed architecture is composed of a common kernel, based on a suitable modification of the A* algorithm, that starts different auxiliary processes depending on the particular line to be tracked. Three auxiliary processes are considered: search strategy generation (SSG) which is responsible for the strategy used to scan the image pixels; low level symbol detection (LSD) which decides if a certain image region around the pixel selected by the SSG is an elementary symbol; cost evaluation (CE) which gives the quality of each symbol with respect to the global course of the line. The whole system has been tested on a 1:50.000 map furnished by the Istituto Geografico Militare Italiano (IGMI). The results were very good for different types of discontinuous lines. Over the whole map (i.e. about 80 Mbytes of digitized data) 95% of the elementary symbols of the lines have been correctly chained. The operator time required to correct misclassifications is a small part of the time needed to manually digitize the discontinuous lines.

  19. Efficient Markov Chain Monte Carlo Implementation of Bayesian Analysis of Additive and Dominance Genetic Variances in Noninbred Pedigrees

    PubMed Central

    Waldmann, Patrik; Hallander, Jon; Hoti, Fabian; Sillanpää, Mikko J.

    2008-01-01

    Accurate and fast computation of quantitative genetic variance parameters is of great importance in both natural and breeding populations. For experimental designs with complex relationship structures it can be important to include both additive and dominance variance components in the statistical model. In this study, we introduce a Bayesian Gibbs sampling approach for estimation of additive and dominance genetic variances in the traditional infinitesimal model. The method can handle general pedigrees without inbreeding. To optimize between computational time and good mixing of the Markov chain Monte Carlo (MCMC) chains, we used a hybrid Gibbs sampler that combines a single site and a blocked Gibbs sampler. The speed of the hybrid sampler and the mixing of the single-site sampler were further improved by the use of pretransformed variables. Two traits (height and trunk diameter) from a previously published diallel progeny test of Scots pine (Pinus sylvestris L.) and two large simulated data sets with different levels of dominance variance were analyzed. We also performed Bayesian model comparison on the basis of the posterior predictive loss approach. Results showed that models with both additive and dominance components had the best fit for both height and diameter and for the simulated data with high dominance. For the simulated data with low dominance, we needed an informative prior to avoid the dominance variance component becoming overestimated. The narrow-sense heritability estimates in the Scots pine data were lower compared to the earlier results, which is not surprising because the level of dominance variance was rather high, especially for diameter. In general, the hybrid sampler was considerably faster than the blocked sampler and displayed better mixing properties than the single-site sampler. PMID:18558655

  20. Efficient Markov chain Monte Carlo implementation of Bayesian analysis of additive and dominance genetic variances in noninbred pedigrees.

    PubMed

    Waldmann, Patrik; Hallander, Jon; Hoti, Fabian; Sillanpää, Mikko J

    2008-06-01

    Accurate and fast computation of quantitative genetic variance parameters is of great importance in both natural and breeding populations. For experimental designs with complex relationship structures it can be important to include both additive and dominance variance components in the statistical model. In this study, we introduce a Bayesian Gibbs sampling approach for estimation of additive and dominance genetic variances in the traditional infinitesimal model. The method can handle general pedigrees without inbreeding. To optimize between computational time and good mixing of the Markov chain Monte Carlo (MCMC) chains, we used a hybrid Gibbs sampler that combines a single site and a blocked Gibbs sampler. The speed of the hybrid sampler and the mixing of the single-site sampler were further improved by the use of pretransformed variables. Two traits (height and trunk diameter) from a previously published diallel progeny test of Scots pine (Pinus sylvestris L.) and two large simulated data sets with different levels of dominance variance were analyzed. We also performed Bayesian model comparison on the basis of the posterior predictive loss approach. Results showed that models with both additive and dominance components had the best fit for both height and diameter and for the simulated data with high dominance. For the simulated data with low dominance, we needed an informative prior to avoid the dominance variance component becoming overestimated. The narrow-sense heritability estimates in the Scots pine data were lower compared to the earlier results, which is not surprising because the level of dominance variance was rather high, especially for diameter. In general, the hybrid sampler was considerably faster than the blocked sampler and displayed better mixing properties than the single-site sampler. PMID:18558655

  1. TaClo as a neurotoxic lead: improved synthesis, stereochemical analysis, and inhibition of the mitochondrial respiratory chain.

    PubMed

    Bringmann, G; God, R; Feineis, D; Janetzky, B; Reichmann, H

    1995-01-01

    "TaClo", a highly halogenated tetrahydro-beta-carboline derived from the biogenic amine tryptamine ("Ta") and the synthetic hypnotic chloral ("Clo"), has to be considered as a dopaminergic neurotoxin potentially occurring in vivo. For the preparation of TaClo on a large scale, an improved synthetic pathway was elaborated. The distinct neurotoxic activity of TaClo warrants its intensive study also under stereochemical aspects. For this reason, an analytic device for the separation and stereochemical attribution of its two enantiomers, (R)-TaClo and (S)-TaClo, was developed, based on chromatography on a chiral HPLC phase. Elucidation of the absolute configuration was achieved by CD spectroscopy and confirmed by X-ray crystallography. TaClo exhibits highly selective in vitro inhibition of complex I of the mitochondrial respiratory chain, the required concentrations being much lower than those needed for related halogen-free beta-carbolines or for MPP+ (1-methyl-4-phenyl-pyridinium ion), the active metabolite of MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine). Furthermore, TaClo as a novel lead structure stimulated chemical and neuropharmacological investigations also on related highly halogenated beta-carbolines. Thus, some of the tested compounds--both potential TaClo metabolites and unnatural derivatives--showed even an enhanced inhibition of the mitochondrial respiration in vitro. PMID:8821061

  2. Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis

    USGS Publications Warehouse

    Chase, D.M.; Elliott, D.G.; Pascho, R.J.

    2006-01-01

    Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.

  3. Randomly amplified polymorphic DNA-polymerase chain reaction analysis of two different populations of cultured Korean catfish Silurus asotus.

    PubMed

    Yoon, J M; Kim, G W

    2001-12-01

    Genetic similarity and diversity of cultured catfish Silurus asotus populations collected from two areas in western Korea were examined using randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). Out of 20 random primers tested, 5 produced 1344 RAPD bands ranging from 8.2 to 13.6 polymorphic bands per primer. The polymorphic bands in these populations ranged from 56.4% to 59.6%. Polymorphic bands per lane within populations ranged from 4.9% to 5.3%. The similarity within the Kunsan population varied from 0.39 to 0.82 with a mean (+/- SD) of 0.56 +/- 0.08. The level of bandsharing values was 0.59 +/- 0.07 within the catfish population from Yesan. The genetic similarity in cultured catfish populations may have been caused because individuals from two populations were reared in the same environmental conditions or by inbreeding during several generations. However, in view of bandsharing values, polymorphic bands and also the specific major bands that were inter-population-specific, significant genetic differentiation between these populations were present even if bandsharing (BS) values were somewhat numerically different. Therefore, the number of RAPD polymorphisms identified in this study may be sufficient to permit estimating genetic similarity and diversity. However, in future, additional populations, sampling sites and individuals will be necessary to make up for these weak points. PMID:11807294

  4. Computational analysis of molecular properties and spectral characteristics of cyano-containing liquid crystals: Role of alkyl chains

    NASA Astrophysics Data System (ADS)

    Praveen, P. Lakshmi; Ojha, Durga P.

    2011-05-01

    The electronic transitions in the uv-visible range of 4'-n-alkyl-4-cyanobiphenyl (nCB) with propyl, pentyl, and heptyl groups, which are of commercial and application interests, have been studied. The uv-visible and circular dichroism spectra of nCB (n = 3,5,7) molecules have been simulated using the time dependent density functional theory Becke3-Lee-Yang-Parr hybrid functional-6-31 + G (d) method. Mulliken atomic charges for each molecule have been compared with Loewdin atomic charges to analyze the molecular charge distribution and phase stability. The highest occupied molecular orbital and lowest unoccupied molecular orbital energies corresponding to the electronic transitions in the uv-visible range have been reported. Excited states have been calculated via the configuration interaction single level with a semiempirical Hamiltonian (intermediate neglect of differential overlap method, as parametrized by Zerner and co-workers). Further, two types of calculations have been performed for model systems containing single and double molecules of nCB. Furthermore, the dimer complexes during the different modes of molecular interactions have also been studied. The interaction energies of dimer complexes have been taken into consideration in order to investigate the most energetically stable configuration. These studies are helpful for understanding the role and flexibility of end chains, in particular, phase behavior and stability.

  5. In vivo analysis of fibroin heavy chain signal peptide of silkworm Bombyx mori using recombinant baculovirus as vector

    SciTech Connect

    Wang Shengpeng; Guo Tingqing; Guo Xiuyang; Huang Junting; Lu Changde . E-mail: cdlu@sibs.ac.cn

    2006-03-24

    In order to investigate the functional signal peptide of silkworm fibroin heavy chain (FibH) and the effect of N- and C-terminal parts of FibH on the secretion of FibH in vivo, N- and C-terminal segments of fibh gene were fused with enhanced green fluorescent protein (EGFP) gene. The fused gene was then introduced into silkworm larvae and expressed in silk gland using recombinant AcMNPV (Autographa californica multiple nuclear polyhedrosis virus) as vector. The fluorescence of EGFP was observed with fluorescence microscope. FibH-EGFP fusion proteins extracted from silk gland were analyzed by Western blot. Results showed that the two alpha helices within N-terminal 163 amino acid residues and the C-terminal 61 amino acid residues were not necessary for cleavage of signal peptide and secretion of the fusion protein into silk gland. Then the C-terminal 61 amino acid residues were substituted with a His-tag in the fusion protein to facilitate the purification. N-terminal sequencing of the purified protein showed that the signal cleavage site is between position 21 and 22 amino acid residues.

  6. Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis.

    PubMed

    Chase, Dorothy M; Elliott, Diane G; Pascho, Ronald J

    2006-07-01

    Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids. PMID:16921877

  7. A Comprehensive Analysis of the Phylogeny, Genomic Organization and Expression of Immunoglobulin Light Chain Genes in Alligator sinensis, an Endangered Reptile Species

    PubMed Central

    Lu, Yan; Zhang, Chenglin; Wu, Xiaobing; Han, Haitang; Zhao, Yaofeng; Ren, Liming

    2016-01-01

    Crocodilians are evolutionarily distinct reptiles that are distantly related to lizards and are thought to be the closest relatives of birds. Compared with birds and mammals, few studies have investigated the Ig light chain of crocodilians. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization of the Alligator sinensis IgL gene loci. The Alligator sinensis has two IgL isotypes, λ and κ, the same as Anolis carolinensis. The Igλ locus contains 6 Cλ genes, each preceded by a Jλ gene, and 86 potentially functional Vλ genes upstream of (Jλ-Cλ)n. The Igκ locus contains a single Cκ gene, 6 Jκs and 62 functional Vκs. All VL genes are classified into a total of 31 families: 19 Vλ families and 12 Vκ families. Based on an analysis of the chromosomal location of the light chain genes among mammals, birds, lizards and frogs, the data further confirm that there are two IgL isotypes in the Alligator sinensis: Igλ and Igκ. By analyzing the cloned Igλ/κ cDNA, we identified a biased usage pattern of V families in the expressed Vλ and Vκ. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed λ and κ sequences. Phylogenetic analysis of the V genes revealed V families shared by mammals, birds, reptiles and Xenopus, suggesting that these conserved V families are orthologous and have been retained during the evolution of IgL. Our data suggest that the Alligator sinensis IgL gene repertoire is highly diverse and complex and provide insight into immunoglobulin gene evolution in vertebrates. PMID:26901135

  8. A Comprehensive Analysis of the Phylogeny, Genomic Organization and Expression of Immunoglobulin Light Chain Genes in Alligator sinensis, an Endangered Reptile Species.

    PubMed

    Wang, Xifeng; Cheng, Gang; Lu, Yan; Zhang, Chenglin; Wu, Xiaobing; Han, Haitang; Zhao, Yaofeng; Ren, Liming

    2016-01-01

    Crocodilians are evolutionarily distinct reptiles that are distantly related to lizards and are thought to be the closest relatives of birds. Compared with birds and mammals, few studies have investigated the Ig light chain of crocodilians. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization of the Alligator sinensis IgL gene loci. The Alligator sinensis has two IgL isotypes, λ and κ, the same as Anolis carolinensis. The Igλ locus contains 6 Cλ genes, each preceded by a Jλ gene, and 86 potentially functional Vλ genes upstream of (Jλ-Cλ)n. The Igκ locus contains a single Cκ gene, 6 Jκs and 62 functional Vκs. All VL genes are classified into a total of 31 families: 19 Vλ families and 12 Vκ families. Based on an analysis of the chromosomal location of the light chain genes among mammals, birds, lizards and frogs, the data further confirm that there are two IgL isotypes in the Alligator sinensis: Igλ and Igκ. By analyzing the cloned Igλ/κ cDNA, we identified a biased usage pattern of V families in the expressed Vλ and Vκ. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed λ and κ sequences. Phylogenetic analysis of the V genes revealed V families shared by mammals, birds, reptiles and Xenopus, suggesting that these conserved V families are orthologous and have been retained during the evolution of IgL. Our data suggest that the Alligator sinensis IgL gene repertoire is highly diverse and complex and provide insight into immunoglobulin gene evolution in vertebrates. PMID:26901135

  9. Frequent expression loss of Inter-alpha-trypsin inhibitor heavy chain (ITIH) genes in multiple human solid tumors: A systematic expression analysis

    PubMed Central

    Hamm, Alexander; Veeck, Juergen; Bektas, Nuran; Wild, Peter J; Hartmann, Arndt; Heindrichs, Uwe; Kristiansen, Glen; Werbowetski-Ogilvie, Tamra; Del Maestro, Rolando; Knuechel, Ruth; Dahl, Edgar

    2008-01-01

    Background The inter-alpha-trypsin inhibitors (ITI) are a family of plasma protease inhibitors, assembled from a light chain – bikunin, encoded by AMBP – and five homologous heavy chains (encoded by ITIH1, ITIH2, ITIH3, ITIH4, and ITIH5), contributing to extracellular matrix stability by covalent linkage to hyaluronan. So far, ITIH molecules have been shown to play a particularly important role in inflammation and carcinogenesis. Methods We systematically investigated differential gene expression of the ITIH gene family, as well as AMBP and the interacting partner TNFAIP6 in 13 different human tumor entities (of breast, endometrium, ovary, cervix, stomach, small intestine, colon, rectum, lung, thyroid, prostate, kidney, and pancreas) using cDNA dot blot analysis (Cancer Profiling Array, CPA), semiquantitative RT-PCR and immunohistochemistry. Results We found that ITIH genes are clearly downregulated in multiple human solid tumors, including breast, colon and lung cancer. Thus, ITIH genes may represent a family of putative tumor suppressor genes that should be analyzed in greater detail in the future. For an initial detailed analysis we chose ITIH2 expression in human breast cancer. Loss of ITIH2 expression in 70% of cases (n = 50, CPA) could be confirmed by real-time PCR in an additional set of breast cancers (n = 36). Next we studied ITIH2 expression on the protein level by analyzing a comprehensive tissue micro array including 185 invasive breast cancer specimens. We found a strong correlation (p < 0.001) between ITIH2 expression and estrogen receptor (ER) expression indicating that ER may be involved in the regulation of this ECM molecule. Conclusion Altogether, this is the first systematic analysis on the differential expression of ITIH genes in human cancer, showing frequent downregulation that may be associated with initiation and/or progression of these malignancies. PMID:18226209

  10. The effects of LIGO detector noise on a 15-dimensional Markov-chain Monte Carlo analysis of gravitational-wave signals

    NASA Astrophysics Data System (ADS)

    Raymond, V.; van der Sluys, M. V.; Mandel, I.; Kalogera, V.; Röver, C.; Christensen, N.

    2010-06-01

    Gravitational-wave signals from inspirals of binary compact objects (black holes and neutron stars) are primary targets of the ongoing searches by ground-based gravitational-wave (GW) interferometers (LIGO, Virgo and GEO-600). We present parameter estimation results from our Markov-chain Monte Carlo code SPINspiral on signals from binaries with precessing spins. Two data sets are created by injecting simulated GW signals either into synthetic Gaussian noise or into LIGO detector data. We compute the 15-dimensional probability-density functions (PDFs) for both data sets, as well as for a data set containing LIGO data with a known, loud artefact ('glitch'). We show that the analysis of the signal in detector noise yields accuracies similar to those obtained using simulated Gaussian noise. We also find that while the Markov chains from the glitch do not converge, the PDFs would look consistent with a GW signal present in the data. While our parameter estimation results are encouraging, further investigations into how to differentiate an actual GW signal from noise are necessary.

  11. A study of acoustic-to-articulatory inversion of speech by analysis-by-synthesis using chain matrices and the Maeda articulatory model

    PubMed Central

    Panchapagesan, Sankaran; Alwan, Abeer

    2011-01-01

    In this paper, a quantitative study of acoustic-to-articulatory inversion for vowel speech sounds by analysis-by-synthesis using the Maeda articulatory model is performed. For chain matrix calculation of vocal tract (VT) acoustics, the chain matrix derivatives with respect to area function are calculated and used in a quasi-Newton method for optimizing articulatory trajectories. The cost function includes a distance measure between natural and synthesized first three formants, and parameter regularization and continuity terms. Calibration of the Maeda model to two speakers, one male and one female, from the University of Wisconsin x-ray microbeam (XRMB) database, using a cost function, is discussed. Model adaptation includes scaling the overall VT and the pharyngeal region and modifying the outer VT outline using measured palate and pharyngeal traces. The inversion optimization is initialized by a fast search of an articulatory codebook, which was pruned using XRMB data to improve inversion results. Good agreement between estimated midsagittal VT outlines and measured XRMB tongue pellet positions was achieved for several vowels and diphthongs for the male speaker, with average pellet-VT outline distances around 0.15 cm, smooth articulatory trajectories, and less than 1% average error in the first three formants. PMID:21476670

  12. Backcountry Adventure as Spiritual Development: A Means-End Study

    ERIC Educational Resources Information Center

    Marsh, Paul E.

    2008-01-01

    What do people mean when they describe backcountry adventure experiences as being "spiritual"? Spiritual aspects of adventure experiences in the wilderness have been recounted anecdotally and recognized in research. This body of research, however, has left the definition of the term spiritual to the individual participants, and has not yet…

  13. Chemical genetics analysis of an aniline mustard anticancer agent reveals complex I of the electron transport chain as a target.

    PubMed

    Fedeles, Bogdan I; Zhu, Angela Y; Young, Kellie S; Hillier, Shawn M; Proffitt, Kyle D; Essigmann, John M; Croy, Robert G

    2011-09-30

    The antitumor agent 11β (CAS 865070-37-7), consisting of a DNA-damaging aniline mustard linked to an androgen receptor (AR) ligand, is known to form covalent DNA adducts and to induce apoptosis potently in AR-positive prostate cancer cells in vitro; it also strongly prevents growth of LNCaP xenografts in mice. The present study describes the unexpectedly strong activity of 11β against the AR-negative HeLa cells, both in cell culture and tumor xenografts, and uncovers a new mechanism of action that likely explains this activity. Cellular fractionation experiments indicated that mitochondria are the major intracellular sink for 11β; flow cytometry studies showed that 11β exposure rapidly induced oxidative stress, mitochondria being an important source of reactive oxygen species (ROS). Additionally, 11β inhibited oxygen consumption both in intact HeLa cells and in isolated mitochondria. Specifically, 11β blocked uncoupled oxygen consumption when mitochondria were incubated with complex I substrates, but it had no effect on oxygen consumption driven by substrates acting downstream of complex I in the mitochondrial electron transport chain. Moreover, 11β enhanced ROS generation in isolated mitochondria, suggesting that complex I inhibition is responsible for ROS production. At the cellular level, the presence of antioxidants (N-acetylcysteine or vitamin E) significantly reduced the toxicity of 11β, implicating ROS production as an important contributor to cytotoxicity. Collectively, our findings establish complex I inhibition and ROS generation as a new mechanism of action for 11β, which supplements conventional DNA adduct formation to promote cancer cell death. PMID:21832047

  14. Avian haemosporidian parasites (Haemosporida): A comparative analysis of different polymerase chain reaction assays in detection of mixed infections.

    PubMed

    Bernotienė, Rasa; Palinauskas, Vaidas; Iezhova, Tatjana; Murauskaitė, Dovilė; Valkiūnas, Gediminas

    2016-04-01

    Mixed infections of different species and genetic lineages of haemosporidian parasites (Haemosporida) predominate in wildlife, and such infections are particularly virulent. However, currently used polymerase chain reaction (PCR)-based detection methods often do not read mixed infections. Sensitivity of different PCR assays in detection of mixed infections has been insufficiently tested, but this knowledge is essential in studies addressing parasite diversity in wildlife. Here, we applied five different PCR assays, which are broadly used in wildlife avian haemosporidian research, and compared their sensitivity in detection of experimentally designed mixed infections of Haemoproteus and Plasmodium parasites. Three of these PCR assays use primer sets that amplify fragments of cytochrome b gene (cyt b), one of cytochrome oxidase subunit I (COI) gene, and one target apicoplast genome. We collected blood from wild-caught birds and, using microscopic and PCR-based methods applied in parallel, identified single infections of ten haemosporidian species with similar parasitemia. Then, we prepared 15 experimental mixes of different haemosporidian parasites, which often are present simultaneously in wild birds. Similar concentration of total DNA was used in each parasite lineage during preparation of mixes. Positive amplifications were sequenced, and the presence of mixed infections was reported by visualising double-base calling in sequence electropherograms. This study shows that the use of each single PCR assay markedly underestimates biodiversity of haemosporidian parasites. The application of at least 3 PCR assays in parallel detected the majority, but still not all lineages present in mixed infections. We determined preferences of different primers in detection of parasites belonging to different genera of haemosporidians during mixed infections. PMID:26821298

  15. Amplification and analysis of specific DNA and RNA sequences of bovine leukemia virus from infected cows by polymerase chain reaction.

    PubMed Central

    Sherman, M P; Ehrlich, G D; Ferrer, J F; Sninsky, J J; Zandomeni, R; Dock, N L; Poiesz, B

    1992-01-01

    Bovine leukemia virus (BLV) is the etiologic agent of leukemia in cattle and is believed to cause decreases in milk productivity, fertility, and life span in infected cows. BLV is a type C retrovirus in the Oncovirinae subfamily. It is most closely related to human T-cell lymphoma/leukemia virus type I (HTLV-I) and type II (HTLV-II). Since the polymerase chain reaction (PCR) provides rapid and efficient amplification of DNA sequences, primers were designed to amplify regions of the polymerase (pol) and pX genes specific for BLV targets. These sets of primers consistently amplified as few as 10 copies of BLV DNA contained in a plasmid in the background of 1 microgram of either human or bovine chromosomal DNA. In addition, no amplification products were detected from cell lines infected with HTLV-I, HTLV-II, or human immunodeficiency virus type 1 or 2 by the BLV PCR systems. Samples of peripheral blood mononuclear cells from 18 cows, previously determined to be serologically positive or negative, were correctly identified in a blind study as containing proviral DNA by use of the BLV primers and probes. Cloning and sequencing of amplified products revealed finite sequence variations among a previously cloned BLV isolate, the wild-type virus, and the published genome. Reverse transcriptase-directed PCR with the primers for both BLV pol and BLV pX was performed on plasma from a BLV-infected cow and detected in vivo BLV RNA expression. In summary, we have developed a specific and sensitive assay using PCR for the detection and identification of BLV infections; this assay can now be applied to clinical and basic research questions in veterinary medicine. Images PMID:1370847

  16. Adjusting the Chain Gear

    NASA Astrophysics Data System (ADS)

    Koloc, Z.; Korf, J.; Kavan, P.

    The adjustment (modification) deals with gear chains intermediating (transmitting) motion transfer between the sprocket wheels on parallel shafts. The purpose of the adjustments of chain gear is to remove the unwanted effects by using the chain guide on the links (sliding guide rail) ensuring a smooth fit of the chain rollers into the wheel tooth gap.

  17. Antibiotic resistance and molecular typing among cockle (Anadara granosa) strains of Vibrio parahaemolyticus by polymerase chain reaction (PCR)-based analysis.

    PubMed

    Sahilah, A M; Laila, R A S; Sallehuddin, H Mohd; Osman, H; Aminah, A; Ahmad Azuhairi, A

    2014-02-01

    Genomic DNA of Vibrio parahaemolyticus were characterized by antibiotic resistance, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) analysis. These isolates originated from 3 distantly locations of Selangor, Negeri Sembilan and Melaka (East coastal areas), Malaysia. A total of 44 (n = 44) of tentatively V. parahaemolyticus were also examined for the presence of toxR, tdh and trh gene. Of 44 isolates, 37 were positive towards toxR gene; while, none were positive to tdh and trh gene. Antibiotic resistance analysis showed the V. parahaemolyticus isolates were highly resistant to bacitracin (92%, 34/37) and penicillin (89%, 33/37) followed by resistance towards ampicillin (68%, 25/37), cefuroxime (38%, 14/37), amikacin (6%, 2/37) and ceftazidime (14%, 5/37). None of the V. parahaemolyticus isolates were resistant towards chloramphenicol, ciprofloxacin, ceftriaxone, enrofloxacin, norfloxacin, streptomycin and vancomycin. Antibiogram patterns exhibited, 9 patterns and phenotypically less heterogenous when compared to PCR-based techniques using ERIC- and RAPD-PCR. The results of the ERIC- and RAPD-PCR were analyzed using GelCompare software. ERIC-PCR with primers ERIC1R and ERIC2 discriminated the V. parahaemolyticus isolates into 6 clusters and 21 single isolates at a similarity level of 80%. While, RAPD-PCR with primer Gen8 discriminated the V. parahaemolyticus isolates into 11 clusters and 10 single isolates and Gen9 into 8 clusters and 16 single isolates at the same similarity level examined. Results in the presence study demonstrated combination of phenotypically and genotypically methods show a wide heterogeneity among cockle isolates of V. parahaemolyticus. PMID:24068534

  18. Field application of a combined pig and poultry market chain and risk pathway analysis within the Pacific Islands region as a tool for targeted disease surveillance and biosecurity.

    PubMed

    Brioudes, Aurélie; Gummow, Bruce

    2016-07-01

    Limited resources are one of the major constraints in effective disease monitoring and control in developing countries. This paper examines the pig and poultry market chains of four targeted Pacific Island countries and territories (PICTs): Fiji, Papua New Guinea, Solomon Islands and Vanuatu and combines them with a risk pathway analysis to identify the highest risk areas (risk hotspots) and risky practices and behaviours (risk factors) of animal disease introduction and/or spread, using highly pathogenic avian influenza (HPAI) and foot-and-mouth disease (FMD) as model diseases because of their importance in the region. The results show that combining a market chain analysis with risk pathways is a practical way of communicating risk to animal health officials and improving biosecurity. It provides a participatory approach that helps officials to better understand the trading regulations in place in their country and to better evaluate their role as part of the control system. Common risk patterns were found to play a role in all four PICTs. Legal trade pathways rely essentially on preventive measures put in place in the exporting countries while no or only limited control measures are undertaken by the importing countries. Legal importations of animals and animal products are done mainly by commercial farms which then supply local smallholders. Targeting surveillance on these potential hotspots would limit the risk of introduction and spread of animal diseases within the pig and poultry industry and better rationalize use of skilled manpower. Swill feeding is identified as a common practice in the region that represents a recognized risk factor for dissemination of pathogens to susceptible species. Illegal introduction of animals and animal products is suspected, but appears restricted to small holder farms in remote areas, limiting the risk of spread of transboundary animal diseases along the market chain. Introduction of undeclared goods hidden within a legal

  19. FECAL INDICATOR BACTERIA MEASUREMENTS BY QUANTITATIVE POLYMERASE CHAIN REACTION (QPCR) ANALYSIS IN FRESH ARCHIVED DNA EXTRACT OF WATER SAMPLE FILTRATES

    EPA Science Inventory

    The U.S. EPA has initiated a new recreational water study to evaluate the correlation between illness rates in swimmers and Enterococcus concentrations determined by the mEI agar membrane filter (MF) method and several new technologies including QPCR analysis. Results of this stu...

  20. COMPARISON OF ENTEROCOCCUS MEASUREMENTS IN FRESHWATER AT TWO RECREATIONAL BEACHES BY QUANTITATIVE POLYMERASE CHAIN REACTION AND MEMBRANE FILER CULTURE ANALYSIS

    EPA Science Inventory

    Cell densities of the fecal pollution indicator genus, Enterococcus, were determined by a rapid (2-3 hr) quantitative PCR (QPCR) analysis based method in 100 ml water samples collected from recreational beaches on Lake Michigan and Lake Erie during the summer of 2003. Enumeration...

  1. Reference Gene Identification for Reverse Transcription-Quantitative Polymerase Chain Reaction Analysis in an Ischemic Wound-Healing Model

    PubMed Central

    Ruedrich, Elizabeth D.; Henzel, Mary K.; Hausman, Bryan S.; Bogie, Kath M.

    2013-01-01

    Reference genes are often used in RT-quantitative PCR (qPCR) analysis to normalize gene expression levels to a gene that is expressed stably across study groups. They ultimately serve as a control in RT-qPCR analysis, producing more accurate interpretation of results. Whereas many reference genes have been used in various wound-healing studies, the most stable reference gene for ischemic wound-healing analysis has yet to be identified. The goal of this study was to determine systematically the most stable reference gene for studying gene expression in a rat ischemic wound-healing model using RT-qPCR. Twelve commonly used reference genes were analyzed using RT-qPCR and geNorm data analysis to determine stability across normal and ischemic skin tissue. It was ultimately determined that Ubiquitin C (UBC) and β-2 Microglobulin (B2M) are the most stably conserved reference genes across normal and ischemic skin tissue. UBC and B2M represent reliable reference genes for RT-qPCR studies in the rat ischemic wound model and are unaffected by sustained tissue ischemia. The geometric mean of these two stable genes provides an accurate normalization factor. These results provide insight on dependence of reference-gene stability on experimental parameters and the importance of such reference-gene investigations. PMID:24294111

  2. Reference gene identification for reverse transcription-quantitative polymerase chain reaction analysis in an ischemic wound-healing model.

    PubMed

    Ruedrich, Elizabeth D; Henzel, Mary K; Hausman, Bryan S; Bogie, Kath M

    2013-12-01

    Reference genes are often used in RT-quantitative PCR (qPCR) analysis to normalize gene expression levels to a gene that is expressed stably across study groups. They ultimately serve as a control in RT-qPCR analysis, producing more accurate interpretation of results. Whereas many reference genes have been used in various wound-healing studies, the most stable reference gene for ischemic wound-healing analysis has yet to be identified. The goal of this study was to determine systematically the most stable reference gene for studying gene expression in a rat ischemic wound-healing model using RT-qPCR. Twelve commonly used reference genes were analyzed using RT-qPCR and geNorm data analysis to determine stability across normal and ischemic skin tissue. It was ultimately determined that Ubiquitin C (UBC) and β-2 Microglobulin (B2M) are the most stably conserved reference genes across normal and ischemic skin tissue. UBC and B2M represent reliable reference genes for RT-qPCR studies in the rat ischemic wound model and are unaffected by sustained tissue ischemia. The geometric mean of these two stable genes provides an accurate normalization factor. These results provide insight on dependence of reference-gene stability on experimental parameters and the importance of such reference-gene investigations. PMID:24294111

  3. Bioactive Glass S53P4 versus Chlorhexidine Gluconate as Intracanal Medicament in Primary Teeth: An In-vivo Study Using Polymerase Chain Reaction Analysis

    PubMed Central

    Goel, Ankit; Sinha, Abhishek; Khandeparker, Rakshit Vijay Sinai; Mehrotra, Rachit; Vashisth, Pallavi; Garg, Anuj

    2015-01-01

    Background: Bacteria have long been recognized as the primary etiology for pulpal and periapical lesions, which necessitates the elimination of bacteria from the root canal system. In primary teeth, irrigation and debridement is the main protocol required to disinfect the canal. Biomechanical preparation cannot be vigorously done on the primary teeth due to anatomical barrier such as thin and flared roots. This calls for the use of an effective intracanal medication that will assist disinfection of root canal system. Aim of the study was to examine the in-vivo susceptibility of root canal bacteria to chlorhexidine (CHX) gluconate-1% gel and bioactive glass (BAG) S53P4 when used as intracanal medicaments using polymerase chain reaction (PCR). Methodology: PCR (analysis used oligonucleotide primers of Escherichia coli) was used to detect and compare the microbial load reduction after medication of 14 teeth for a week with either CHX gel - 1% or BAG S53P4. The pre and post microbial load was checked in the form of colony forming units. When analysis was done, a statistically significant difference was observed between the two groups. Results: The study revealed that both medicaments caused a considerable amount of microbial load reduction. BAG S53P4 caused much more reduction than CHX 1% gel. Statistical analysis showed a significant difference between the two groups. Conclusion: BAG S53P4 has superior antibacterial property as compared to CHX 1% gel. PMID:26464542

  4. Comparative evaluation of Polymerase Chain Reaction-Restriction Enzyme Analysis (PRA) and sequencing of heat shock protein 65 (hsp65) gene for identification of aquatic mycobacteria.

    PubMed

    Pourahmad, F; Thompson, K D; Adams, A; Richards, R H

    2009-02-01

    Traditional identification of mycobacteria based on cultural and biochemical tests can take several weeks and may fail to provide a precise identification. Polymerase Chain Reaction-Restriction Enzyme Analysis (PRA) of the gene encoding heat shock protein 65 kDa (hsp65) gene has been proposed as a rapid and inexpensive alternative approach. Despite being widely used for differentiation of mammalian mycobacteria, this method has only been applied in the identification of a small number of aquatic mycobacteria. The present study aimed to evaluate the potential use of PRA of hsp65 for the identification of aquatic mycobacteria compared with sequence analysis. Seventy one mycobacterial isolates including, 10 type/reference strains and the remainder field isolates, were subjected to PRA of a 441 bp fragment of this gene. For 68 representative isolates, sequence analysis was performed. All rapidly and slowly growing mycobacteria had best matches with 99.3% to 100% similarity with their corresponding species in the databanks. PRA proved to be a simple and rapid method for identifying aquatic mycobacteria. However, the incidence of similar or identical restriction patterns for some species of mycobacteria, and in particular, identification of new species of mycobacteria is a major problem using such a method. In contrast, the nucleic acid sequencing of the hsp65 gene yielded unambiguous results. PMID:18950664

  5. Rapid deoxyribonucleic acid analysis by allele-specific polymerase chain reaction for detection of mutations in the steroid 21-hydroxylase gene

    SciTech Connect

    Wilson, R.C.; Wei, J.Q.; Cheng, K.C.

    1995-05-01

    Rapid DNA analysis based on allele-specific polymerase chain reaction (PCR) using mutation site-specific primers was developed to detect mutations in the CYP21 gene known to cause steroid 21-hydroxylase deficiency. In contrast to the previous method, in which PCR of genomic DNA was followed by dot blot analysis with radio active probes and multiple rounds of stripping and reprobing for each of the 8 most common mutation sites, the results using this new method were immediately visualized after the PCR run by ethidium bromide-stained agarose gel electrophoresis. Using allele-specific PCR, mutation(s) were identified on 148 affected chromosomes out of 160 tested. Although mutation(s) were identified on only one chromosome of 11 of these patients, their parents showed a consistent pattern on DNA analysis. The only exception was that in one family, in which the parents each had a detectable mutation, a mutation was detected on only one allele of the patient. Most likely there is a mutation in the patient`s other allele that could have arisen de novo or was inherited from the parent and was not evident in the transmitting parent`s phenotype. When compared with the dot blot procedure, allele-specific PCR is more rapid, less labor-intensive, and avoids the use of radioactivity. 26 refs., 3 figs., 2 tabs.

  6. Comparison of detection platforms and post-polymerase chain reaction DNA purification methods for use in conjunction with Cleavase fragment length polymorphism analysis.

    PubMed

    Sander, T; Olson, S; Hall, J; Siebert, M; Grooms, K; Heisler, L; de Arruda, M; Neri, B

    1999-06-01

    The removal of impurities and contaminants from PCR-amplified fragments is important for mutation detection methods which identify mutations based on shifts in electrophoretic mobility. This is particularly critical for assays and detection methods which use target DNA that is labeled prior to analysis and electrophoretic detection. We examined several procedures for purifying DNA amplified by the polymerase chain reaction (PCR) and their use in conjunction with a novel DNA scanning method, the Cleavase fragment length polymorphism (CFLP)* assay. In this study, a 480 bp DNA fragment, fluorescently labeled on the 5'-end of one strand, was amplified and subjected to various widely used purification procedures, including several commercially available clean-up kits. We demonstrate that visualization of the fluorescent label, as opposed to simple ethidium bromide staining, reveals the presence of considerable levels of labeled, truncated, amplification products. The various procedures were evaluated on the basis of their ability to remove these unwanted DNA fragments as well as on the degree to which they inhibited or promoted the CFLP reaction. Several procedures are recommended for use with CFLP analysis, including isopropanol precipitation, gel excision, and several commercially available spin columns. Concurrently, we evaluated (compared) a number of commonly used visualization platforms, including fluorescence imaging, chemiluminescence, and post-electrophoretic staining, for the ability to detect CFLP pattern changes. The advantages and disadvantages of different methods are discussed and amounts of DNA to be used for CFLP analysis on different detection platforms are recommended. PMID:10380752

  7. Genome shuffling of Saccharomyces cerevisiae for enhanced glutathione yield and relative gene expression analysis using fluorescent quantitation reverse transcription polymerase chain reaction.

    PubMed

    Yin, Hua; Ma, Yanlin; Deng, Yang; Xu, Zhenbo; Liu, Junyan; Zhao, Junfeng; Dong, Jianjun; Yu, Junhong; Chang, Zongming

    2016-08-01

    Genome shuffling is an efficient and promising approach for the rapid improvement of microbial phenotypes. In this study, genome shuffling was applied to enhance the yield of glutathione produced by Saccharomyces cerevisiae YS86. Six isolates with subtle improvements in glutathione yield were obtained from populations generated by ultraviolet (UV) irradiation and nitrosoguanidine (NTG) mutagenesis. These yeast strains were then subjected to recursive pool-wise protoplast fusion. A strain library that was likely to yield positive colonies was created by fusing the lethal protoplasts obtained from both UV irradiation and heat treatments. After two rounds of genome shuffling, a high-yield recombinant YSF2-19 strain that exhibited 3.2- and 3.3-fold increases in glutathione production in shake flask and fermenter respectively was obtained. Comparative analysis of synthetase gene expression was conducted between the initial and shuffled strains using FQ (fluorescent quantitation) RT-PCR (reverse transcription polymerase chain reaction). Delta CT (threshold cycle) relative quantitation analysis revealed that glutathione synthetase gene (GSH-I) expression at the transcriptional level in the YSF2-19 strain was 9.9-fold greater than in the initial YS86. The shuffled yeast strain has a potential application in brewing, other food, and pharmaceutical industries. Simultaneously, the analysis of improved phenotypes will provide more valuable data for inverse metabolic engineering. PMID:27302037

  8. Identification of anisotropic geoelectric structures using dimensionality analysis of magnetotelluric data. Application to the Spanish Betic Chain

    NASA Astrophysics Data System (ADS)

    Martí, A.; Rosell, O.; Queralt, P.; Ledo, J.; Marcuello, A.

    2012-04-01

    In this work we investigate how to identify and characterise anisotropic structures in the Earth using the dimensionality analysis of the magnetotelluric (MT) responses, and apply it to the dataset from the Betics (SE Spain), which geoelectric lithospheric structure is well known from a 3D model. The methodology employed is based on a previous work (Martí et al., 2010), which extended the use of the rotational invariants of the MT tensor to define new criteria to identify anisotropic structures, based on 1D and 2D synthetic models. Now, we apply these criteria to a broad grid of MT sites which data are affected by 3D structures. In order to obtain as much information from the data as possible, we include the study of the induction arrows and compare the analysis with the phase tensor.

  9. A Markov chain analysis of the movements of juvenile salmonids in the forebay of McNary Dam, Washington and Oregon, 2006-09

    USGS Publications Warehouse

    Adams, Noah S.; Hatton, Tyson W.

    2012-01-01

    Passage and survival data for yearling and subyearling Chinook salmon and juvenile steelhead were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the information collected at McNary Dam was in the form of three-dimensional tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and test configurations of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting three-dimensional results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we investigated the feasibility of using a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis is one way that can be used to summarize numerically the behavior of fish in the forebay. Numerically summarizing the behavior of juvenile salmonids in the forebay of McNary Dam using the Markov chain analysis allowed us to confirm what had been previously summarized using visualization software. For example, proportions of yearling and subyearling Chinook salmon passing the three powerhouse areas was often greater in the southern and middle areas, compared to the northern area. The opposite generally was observed for steelhead. Results of this analysis also allowed us to confirm and quantify the extent of milling behavior that had been observed for steelhead. For fish that were first detected in the powerhouse region, less than 0.10 of the steelhead, on average, passed within each of the powerhouse areas. Instead, steelhead transitioned to adjoining areas in the

  10. Application of an immunoaffinity-based preconcentration method for mass spectrometric analysis of the O-chain polysaccharide of Aeromonas salmonicida from in vitro- and in vivo-grown cells.

    PubMed

    Wang, Zhan; Liu, Xin; Garduño, Elizabeth; Garduño, Rafael A; Li, Jianjun; Altman, Eleonora

    2009-06-01

    In this study, application of magnetic beads (Dynabeads) coated with Aeromonas salmonicida lipopolysaccharide-specific polyclonal antisera to MS-based characterization of bacterial lipopolysaccharides has been evaluated. The results showed that the affinity-based preconcentration strategy resulted in at least a 100-fold increase in the detection of sensitivity, affording direct capillary electrophoresis (CE)-MS analysis of A. salmonicida lipopolysaccharide O-chain polysaccharide from in vitro-cultured cells. Subsequent CE-MS analysis of in vivo-grown cells of A. salmonicida confirmed significant changes in the structure of the lipopolysaccharide O-chain polysaccharide as a result of in vivo cultivation. PMID:19456871

  11. Laser amplifier chain

    DOEpatents

    Hackel, R.P.

    1992-10-20

    A laser amplifier chain has a plurality of laser amplifiers arranged in a chain to sequentially amplify a low-power signal beam to produce a significantly higher-power output beam. Overall efficiency of such a chain is improved if high-gain, low efficiency amplifiers are placed on the upstream side of the chain where only a very small fraction of the total pumped power is received by the chain and low-gain, high-efficiency amplifiers are placed on the downstream side where a majority of pumping energy is received by the chain. 6 figs.

  12. Laser amplifier chain

    DOEpatents

    Hackel, Richard P.

    1992-01-01

    A laser amplifier chain has a plurality of laser amplifiers arranged in a chain to sequentially amplify a low-power signal beam to produce a significantly higher-power output beam. Overall efficiency of such a chain is improved if high-gain, low efficiency amplifiers are placed on the upstream side of the chain where only a very small fraction of the total pumped power is received by the chain and low-gain, high-efficiency amplifiers are placed on the downstream side where a majority of pumping energy is received by the chain.

  13. The Collaborative Study on the Enzymatic Analysis of Positional Distribution of Short- and Medium-chain Fatty Acids in Milk Fat Using Immobilized Candida antarctica Lipase B.

    PubMed

    Yoshinaga, Kazuaki; Sato, Shinichi; Sasaki, Ryo; Asada, Mihoko; Hori, Ryuji; Imagi, Jun; Miyazaki, Yosuke; Nagai, Toshiharu; Saito, Katsuyoshi; Sano, Takashi; Sasaki, Akiko; Sato, Chiemi; Tsukahara, Yuki; Yamashita, Atsushi; Watanabe, Shimpei; Watanabe, Yomi

    2016-01-01

    The positional distributions of fatty acids (FAs) in milk fat containing short- and medium-chain FAs were analyzed by sn-1(3)-selective transesterification of triacylglycerols (TAGs) with ethanol using immobilized Candida antarctica lipase B (CALB), in a collaborative study conducted by 10 laboratories. The mean C4:0, C6:0, and C8:0 FA contents, when analyzed as propyl esters (PEs) using gas chromatography (GC) with a DB-23 capillary column, were found to be 3.0, 2.0, and, 1.3 area%, respectively. Their reproducibility standard deviations were 0.33, 0.18, and 0.19, respectively. The mean C4:0, C6:0, and C8:0 contents at the sn-2 position were 0.3, 0.4, and 1.0 area%, respectively. Their reproducibility standard deviations were 0.17, 0.11, and 0.19, respectively. The reproducibility standard deviations of C4:0, C6:0, and C8:0 FAs at the sn-2 position were either the same as or smaller than those for milk fat, although the FA contents at the sn-2 position were smaller than those in the milk fat. Therefore, it was concluded that the CALB method for estimating the regiospecific distribution is applicable to TAGs containing short- and medium-chain FAs. When estimating the short-chain (SC) FA contents in fats and oils by GC, it is better to analyze SCFAs as PEs or butyl esters, and not as methyl esters, in order to prevent loss of SCFAs during the experimental procedure because of their volatility and water solubility. This study also revealed that the stationary phase of the GC capillary column affected the flame ionization detector (FID) response of SCFAs. The theoretical FID correction factor (MWFA / active carbon number / atomic weight of carbon) fitted well with the actual FID responses of C4:0-C12:0 FAs when they were analyzed as PEs using a DB-23 column; however, this was not the case when the GC analysis was performed using wax-type columns. PMID:26972465

  14. Quantitative polymerase chain reaction analysis with allele-specific oligonucleotide primers for individual IgH VDJ regions to evaluate tumor burden in myeloma patients.

    PubMed

    Sata, Hiroshi; Shibayama, Hirohiko; Maeda, Ikuhiro; Habuchi, Yoko; Nakatani, Eiji; Fukushima, Kentaro; Fujita, Jiro; Ezoe, Sachiko; Tadokoro, Seiji; Maeda, Tetsuo; Mizuki, Masao; Kosugi, Satoru; Nakagawa, Masashi; Ueda, Shuji; Iida, Masato; Tokumine, Yukihiro; Azenishi, Yasuhiko; Mitsui, Hideki; Oritani, Kenji; Kanakura, Yuzuru

    2015-05-01

    Quantitative polymerase chain reaction (PCR) with patient-specific, allele-specific oligonucleotide (ASO) primers for individual immunoglobulin H VDJ region (ASO-PCR) amplification was performed using several sources of clinical material, including mRNA from peripheral blood cells (PBMNCs), whole bone marrow cells (BMMNCs), and the CD20+ CD38- B-cell population in bone marrow, as well as cell-free DNA from the sera of patients with multiple myeloma (MM). We designed the ASO primers and produced sufficient PCR fragments to evaluate tumor burden in 20 of 30 bone marrow samples at diagnosis. Polymerase chain reaction amplification efficiency depended on primer sequences because the production of ASO-PCR fragments did not correlate with serum M-protein levels. However, the ASO-PCR levels in BMMNCs showed statistically significant correlations with those in PBMNCs and CD20+ CD38- B-cells. The good association between the BMMNC and PBMNC data indicated that PBMNCs could be a suitable source for monitoring minimal residual disease (MRD). In the case of cell-free DNA, ASO-PCR levels showed a unique pattern and remained high even after treatment. Because the sequence information for each ASO-PCR product was identical to the original, the cell-free DNA might also be useful for evaluating MRD. Moreover, the ASO-PCR products were clearly detected in 17 of 22 mRNA samples from CD20+ CD38- populations, suggesting that MM clones might exist in relatively earlier stages of B cells than in plasma cells. Thus, ASO-PCR analysis using various clinical materials is useful for detecting MRD in MM patients as well as for clarifying MM pathogenesis. PMID:25591497

  15. Multiscale and Fractal Analysis of Silicon Content Time Series Observed in Blast Furnace Hot Metal Using Hurst Exponent Chain

    NASA Astrophysics Data System (ADS)

    Luo, Shihua; Guo, Fan; Lai, Dejian; Yan, Fang; Tang, Feilai

    2015-09-01

    Hurst exponent is an important measure of nonlinearity of dynamical time series. In this paper, using rescaled-range (R/S) analysis, multi-fractal detrended fluctuation analysis (MF-DFA) methods, the multiscale Hurst exponent (MHE) and the multiscale generalized Hurst exponent (MGHE) of coarse-grained silicon content ([Si]) time series in blast furnace (BF) hot metal were calculated. First, we collected these [Si] time series from No. 1 BF of Nanchang Iron and Steel Co. and No. 10 BF of Xinyu Iron and Steel Co. in Jiangxi Province, China. Then, we analyzed and compared the estimated Hurst exponents and the generalized Hurst exponent of these observed time series with some simulated time series. Our results show that the observed time series from these BFs have negative correlation with the Hurst exponent less than 0.5, the generalized Hurst exponent H(q) is a nonlinear function of q, and such negative correlation and local various structure persist in their moving averages of the observed time series up to lag 5 or 10.

  16. Comparison of polymerase chain reaction methods and plating for analysis of enriched cultures of Listeria monocytogenes when using the ISO11290-1 method.

    PubMed

    Dalmasso, Marion; Bolocan, Andrei Sorin; Hernandez, Marta; Kapetanakou, Anastasia E; Kuchta, Tomáš; Manios, Stavros G; Melero, Beatriz; Minarovičová, Jana; Muhterem, Meryem; Nicolau, Anca Ioana; Rovira, Jordi; Skandamis, Panagiotis N; Stessl, Beatrix; Wagner, Martin; Jordan, Kieran; Rodríguez-Lázaro, David

    2014-03-01

    Analysis for Listeria monocytogenes by ISO11290-1 is time-consuming, entailing two enrichment steps and subsequent plating on agar plates, taking five days without isolate confirmation. The aim of this study was to determine if a polymerase chain reaction (PCR) assay could be used for analysis of the first and second enrichment broths, saving four or two days, respectively. In a comprehensive approach involving six European laboratories, PCR and traditional plating of both enrichment broths from the ISO11290-1 method were compared for the detection of L. monocytogenes in 872 food, raw material and processing environment samples from 13 different dairy and meat food chains. After the first and second enrichments, total DNA was extracted from the enriched cultures and analysed for the presence of L. monocytogenes DNA by PCR. DNA extraction by chaotropic solid-phase extraction (spin column-based silica) combined with real-time PCR (RTi-PCR) was required as it was shown that crude DNA extraction applying sonication lysis and boiling followed by traditional gel-based PCR resulted in fewer positive results than plating. The RTi-PCR results were compared to plating, as defined by the ISO11290-1 method. For first and second enrichments, 90% of the samples gave the same results by RTi-PCR and plating, whatever the RTi-PCR method used. For the samples that gave different results, plating was significantly more accurate for detection of positive samples than RTi-PCR from the first enrichment, but RTi-PCR detected a greater number of positive samples than plating from the second enrichment, regardless of the RTi-PCR method used. RTi-PCR was more accurate for non-food contact surface and food contact surface samples than for food and raw material samples especially from the first enrichment, probably because of sample matrix interference. Even though RTi-PCR analysis of the first enrichment showed less positive results than plating, in outbreak scenarios where a rapid result is

  17. Quality assurance of temporal variability of natural decay chain and neutron induced background for low-level NORM analysis

    SciTech Connect

    Yoho, Michael; Porterfield, Donivan R.; Landsberger, Sheldon

    2015-09-22

    In this study, twenty-one high purity germanium (HPGe) background spectra were collected over 2 years at Los Alamos National Laboratory. A quality assurance methodology was developed to monitor spectral background levels from thermal and fast neutron flux levels and naturally occurring radioactive material decay series radionuclides. 238U decay products above 222Rn demonstrated minimal temporal variability beyond that expected from counting statistics. 238U and 232Th progeny below Rn gas displayed at most twice the expected variability. Further, an analysis of the 139 keV 74Ge(n, γ) and 691 keV 72Ge(n, n') spectral features demonstrated temporal stability for both thermal and fast neutron fluxes.

  18. Quality assurance of temporal variability of natural decay chain and neutron induced background for low-level NORM analysis

    DOE PAGESBeta

    Yoho, Michael; Porterfield, Donivan R.; Landsberger, Sheldon

    2015-09-22

    In this study, twenty-one high purity germanium (HPGe) background spectra were collected over 2 years at Los Alamos National Laboratory. A quality assurance methodology was developed to monitor spectral background levels from thermal and fast neutron flux levels and naturally occurring radioactive material decay series radionuclides. 238U decay products above 222Rn demonstrated minimal temporal variability beyond that expected from counting statistics. 238U and 232Th progeny below Rn gas displayed at most twice the expected variability. Further, an analysis of the 139 keV 74Ge(n, γ) and 691 keV 72Ge(n, n') spectral features demonstrated temporal stability for both thermal and fast neutronmore » fluxes.« less

  19. Lineage-specific detection of influenza B virus using real-time polymerase chain reaction with melting curve analysis.

    PubMed

    Tewawong, Nipaporn; Chansaenroj, Jira; Klinfueng, Sirapa; Vichiwattana, Preeyaporn; Korkong, Sumeth; Thongmee, Thanunrat; Theamboonlers, Apiradee; Payungporn, Sunchai; Vongpunsawad, Sompong; Poovorawan, Yong

    2016-06-01

    Influenza B viruses comprise two lineages, Victoria (B/Vic) and Yamagata (B/Yam), which co-circulate globally. The surveillance data on influenza B virus lineages in many countries often underestimate the true prevalence due to the lack of a rapid, accurate, and cost-effective method for virus detection. We have developed a real-time PCR with melting curve analysis for lineage-specific differential detection of influenza B virus. By amplifying a region of the hemagglutinin gene using real-time PCR with SYBR Green I dye, B/Vic and B/Yam could be differentiated based on their melting temperature peaks. This method was efficient (B/Vic = 93.2 %; B/Yam 97.7 %), sensitive (B/Vic, 94.6 %; B/Yam, 96.3 %), and specific (B/Vic, 97.7 %; B/Yam, 97.1 %). The lower detection limit was 10(2) copies per microliter. The assay was evaluated using 756 respiratory specimens that were positive for influenza B virus, obtained between 2010 and 2015. The incidence of influenza B virus was approximately 18.9 % of all influenza cases, and the percentage was highest among children aged 6-17 years (7.57 %). The overall percentage of mismatched influenza B vaccine was 21.1 %. Our findings suggest that real-time PCR with melting curve analysis can provide a rapid, simple, and sensitive lineage-specific influenza B virus screening method to facilitate influenza surveillance. PMID:26923928

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

    PubMed Central

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

    2014-01-01

    An analysis of the dietary content of haematophagous insects can provide important information about the transmission networks of certain zoonoses. The present study evaluated the potential of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mitochondrial cytochrome B (cytb) gene to differentiate between vertebrate species that were identified as possible sources of sandfly meals. The complete cytb gene sequences of 11 vertebrate species available in the National Center for Biotechnology Information database were digested with Aci I, Alu I, Hae III and Rsa I restriction enzymes in silico using Restriction Mapper software. The cytb gene fragment (358 bp) was amplified from tissue samples of vertebrate species and the dietary contents of sandflies and digested with restriction enzymes. Vertebrate species presented a restriction fragment profile that differed from that of other species, with the exception of Canis familiaris and Cerdocyon thous. The 358 bp fragment was identified in 76 sandflies. Of these, 10 were evaluated using the restriction enzymes and the food sources were predicted for four: Homo sapiens (1), Bos taurus (1) and Equus caballus (2). Thus, the PCR-RFLP technique could be a potential method for identifying the food sources of arthropods. However, some points must be clarified regarding the applicability of the method, such as the extent of DNA degradation through intestinal digestion, the potential for multiple sources of blood meals and the need for greater knowledge regarding intraspecific variations in mtDNA. PMID:24821056

  1. Market surveillance on non-halal additives incorporated in surimi based products using polymerase chain reaction (PCR)-southern hybridization analysis

    NASA Astrophysics Data System (ADS)

    Aravindran, S.; Sahilah, A. M.; Aminah, A.

    2014-09-01

    Halal surveillance on halal ingredients incorporated in surimi based products were studied using polymerase chain reaction (PCR)-southern hybridization on chip analysis. The primers used in this technique were targeted on mitochondria DNA (mtDNA) of cytochrome b (cyt b) gene sequence which able to differentiate 7 type (beef, chicken, duck, goat, buffalo, lamb and pork) of species on a single chip. 17 (n = 17*3) different brands of surimi-based product were purchased randomly from Selangor local market in January 2013. Of 17 brands, 3 (n = 3*3) brands were positive for chicken DNA, 1 (n = 1*3) brand was positive for goat DNA, and the remainder 13 brands (n = 13*3) have no DNA species detected. The sensitivity of PCR-southern hybridization primers to detect each meat species was 0.1 ng. In the present study, it is evidence that PCR-Southern Hybridization analysis offered a reliable result due to its highly specific and sensitive properties in detecting non-halal additive such as plasma protein incorporation in surimi-based product.

  2. Markov chains-cellular automata modeling and multicriteria analysis of land cover change in the Lower Nhecolândia subregion of the Brazilian Pantanal wetland

    NASA Astrophysics Data System (ADS)

    Bacani, Vitor Matheus; Sakamoto, Arnaldo Yoso; Quénol, Hervé; Vannier, Clémence; Corgne, Samuel

    2016-01-01

    The dynamics of land use/land cover change in the Lower Nhecolândia wetland are marked by deforestation for pasture expansion, resulting in a real threat to the ecological stability. The aim of our work was to analyze the spatial distribution of land cover changes in the Lower Nhecolândia from 1985 to 2013 and to predict changes in trends for 2040. The mapping of land cover changes was developed using Landsat satellite images of 1985, 1999, 2007, and 2013, based on geographic object-based image analysis approach. This study uses integrated Markov chains and cellular automata modeling and multicriteria evaluation techniques to produce transition probability maps and describe the trajectory analysis methodology to construct a continuity of spatial and temporal changes for the wetland. The results of the multitemporal change detection classification show that, from 1985 to 2013, the forest woodland decreased by 6.89% and the grassland class increased by 18.29%. On the other hand, all water bodies showed a reducing trend, while the bare soil class increased compared to 1985, but did not present a regular trend of increase or decrease. From the present day, the trend for the future is a reduction of almost 6.4% by 2040. We found that deforestation actions will be concentrated in the areas with the highest concentration of saline lakes, constituting a serious threat to the natural functioning of this environmental system.

  3. Polymerase chain reaction-based analysis using deaminated DNA of dodecamer expansions in CSTB, associated with Unverricht-Lundborg myoclonus epilepsy.

    PubMed

    Horiuchi, H; Osawa, M; Furutani, R; Morita, M; Tian, W; Awatsu, Y; Shimazaki, H; Umetsu, K

    2005-01-01

    Progressive myoclonus epilepsy of the Unverricht-Lundborg type is an autosomal recessive disorder that is characterized clinically by myoclonic seizures and ataxia. The majority of affected individuals carry repeat expansions of a dodecamer in the promoter region of the cystatin B gene. The unusually high GC content of this tract is refractory to conventional polymerase chain reaction (PCR), and, as a result, a circumventive procedure involving the deamination of DNA with sodium bisulfite has been proposed. This study evaluates the effectiveness of this deamination modification for the detection of dodecamer repeat variants. An analysis of 258 healthy Japanese individuals revealed an allele with four copies of the dodecamer repeat with a frequency of 0.01, in addition to the more commonly observed two and three copy repeat alleles. Homozygous repeat expansions 600 and 680 base pairs in length were detected in the analyses of two affected individuals. For these cases, sequencing, along with an alternative PCR-stutter formation, revealed 41 and 48 copies, respectively, of the dodecamer repeat. The complete conversion of C to T was observed in the expanded tracts, indicating that no methylation occurred at the CpG sites. Based on these results, it was concluded that the use of deaminated DNA allows for a precise analysis of consecutive GC tracts. PMID:16379547

  4. Optimization of DNA extraction from seeds and fresh leaf tissues of wild marigold (Tagetes minuta) for polymerase chain reaction analysis.

    PubMed

    Shahzadi, I; Ahmed, R; Hassan, A; Shah, M M

    2010-01-01

    Tagetes, a genus of flowering marigolds in the family Asteraceae (Compositeae), is reported to be a medicinal plant with hypotensive, spasmolytic, anti-inflammatory, antimicrobial, and antifungal properties. Tagetes minuta characteristically contains high concentrations of essential oils, flavonoids, polyphenols, and polysaccharides that interfere with DNA, causing erroneous or no PCR products. We tested and modified various standard protocols in an effort to isolate high-quality DNA from different plant tissues of T. minuta. We used sun-dried, shade-dried and fresh-leaf tissues, as well as seeds for DNA analysis. The DNA obtained from seeds and fresh-leaf tissues with a modified cetyltrimethylammonium bromide buffer protocol was of good quality, with no colored pigments and contaminants. We were able to obtain good quality DNA from fresh leaf tissues without using liquid nitrogen. A relatively large amount of DNA was also extracted from the sun- and shade-dried tissues, but its quality was not as good as that from seeds. The DNA extracted from seeds and fresh leaves was successfully amplified by PCR using arbitrary RAPD primers. The same protocol will probably be useful for extracting high-molecular weight DNA from other plant materials containing large amounts of secondary metabolites and essential oils. PMID:20309824

  5. Molecular Analysis of Oral Bacteria in Heart Valve of Patients With Cardiovascular Disease by Real-Time Polymerase Chain Reaction.

    PubMed

    Oliveira, Francisco Artur Forte; Forte, Clarissa Pessoa Fernandes; Silva, Paulo Goberlânio de Barros; Lopes, Camile B; Montenegro, Raquel Carvalho; Santos, Ândrea Kely Campos Ribeiro Dos; Sobrinho, Carlos Roberto Martins Rodrigues; Mota, Mário Rogério Lima; Sousa, Fabrício Bitu; Alves, Ana Paula Negreiros Nunes

    2015-11-01

    Structural deficiencies and functional abnormalities of heart valves represent an important cause of cardiovascular morbidity and mortality, and a number of diseases, such as aortic stenosis, have been recently associated with infectious agents. This study aimed to analyze oral bacteria in dental plaque, saliva, and cardiac valves of patients with cardiovascular disease. Samples of supragingival plaque, subgingival plaque, saliva, and cardiac valve tissue were collected from 42 patients with heart valve disease. Molecular analysis of Streptococcus mutans, Prevotella intermedia, Porphyromonas gingivalis, and Treponema denticola was performed through real-time PCR. The micro-organism most frequently detected in heart valve samples was the S. mutans (89.3%), followed by P. intermedia (19.1%), P. gingivalis (4.2%), and T. denticola (2.1%). The mean decayed, missing, filled teeth (DMFT) was 26.4 ± 6.9 (mean ± SD), and according to the highest score of periodontal disease observed for each patient, periodontal pockets > 4 mm and dental calculus were detected in 43.4% and 34.7% of patients, respectively. In conclusion, oral bacteria, especially S. mutans, were found in the cardiac valve samples of patients with a high rate of caries and gingivitis/periodontitis. PMID:26632711

  6. Effective quantitative real-time polymerase chain reaction analysis of the parkin gene (PARK2) exon 1–12 dosage

    PubMed Central

    Shadrina, Maria I; Semenova, Elena V; Slominsky, Petr A; Bagyeva, Gulbahar H; Illarioshkin, Sergei N; Ivanova-Smolenskaia, Irina I; Limborska, Svetlana A

    2007-01-01

    Background One of the causes of Parkinson's disease is mutations in the PARK2 gene. Deletions and duplications of single exons or exon groups account for a large proportion of the gene mutations. Direct detection of these mutations can be used for the diagnosis of Parkinson's disease. Methods To detect these mutations, we developed an effective technique based on the real-time TaqMan PCR system, which allows us to evaluate the copynumbers of the PARK2 gene exons by comparing the intensity of the amplification signals from some exon of this gene with that of the β-globin gene (the internal control). Results We analyzed rearrangements in exons 1–12 of the PARK2 gene in 64 patients from Russia with early-onset Parkinson's disease. The frequency of these mutations in our patients was 14%. Conclusion We have developed a simple, accurate, and reproducible method applicable to the rapid detection of exon rearrangements in the PARK2 gene. It is suitable for the analysis of large patient groups, and it may become the basis for a diagnostic test. PMID:17324265

  7. Functional analysis, a resilience improvement tool applied to a waste management system - application to the "household waste management chain"

    NASA Astrophysics Data System (ADS)

    Beraud, H.; Barroca, B.; Hubert, G.

    2012-12-01

    A waste management system plays a leading role in the capacity of an area to restart after flooding, as their impact on post-crisis management can be very considerable. Improving resilience, i.e. enabling it to maintain or recover acceptable operating levels after flooding is primordial. To achieve this, we must understand how the system works for bringing any potential dysfunctions to light and taking preventive measures. Functional analysis has been used for understanding the complexity of this type of system. The purpose of this article is to show the interest behind this type of method and the limits in its use for improving resilience of waste management system as well as other urban technical systems1, by means of theoretical modelling and its application on a study site. 1In a systemic vision of the city, urban technical systems combine all the user service systems that are essential for the city to operate (electricity, water supplies, transport, sewerage, etc.). These systems are generally organised in the form of networks (Coutard, 2010; CERTU, 2005).

  8. Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.

    PubMed

    Fogolari, F; Esposito, G; Viglino, P; Cattarinussi, S

    1996-03-01

    In an effort to reduce the number of degrees of freedom necessary to describe a polypeptide chain we analyze the statistical behavior of polypeptide chains when represented as C alpha chains, C alpha chains with C beta atoms attached, and C alpha chains with rotational ellipsoids as models of side chains. A statistical analysis on a restricted data set of 75 unrelated protein structures is performed. The comparison of the database distributions with those obtained by model calculation on very short polypeptide stretches allows the dissection of local versus nonlocal features of the distributions. The database distribution of the bend angles of polypeptide chains of pseudo bonded C alpha atoms spans a restricted range of values and shows a bimodal structure. On the other hand, the torsion angles of the C alpha chain may assume almost all possible values. The distribution is bimodal, but with a much broader probability distribution than for bend angles. The C alpha - C beta vectors may be taken as representative of the orientation of the lateral chain, as the direction of the bond is close to the direction of the vector joining C alpha to the ad hoc defined center of the "steric mass" of the side chain. Interestingly, both the bend angle defined by C alpha i-C alpha i+1-C beta i+1 and the torsional angle offset of the pseudo-dihedral C alpha i-C alpha i+1-C alpha i+2-C beta i+2 with respect to C alpha i-C alpha i+1-C alpha i+2-C alpha i+3 span a limited range of values. The latter results show that it is possible to give a more realistic representation of polypeptide chains without introducing additional degrees of freedom, i.e., by just adding to the C alpha chain a C beta with given side-chain properties. However, a more realistic description of side chains may be attained by modeling side chains as rotational ellipsoids that have roughly the same orientation and steric hindrance. To this end, we define the steric mass of an atom as proportional to its van der

  9. Relations in Chains

    ERIC Educational Resources Information Center

    Mineur, B. W.

    1973-01-01

    The criticisms made against chain indexing are reviewed, and PRECIS briefly considered as a possible (but improbable) general substitute for indexing. The failures of chain indexing arise mainly from an overemphasis on generic relationships. The use of symbols to represent relations between terms is suggested for the chain index. (80 references)…

  10. Improvement and comparison of likelihood functions for model calibration and parameter uncertainty analysis within a Markov chain Monte Carlo scheme

    NASA Astrophysics Data System (ADS)

    Cheng, Qin-Bo; Chen, Xi; Xu, Chong-Yu; Reinhardt-Imjela, Christian; Schulte, Achim

    2014-11-01

    In this study, the likelihood functions for uncertainty analysis of hydrological models are compared and improved through the following steps: (1) the equivalent relationship between the Nash-Sutcliffe Efficiency coefficient (NSE) and the likelihood function with Gaussian independent and identically distributed residuals is proved; (2) a new estimation method of the Box-Cox transformation (BC) parameter is developed to improve the effective elimination of the heteroscedasticity of model residuals; and (3) three likelihood functions-NSE, Generalized Error Distribution with BC (BC-GED) and Skew Generalized Error Distribution with BC (BC-SGED)-are applied for SWAT-WB-VSA (Soil and Water Assessment Tool - Water Balance - Variable Source Area) model calibration in the Baocun watershed, Eastern China. Performances of calibrated models are compared using the observed river discharges and groundwater levels. The result shows that the minimum variance constraint can effectively estimate the BC parameter. The form of the likelihood function significantly impacts on the calibrated parameters and the simulated results of high and low flow components. SWAT-WB-VSA with the NSE approach simulates flood well, but baseflow badly owing to the assumption of Gaussian error distribution, where the probability of the large error is low, but the small error around zero approximates equiprobability. By contrast, SWAT-WB-VSA with the BC-GED or BC-SGED approach mimics baseflow well, which is proved in the groundwater level simulation. The assumption of skewness of the error distribution may be unnecessary, because all the results of the BC-SGED approach are nearly the same as those of the BC-GED approach.

  11. Long-chain fatty acid metabolism in dairy cows: a meta-analysis of milk fatty acid yield in relation to duodenal flows and de novo synthesis.

    PubMed

    Glasser, F; Ferlay, A; Doreau, M; Schmidely, P; Sauvant, D; Chilliard, Y

    2008-07-01

    This study is a meta-analysis of the response of milk long-chain fatty acid (FA) yield and composition to lipid supply, based on published experiments reporting duodenal FA flows or duodenal lipid infusions and milk FA composition (i.e., 39 experiments reporting 139 experimental treatments). Analysis of these data underlined the interdependence between milk yields of C18 and short- and medium-chain (C4 to C16) FA. Lipid supplementation (producing an increase in duodenal C18 flow) decreased linearly milk C4 to C16 yield (-0.26 g of C4 to C16 produced per gram of duodenal C18 flow increase) and increased quadratically milk C18 yield. When these 2 effects increased the percentage of C18 in milk FA up to a threshold value (around 52% of total FA), then milk C18 yield was limited by C4 to C16 yield, decreasing the C18 transfer efficiency from duodenum to milk with high-lipid diets. Moreover, for a given duodenal C18 flow, a decrease in milk C4 to C16 yield induced a decrease in milk C18 yield. Despite high variations in C18 transfer efficiency between duodenum and milk, for a given experimental condition, the percentages of C18 FA in milk total C18 could be predicted from their percentages in duodenal C18, and the percentages at the duodenum and in milk were very similar when mammary desaturation was taken into account (i.e., considering the sums of substrates and products of mammary desaturase). The estimated amounts of 18:0, trans-11-, and trans-13-18:1 desaturated by the mammary gland were a linear function of their mammary uptake, and mammary desaturation was responsible for 80, 95, and 81%, respectively, of the yield of their products (i.e., cis-9-18:1; cis-9, trans-11-, and cis-9, trans-13-18:2). Thus, mammary FA desaturation capacity did not seem to be a limiting factor in the experimental conditions published so far. PMID:18565935

  12. WASTOX (WATER QUALITY ANALYSIS SIMULATION FOR TOXICS), A FRAMEWORK FOR MODELING THE FATE OF TOXIC CHEMICALS IN AQUATIC ENVIRONMENTS. PART 2. FOOD CHAIN

    EPA Science Inventory

    A food chain bioaccumulation mathematical framework was developed as part of a broader framework for modeling the fate of toxic chemicals in natural water systems, entitled WASTOX. A user's guide for WASTOX (PB85-152882) was published in August 1984. The food chain component of W...

  13. RAPID DNA SEQUENCE ANALYSIS OF REVERTANTS OF THE HISD3052 ALLELE OF SALMONELLA TYPHIMURIUM TA98 USING THE POLYMERASE CHAIN REACTION AND DIRECT SEQUENCING: APPLICATION TO 1-NITROPYRENE-INDUCED REVERTANTS

    EPA Science Inventory

    We have used the polymerase chain reaction (PCR) to speed the processing of revertants of Salmonella typhimurium TA98 for DNA sequence analysis. riefly, a crude DNA extract from a single colony was prepared and used in an asymmetric PCR to amplify a 228-bp fragment containing the...

  14. Use of Length Heterogeneity Polymerase Chain Reaction (LH-PCR) as Non-Invasive Approach for Dietary Analysis of Svalbard Reindeer, Rangifer tarandus platyrhynchus

    PubMed Central

    Joo, Sungbae; Han, Donguk; Lee, Eun Ju; Park, Sangkyu

    2014-01-01

    To efficiently investigate the forage preference of Svalbard reindeer (Rangifer tarandus platyrhynchus), we applied length-heterogeneity polymerase chain reaction (LH-PCR) based on length differences of internal transcribed spacer (ITS) regions of ribosomal RNA (rRNA) to fecal samples from R. tarandus platyrhynchus. A length-heterogeneity (LH) database was constructed using both collected potential food sources of Svalbard reindeer and fecal samples, followed by PCR, cloning and sequencing. In total, eighteen fecal samples were collected between 2011 and 2012 from 2 geographic regions and 15 samples were successfully amplified by PCR. The LH-PCR analysis detected abundant peaks, 18.6 peaks on an average per sample, ranging from 100 to 500 bp in size and showing distinct patterns associated with both regions and years of sample collection. Principal component analysis (PCA) resulted in clustering of 15 fecal samples into 3 groups by the year of collection and region with a statistically significant difference at 99.9% level. The first 2 principal components (PCs) explained 71.1% of the total variation among the samples. Through comparison with LH database and identification by cloning and sequencing, lichens (Stereocaulon sp. and Ochrolechia sp.) and plant species (Salix polaris and Saxifraga oppositifolia) were detected as the food sources that contributed most to the Svalbard reindeer diet. Our results suggest that the use of LH-PCR analysis would be a non-invasive and efficient monitoring tool for characterizing the foraging strategy of Svalbard reindeer. Additionally, combining sequence information would increase its resolving power in identification of foraged diet components. PMID:24618847

  15. Comparing the Southern blot method and polymerase chain reaction product analysis for chimeric RCCX detection in CYP21A2 deficiency.

    PubMed

    Lee, Hsien-Hsiung; Lee, Yann-Jinn; Chao, Mei-Chyn

    2010-04-15

    The 3.2-kb TaqI-produced fragment of the CYP21A1P pseudogene and the 3.7-kb TaqI-produced fragment of the functional CYP21A2 gene exist on chromosome 6p21.3. We used the polymerase chain reaction (PCR) product and Southern blot method with TaqI endonuclease digestion to identify a chimeric RCCX module in two unrelated patients with congenital adrenal hyperplasia (CAH). After TaqI cleavage, the PCR product analysis revealed that patient 1 with the chimeric CYP21A1P/CYP21A2 gene in one allele and IVS2-12A/C>G in combination with the 707-714del mutation in the other allele produced a configuration of 3.2- and 2.4-kb fragments. Patient 2, who carried IVS2-12A/C>G in combination with the 707-714del mutation in one allele and the chimeric TNXA/TNXB gene in the other allele, presented with 3.2- and 2.3-kb fragments. However, Southern blot analysis showed that patients 1 and 2 produced 3.2-, 2.4-, and 2.5-kb fragments. We conclude that the chimeric CYP21A1P/CYP21A2 gene, IVS2-12A/C>G in combination with the 707-714del mutation, and the chimeric TNXA/TNXB gene cannot be distinguished by the Southern blot method. Conversely, the chimeric TNXA/TNXB gene was identified in the PCR product analysis due to the appearance of the 2.37-kb fragment, which indicates the occurrence of the chimeric TNXA/TNXB formation extending to the boundary of TNXA in the RCCX region. PMID:19961824

  16. A Markov chain analysis of the movements of juvenile salmonids, including sockeye salmon, in the forebay of McNary Dam, Washington and Oregon, 2006-09

    USGS Publications Warehouse

    Adams, Noah S.; Hatton, Tyson W.

    2012-01-01

    Passage and survival data were collected at McNary Dam between 2006 and 2009. These data have provided critical information for resource managers to implement structural and operational changes designed to improve the survival of juvenile salmonids as they migrate past the dam. Much of the valuable information collected at McNary Dam was in the form of three-dimensional (hereafter referred to as 3-D) tracks of fish movements in the forebay. These data depicted the behavior of multiple species (in three dimensions) during different diel periods, spill conditions, powerhouse operations, and testing of the surface bypass structures (temporary spillway weirs; TSWs). One of the challenges in reporting 3-D results is presenting the information in a manner that allows interested parties to summarize the behavior of many fish over many different conditions across multiple years. To accomplish this, we used a Markov chain analysis to characterize fish movement patterns in the forebay of McNary Dam. The Markov chain analysis allowed us to numerically summarize the behavior of fish in the forebay. This report is the second report published in 2012 that uses this analytical method. The first report included only fish released as part of the annual studies conducted at McNary Dam. This second report includes sockeye salmon that were released as part of studies conducted by the Chelan and Grant County Public Utility Districts at mid-Columbia River dams. The studies conducted in the mid-Columbia used the same transmitters as were used for McNary Dam studies, but transmitter pulse width was different between studies. Additionally, no passive integrated transponder tags were implanted in sockeye salmon. Differences in transmitter pulse width resulted in lower detection probabilities for sockeye salmon at McNary Dam. The absence of passive integrated transponder tags prevented us from determining if fish passed the powerhouse through the juvenile bypass system (JBS) or turbines. To

  17. Jetfighter: An Experiential Value Chain Exercise

    ERIC Educational Resources Information Center

    Sheehan, Norman T.; Gamble, Edward N.

    2010-01-01

    Value chain analysis is widely taught in business schools and applied by practitioners to improve business performance. Despite its ubiquity, many students struggle to understand and apply value chain concepts in practice. JetFighter uses a complex manufacturing process (making intricate paper planes) to provide students an opportunity to enhance…

  18. Gushing metal chain

    NASA Astrophysics Data System (ADS)

    Belyaev, Alexander; Sukhanov, Alexander; Tsvetkov, Alexander

    2016-03-01

    This article addresses the problem in which a chain falls from a glass from some height. This phenomenon demonstrates a paradoxical rise of the chain over the glass. To explain this effect, an initial hypothesis and an appropriate theory are proposed for calculating the steady fall parameters of the chain. For this purpose, the modified Cayley's problem of falling chain given its rise due to the centrifugal force of upward inertia is solved. Results show that the lift caused by an increase in linear density at the part of chain where it is being bent (the upper part) is due to the convergence of the chain balls to one another. The experiments confirm the obtained estimates of the lifting chain.

  19. Analysis of cytomegalovirus (CMV) viremia using the pp65 antigenemia assay, the amplicor CMV test, and a semi-quantitative polymerase chain reaction test after allogeneic marrow transplantation.

    PubMed

    Ksouri, H; Eljed, H; Greco, A; Lakhal, A; Torjman, L; Abdelkefi, A; Ben Othmen, T; Ladeb, S; Slim, A; Zouari, B; Abdeladhim, A; Ben Hassen, A

    2007-03-01

    A pp65 antigenemia assay for polymorphonuclear leukocytes (PMNLs) (CINAkit Rapid Antigenemia), and a qualitative polymerase chain reaction (PCR) test for plasma 'PCR-P qual' (Amplicor cytomegalovirus [CMV] test) were performed for 126 samples (blood and plasma) obtained from 18 bone marrow transplant patients, over a 9-month surveillance period. Among those samples, 92 were assayed with a semi-quantitative PCR test for PMNLs 'PCR-L quant.' The number of samples with a positive CMV test for antigenemia and PCR-P qual assays was 20.63% and 12.7%, respectively, whereas the PCR-L quant assay was positive in 48 of the 92 samples assayed (52.17%). The rates of concordance of the results of PCR-P qual and antigenemia, PCR-P qual and PCR-L quant, antigenemia and PCR-L quant were 92%, 65.2% and 66.8%, respectively. The analysis of the results for the 92 specimens tested by all 3 methods showed a rate of concordance of 63% among all methods. Good agreement (kappa=0.72) was found only between pp65 Ag and PCR-P qual assays. Clinical disease correlates with an antigenemia high viral load. Three patients had CMV disease despite preemptive therapy, and all of them had graft-versus-host-disease (GVHD). PMNLs-based assays are more efficient in monitoring CMV reactivation, but for high-risk patients with GVHD, more sensitive assays (real-time PCR) must be done. PMID:17313466

  20. A resilience assessment framework for infrastructure and economic systems : quantitative and qualitative resilience analysis of petrochemical supply chains to a hurricane.

    SciTech Connect

    Ehlen, Mark Andrew; Vugrin, Eric D.; Warren, Drake E.

    2010-03-01

    In recent years, the nation has recognized that critical infrastructure protection should consider not only the prevention of disruptive events, but also the processes that infrastructure systems undergo to maintain functionality following disruptions. This more comprehensive approach has been termed critical infrastructure resilience (CIR). Given the occurrence of a particular disruptive event, the resilience of a system to that event is the system's ability to efficiently reduce both the magnitude and duration of the deviation from targeted system performance levels. Sandia National Laboratories (Sandia) has developed a comprehensive resilience assessment framework for evaluating the resilience of infrastructure and economic systems. The framework includes a quantitative methodology that measures resilience costs that result from a disruption to infrastructure function. The framework also includes a qualitative analysis methodology that assesses system characteristics that affect resilience in order to provide insight and direction for potential improvements to resilience. This paper describes the resilience assessment framework. This paper further demonstrates the utility of the assessment framework through application to a hypothetical scenario involving the disruption of a petrochemical supply chain by a hurricane.

  1. Analysis of transtheoretical model of health behavioral changes in a nutrition intervention study--a continuous time Markov chain model with Bayesian approach.

    PubMed

    Ma, Junsheng; Chan, Wenyaw; Tsai, Chu-Lin; Xiong, Momiao; Tilley, Barbara C

    2015-11-30

    Continuous time Markov chain (CTMC) models are often used to study the progression of chronic diseases in medical research but rarely applied to studies of the process of behavioral change. In studies of interventions to modify behaviors, a widely used psychosocial model is based on the transtheoretical model that often has more than three states (representing stages of change) and conceptually permits all possible instantaneous transitions. Very little attention is given to the study of the relationships between a CTMC model and associated covariates under the framework of transtheoretical model. We developed a Bayesian approach to evaluate the covariate effects on a CTMC model through a log-linear regression link. A simulation study of this approach showed that model parameters were accurately and precisely estimated. We analyzed an existing data set on stages of change in dietary intake from the Next Step Trial using the proposed method and the generalized multinomial logit model. We found that the generalized multinomial logit model was not suitable for these data because it ignores the unbalanced data structure and temporal correlation between successive measurements. Our analysis not only confirms that the nutrition intervention was effective but also provides information on how the intervention affected the transitions among the stages of change. We found that, compared with the control group, subjects in the intervention group, on average, spent substantively less time in the precontemplation stage and were more/less likely to move from an unhealthy/healthy state to a healthy/unhealthy state. PMID:26123093

  2. Development of Fok-I based nested polymerase chain reaction-restriction fragment length polymorphism analysis for detection of hepatitis B virus X region V5M mutation

    PubMed Central

    Kim, Hong; Hong, Seok-Hyun; Lee, Seoung-Ae; Gong, Jeong-Ryeol; Kim, Bum-Joon

    2015-01-01

    AIM: To develop a Fok-I nested polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) method for the detection of hepatitis B virus X region (HBx) V5M mutation. METHODS: Nested PCR was applied into DNAs from 198 chronic patients at 2 different stages [121 patients with hepatocellular carcinoma (HCC) and 77 carrier patients]. To identify V5M mutants, digestion of nested PCR amplicons by the restriction enzyme Fok-I (GGA TGN9↓) was done. For size comparison, the enzyme-treated products were analyzed by electrophoresis on 2.5% agarose gels, stained with ethidium bromide, and visualized on a UV transilluminator. RESULTS: The assay enabled the identification of 69 patients (sensitivity of 34.8%; 46 HCC patients and 23 carrier patients). Our data also showed that V5M prevalence in HCC patients was significantly higher than in carrier patients (47.8%, 22/46 patients vs 0%, 0/23 patients, P < 0.001), suggesting that HBxAg V5M mutation may play a pivotal role in HCC generation in chronic patients with genotype C infections. CONCLUSION: The Fok-I nested PRA developed in this study is a reliable and cost-effective method to detect HBxAg V5M mutation in chronic patients with genotype C2 infection. PMID:26715821

  3. Hybrid metabolic flux analysis and recombinant protein prediction in Pichia pastoris X-33 cultures expressing a single-chain antibody fragment.

    PubMed

    Isidro, Inês A; Portela, Rui M; Clemente, João J; Cunha, António E; Oliveira, Rui

    2016-09-01

    Despite the growing importance of the Pichia pastoris expression system as industrial workhorse, the literature is almost absent in systematic studies on how culture medium composition affects central carbon fluxes and heterologous protein expression. In this study we investigate how 26 variations of the BSM+PTM1 medium impact central carbon fluxes and protein expression in a P. pastoris X-33 strain expressing a single-chain antibody fragment. To achieve this goal, we adopted a hybrid metabolic flux analysis (MFA) methodology, which is a modification of standard MFA to predict the rate of synthesis of recombinant proteins. Hybrid MFA combines the traditional parametric estimation of central carbon fluxes with non-parametric statistical modeling of product-related quantitative or qualitative measurements as a function of central carbon fluxes. It was observed that protein yield variability was 53.6 % (relative standard deviation) among the different experiments. Protein yield is much more sensitive to medium composition than biomass growth, which is mainly determined by the carbon source availability and main salts. Hybrid MFA was able to describe accurately the protein yield with normalized RMSE of 6.3 % over 5 independent experiments. The metabolic state that promotes high protein yields is characterized by high overall metabolic rates through main central carbon pathways concomitantly with a relative shift of carbon flux from biosynthetic towards energy generating pathways. PMID:27129458

  4. Commercial enzyme-linked immunosorbent assay versus polymerase chain reaction for the diagnosis of chronic Chagas disease: a systematic review and meta-analysis

    PubMed Central

    do Brasil, Pedro Emmanuel Alvarenga Americano; Castro, Rodolfo; de Castro, Liane

    2016-01-01

    Chronic Chagas disease diagnosis relies on laboratory tests due to its clinical characteristics. The aim of this research was to review commercial enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) diagnostic test performance. Performance of commercial ELISA or PCR for the diagnosis of chronic Chagas disease were systematically searched in PubMed, Scopus, Embase, ISI Web, and LILACS through the bibliography from 1980-2014 and by contact with the manufacturers. The risk of bias was assessed with QUADAS-2. Heterogeneity was estimated with the I2 statistic. Accuracies provided by the manufacturers usually overestimate the accuracy provided by academia. The risk of bias is high in most tests and in most QUADAS dimensions. Heterogeneity is high in either sensitivity, specificity, or both. The evidence regarding commercial ELISA and ELISA-rec sensitivity and specificity indicates that there is overestimation. The current recommendation to use two simultaneous serological tests can be supported by the risk of bias analysis and the amount of heterogeneity but not by the observed accuracies. The usefulness of PCR tests are debatable and health care providers should not order them on a routine basis. PCR may be used in selected cases due to its potential to detect seronegative subjects. PMID:26814640

  5. Bulk and Compound-Specific Isotope Analysis of Long-Chain, n-alkanes From a 85-kyr Core From Lake Peten Itza, Guatemala

    NASA Astrophysics Data System (ADS)

    Mays, J. L.; Brenner, M.; Bush, M. B.; Correa, A.; Curtis, J. H.; Hodell, D. A.

    2007-12-01

    Drill cores obtained from Lake Petén Itzá, Guatemala, contain a ~85-kyr record of terrestrial climate from lowland Central America. Variations in sediment lithology suggest rapid changes in precipitation during the last glacial and deglacial periods. Previous work in nearby Lake Quexil demonstrated the utility of using the carbon isotopic compositions of leaf wax n-alkanes to infer changes in terrestrial vegetation (Huang et al., 2001). Here we report carbon isotopes of bulk organic and long-chain n-alkanes in 60 samples to reconstruct changes in the relative proportion of C3 and C4 biomass in the watershed under changing climate and atmospheric CO2 conditions during the past 85 kyrs. Compound-specific carbon isotope results are compared directly with pollen analysis from the same samples. Huang, Y., F.A. Street-Perrott, S.E. Metcalfe, M. Brenner, M. Moreland, and K.H. Freeman. 2001. Climate change as the dominant control on glacial-interglacial variations in C3 and C4 plant abundance. Science 293:1647-1651.

  6. Molecular variation analysis of Aspergillus flavus using polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer rDNA region

    PubMed Central

    Zarrin, Majid; Erfaninejad, Maryam

    2016-01-01

    Aspergillus flavus is the second most common disease-causing species of Aspergillus in humans. The fungus is frequently associated with life-threatening infections in immunocompromised hosts. The primary aim of the present study was to analyze the genetic variability among different isolates of A. flavus using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP). A total of 62 A. flavus isolates were tested in the study. Molecular variability was searched for by analysis of the PCR amplification of the internal transcribed spacer (ITS) regions of ribosomal DNA using restriction enzymes. PCR using primers for ITS1 and ITS4 resulted in a product of ~600 bp. Amplicons were subjected to digestion with restriction endonucleases EcoRI, HaeIII and TaqI. Digestion of the PCR products using these restriction enzymes produced different patterns of fragments among the isolates, with different sizes and numbers of fragments, revealing genetic variability. In conclusion, ITS-RFLP is a useful molecular tool in screening for nucleotide polymorphisms among A. flavus isolates. PMID:27588085

  7. Contribution to the modelling and analysis of logistics system performance by Petri nets and simulation models: Application in a supply chain

    NASA Astrophysics Data System (ADS)

    Azougagh, Yassine; Benhida, Khalid; Elfezazi, Said

    2016-02-01

    In this paper, the focus is on studying the performance of complex systems in a supply chain context by developing a structured modelling approach based on the methodology ASDI (Analysis, Specification, Design and Implementation) by combining the modelling by Petri nets and simulation using ARENA. The linear approach typically followed in conducting of this kind of problems has to cope with a difficulty of modelling due to the complexity and the number of parameters of concern. Therefore, the approach used in this work is able to structure modelling a way to cover all aspects of the performance study. The modelling structured approach is first introduced before being applied to the case of an industrial system in the field of phosphate. Results of the performance indicators obtained from the models developed, permitted to test the behaviour and fluctuations of this system and to develop improved models of the current situation. In addition, in this paper, it was shown how Arena software can be adopted to simulate complex systems effectively. The method in this research can be applied to investigate various improvements scenarios and their consequences before implementing them in reality.

  8. Analysis of the rDNA internal transcribed spacer region of the Fusarium species by polymerase chain reaction-restriction fragment length polymorphism

    PubMed Central

    ZARRIN, MAJID; GANJ, FARZANEH; FARAMARZI, SAMA

    2016-01-01

    The Fusarium species are a widely spread phytopathogen identified in an extensive variety of hosts. The Fusarium genus is one of the most heterogeneous fungi and is difficult to classify. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis is a useful method in detection of DNA polymorphism in objective sequences. The aim of the present study was to identify the phylogenetic associations and usefulness of the internal transcribed spacer (ITS) region as a genetic marker within the most clinically important strain of the Fusarium species. A total of 50 strains of Fusarium spp. were used in the study, including environmental, clinical and reference isolates. The primers ITS1 and ITS4 were used in the study. Two restriction enzymes, HaeIII and SmaI, were assessed for the digestion of PCR products. A PCR product of ~550-base pairs was generated for each Fusarium species. The digested products with HaeIII and SmaI demonstrated that the bands generated for the medically significant Fusarium species, including F. solani, F. oxysporum, F. verticillidea, F. proliferatum and F. fujikuri, have different restriction enzyme patterns. In conclusion, it appears that the PCR-RFLP method used in the present study produces a sufficient restriction profile for differentiation of the most medically significant Fusarium species. PMID:27073635

  9. Analysis of T cell antigen receptors of myelin basic protein specific T cells in SJL/J mice demonstrates an alpha chain CDR3 motif associated with encephalitogenic T cells.

    PubMed

    Yamamura, T; Kondo, T; Sakanaka, S; Kozovska, M; Geng, T C; Takahashi, K; Tabira, T

    1994-07-01

    Experimental autoimmune encephalomyelitis (EAE) is an animal autoimmune disease mediated by CD4+ T cells. Analysis of TCR expression revealed that limited TCR elements (V beta 8.2, V alpha 2 or 4) were utilized by myelin basic protein (MBP) specific T cells in mice with H-2u haplotype and Lewis rats. The usage of a particular beta chain complementarity determining region 3 (CDR3) motif has also been shown. However, it remains unclear to what extent these observations can be extrapolated. Here we studied the TCR sequences of MBP 89-101/I-A(s) specific T cell clones derived from SJL/J mice, using the polymerase chain reaction on reverse transcribed mRNA. Although the V beta usage was less restricted than in H-2u mice, they predominantly utilized V beta 17a and expressed LGG or related motifs in the V beta-D beta-J beta junctions. Furthermore, a single alpha chain rearrangement between V alpha 1.1 and J alpha BBM142 with no N region diversity was preferentially used. Concordantly, immunization with a peptide corresponding to the alpha chain CDR3 was found to significantly alter the clinical course of EAE. Comparison of the published TCR junctional regions demonstrates that the CDR3 motifs (LGG in beta chain, CA*R*NY motif in alpha chains) are expressed by other encephalitogenic clones. Notably, the CA*R*NY was conserved in PL/J mice clones that recognize a distinct MBP-MHC determinant. It suggests that an antigen-independent mechanism may contribute to conserving the alpha chain motif. The implications of these observations are discussed. PMID:7524642

  10. Vibrational analysis of amino acids and short peptides in hydrated media. VIII. Amino acids with aromatic side chains: L-phenylalanine, L-tyrosine, and L-tryptophan.

    PubMed

    Hernández, Belén; Pflüger, Fernando; Adenier, Alain; Kruglik, Sergei G; Ghomi, Mahmoud

    2010-11-25

    Four out of the 20 natural α-amino acids (α-AAs) contain aromatic rings in their side chains. In a recent paper (J. Phys. Chem. B 2010, 114, 9072-9083), we have analyzed the structural and vibrational features of l-histidine, one of the potent elements of this series. Here, we report on the three remaining members of this family, i.e., l-phenylalanine, l-tyrosine, and l-tryptophan. Their solution (H(2)O and D(2)O) Raman scattering and Fourier transform infrared absorption attenuated total reflection (FT-IR ATR) spectra were measured at room temperature from the species corresponding to those existing at physiological conditions. Because of the very low water solubility of tyrosine, special attention was paid to avoid any artifact concerning the report of the vibrational spectra corresponding to nondissolved powder of this AA in aqueous solution. Finally, we could obtain for the first time the Raman and FT-IR spectra of tyrosine at very low concentration (2.3 mM) upon long accumulation time. To clarify this point, those vibrational spectra of tyrosine recorded either in the solid phase or in a heterogeneous state, where dissolved and nondissolved species of this AA coexist in aqueous solution, are also provided as Supporting Information . To carry out a discussion on the general geometrical and vibrational behavior of these AAs, we resorted to quantum mechanical calculations at the DFT/B3LYP/6-31++G* level, allowing (i) determination of potential energy surfaces of these AAs in a continuum solvent as a function of the torsion angles χ(1) and χ(2), defining the conformation of each aromatic side chain around C(α)-C(β) and C(β)-C(γ) bonds, respectively; (ii) analysis of geometrical features of the AAs surrounded by clusters of n explicit (n = 5-7) water molecules interacting with the backbone and aromatic rings; and (iii) assignment of the observed vibrational modes by means of the theoretical data provided by the lowest energy conformers of explicitly

  11. Crater chains on Mercury

    NASA Astrophysics Data System (ADS)

    Shevchenko, V.; Skobeleva, T.

    After discovery of disruption comet Shoemaker-Levy 9 into fragment train before it's collision with Jupiter there was proposed that linear crater chains on the large satellites of Jupiter and on the Moon are impact scars of past tidally disrupted comets.It's known that radar images have revealed the possible presence of water ice deposits in polar regions of Mercury. Impacts by a few large comets seem to provide the best explanation for both the amount and cleanliness of the ice deposits on Mercury because they have a larger volatile content that others external sources, for example, asteroid. A number of crater chains on the surface of Mercury are most likely the impact tracks of "fragment trains" of comets tidally disrupted by Sun or by Mercury and are not secondary craters. Mariner 10 image set (the three Mariner 10 flybys in 1974-1975) was used to recognize the crater chains these did not associate with secondary crater ejecta from observed impact structures. As example, it can be shown such crater chain located near crater Imhotep and crater Ibsen (The Kuiper Quadrangle of Mercury). Resolution of the Mariner 10 image is about 0.54 km/pixel. The crater chain is about 50 km long. It was found a similar crater chain inside large crater Sophocles (The Tolstoj Quadrangle of Mercury). The image resolution is about 1.46 km/pixel. The chain about 50 km long is located in northen part of the crater. Image resolution limits possibility to examine the form of craters strongly. It seems the craters in chains have roughly flat floor and smooth form. Most chain craters are approximately circular. It was examined many images from the Mariner 10 set and there were identified a total 15 crater chains and were unable to link any of these directly to any specific large crater associated with ejecta deposits. Chain craters are remarkably aligned. All distinguished crater chains are superposed on preexisting formations. A total of 127 craters were identified in the 15 recognized

  12. The immunoglobulin heavy-chain variable region in insulin-dependent diabetes mellitus: affected-sib-pair analysis and association studies.

    PubMed Central

    Veijola, R.; Knip, M.; Puukka, R.; Reijonen, H.; Cox, D. W.; Ilonen, J.

    1996-01-01

    We have analyzed immunoglobulin heavy-chain variable-region (VH) polymorphisms and genetic susceptibility to insulin-dependent diabetes mellitus (IDDM) by using a set of polymorphic loci that span approximately 1,000 kb of the VH region on chromosome 14q32. One hundred one Finnish families with at least two children affected with IDDM were studied. Conventional RFLPs determined by hybridization were used, since no microsatellite repeat markers have been available for this gene region. No evidence for linkage between the VH genes and IDDM could be obtained from haplotype-sharing analysis among the 133 diabetic sib pairs. The frequencies of various VH genotypes were also compared between 101 familial IDDM cases and 114 controls derived from the Finnish background population. The distribution of the genotypes at the VH2-B5 locus was significantly different between these groups (P=.004), the 3.4/3.4 genotype being less common in the IDDM cases. In addition, a different genotype distribution at the VH5-B2 locus was observed in the diabetic subjects (P = .022). When the IDDM cases were stratified by presence or absence of the high-risk HLA-DQB1*0302 allele, no differences in VH genotype frequencies were observed between the 0302-positive and 0302-negative cases. In the transmission test for linkage disequilibrium (TDT), no differences were found between the expected and observed frequencies of the transmitted alleles at the VH2-B5 or VH5-B2 locus. In conclusion, significant differences in VH genotype distributions were observed between the familial IDDM cases and the controls, but the observed associations could not be confirmed by the TDT. Haplotype sharing analysis provided no evidence for genetic linkage between the VH gene region and IDDM. Images Figure 1 PMID:8755935

  13. High Throughput Sequencing Analysis of the Immunoglobulin Heavy Chain Gene from Flow-Sorted B Cell Sub-Populations Define the Dynamics of Follicular Lymphoma Clonal Evolution

    PubMed Central

    Carlotti, Emanuela; Wrench, David; Rosignoli, Guglielmo; Marzec, Jacek; Sangaralingam, Ajanthah; Hazanov, Lena; Michaeli, Miri; Hallam, Simon; Chaplin, Tracy; Iqbal, Sameena; Calaminici, Maria; Young, Bryan; Mehr, Ramit; Campbell, Peter; Fitzgibbon, Jude; Gribben, John G.

    2015-01-01

    Understanding the dynamics of evolution of Follicular Lymphoma (FL) clones during disease progression is important for monitoring and targeting this tumor effectively. Genetic profiling of serial FL biopsies and examples of FL transmission following bone marrow transplant suggest that this disease may evolve by divergent evolution from a common ancestor cell. However where this ancestor cell resides and how it evolves is still unclear. The analysis of the pattern of somatic hypermutation of the immunoglobulin gene (Ig) is traditionally used for tracking the physiological clonal evolution of B cells within the germinal center and allows to discriminate those cells that have just entered the germinal center and display features of ancestor cells from those B cells that keep re-circulating across different lymphoid organs. Here we investigated the pattern of somatic hypermutation of the heavy chain of the immunoglobulin gene (IgH-VH) in 4 flow-sorted B cells subpopulations belonging to different stages of differentiation, from sequential lymph node biopsies of cases displaying diverse patterns of evolution, using the GS-FLX Titanium sequencing platform. We observed an unexpectedly high level of clonality, with hundreds of distinct tumor subclones in the different subpopulations from the same sample, the majority detected at a frequency <10−2. By using a lineage trees analysis we observed in all our FL and t-FL cases that the oligoclonal FL population was trapped in a narrow intermediate stage of maturation that maintains the capacity to undergo SHM, but was unable to further differentiate. The presence of such a complex architecture highlights challenges currently encountered in finding a cure for this disease. PMID:26325507

  14. N-3 long-chain polyunsaturated fatty acids and risk of all-cause mortality among general populations: a meta-analysis

    PubMed Central

    Chen, Guo-Chong; Yang, Jing; Eggersdorfer, Manfred; Zhang, Weiguo; Qin, Li-Qiang

    2016-01-01

    Prospective observational studies have shown inconsistent associations of dietary or circulating n-3 long-chain polyunsaturated fatty acids (LCPUFA) with risk of all-cause mortality. A meta-analysis was performed to evaluate the associations. Potentially eligible studies were identified by searching PubMed and EMBASE databases. The summary relative risks (RRs) with 95% confidence intervals (CIs) were calculated using the random-effects model. Eleven prospective studies involving 371 965 participants from general populations and 31 185 death events were included. The summary RR of all-cause mortality for high-versus-low n-3 LCPUFA intake was 0.91 (95% CI: 0.84–0.98). The summary RR for eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) intake was 0.83 (95% CI: 0.75–0.92) and 0.81 (95% CI: 0.74–0.95), respectively. In the dose-response analysis, each 0.3 g/d increment in n-3 LCPUFA intake was associated with 6% lower risk of all-cause mortality (RR = 0.94, 95% CI: 0.89–0.99); and each 1% increment in the proportions of circulating EPA and DHA in total fatty acids in blood was associated with 20% (RR = 0.80, 95% CI: 0.65–0.98) and 21% (RR = 0.79, 95% CI: 0.63–0.99) decreased risk of all-cause mortality, respectively. Moderate to high heterogeneity was observed across our anlayses. Our findings suggest that both dietary and circulating LCPUFA are inversely associated with all-cause mortality. PMID:27306836

  15. Non-additive Empirical Force Fields for Short-Chain Linear Alcohols: Methanol to Butanol. Hydration Free Energetics and Kirkwood-Buff Analysis Using Charge Equilibration Models

    PubMed Central

    Zhong, Yang; Patel, Sandeep

    2010-01-01

    Building upon the nonadditive electrostatic force field for alcohols based on the CHARMM charge equilibration (CHEQ) formalism, we introduce atom-pair specific solute-solvent Lennard-Jones (LJ) parameters for alcohol-water interaction force fields targeting improved agreement with experimental hydration free energies of a series of small molecule linear alcohols as well as ab initio water-alcohol geometries and energetics. We consider short-chain, linear alcohols from methanol to butanol as they are canonical small-molecule organic model compounds to represent the hydroxyl chemical functionality for parameterizing biomolecular force fields for proteins. We discuss molecular dynamics simulations of dilute aqueous solutions of methanol and ethanol in TIP4P-FQ water, with particular discussion of solution densities, structure defined in radial distribution functions, electrostatic properties (dipole moment distributions), hydrogen bonding patterns of water, as well as a Kirkwood-Buff (KB) integral analysis. Calculation of the latter provides an assessment of how well classical force fields parameterized to at least semi-quantitatively match experimental hydration free energies capture the microscopic structures of dilute alcohol solutions; the latter translate into macroscopic thermodynamic properties through the application of KB analysis. We find that the CHEQ alcohol force fields of this work semi-quantitatively match experimental KB integrals for methanol and ethanol mole fractions of 0.1 and 0.2. The force field combination qualitatively captures the concentration dependence of the alcohol-alcohol and water-water KB integrals, but due to inadequacies in the representation of the microscopic structures in such systems (which cannot be parameterized in any systematic fashion), a priori quantitative description of alcohol-water KB integrals remains elusive. PMID:20687517

  16. Quantitation of Bt-176 maize genomic sequences by surface plasmon resonance-based biospecific interaction analysis of multiplex polymerase chain reaction (PCR).

    PubMed

    Feriotto, Giordana; Gardenghi, Sara; Bianchi, Nicoletta; Gambari, Roberto

    2003-07-30

    Surface plasmon resonance (SPR) based biosensors have been described for the identification of genetically modified organisms (GMO) by biospecific interaction analysis (BIA). This paper describes the design and testing of an SPR-based BIA protocol for quantitative determinations of GMOs. Biotinylated multiplex Polymerase Chain Reaction (PCR) products from nontransgenic maize as well as maize powders containing 0.5 and 2% genetically modified Bt-176 sequences were immobilized on different flow cells of a sensor chip. After immobilization, different oligonucleotide probes recognizing maize zein and Bt-176 sequences were injected. The results obtained were compared with Southern blot analysis and with quantitative real-time PCR assays. It was demonstrated that sequential injections of Bt-176 and zein probes to sensor chip flow cells containing multiplex PCR products allow discrimination between PCR performed using maize genomic DNA containing 0.5% Bt-176 sequences and that performed using maize genomic DNA containing 2% Bt-176 sequences. The efficiency of SPR-based BIA in discriminating material containing different amounts of Bt-176 maize is comparable to real-time quantitative PCR and much more reliable than Southern blotting, which in the past has been used for semiquantitative purposes. Furthermore, the approach allows the BIA assay to be repeated several times on the same multiplex PCR product immobilized on the sensor chip, after washing and regeneration of the flow cell. Finally, it is emphasized that the presented strategy to quantify GMOs could be proposed for all of the SPR-based, commercially available biosensors. Some of these optical SPR-based biosensors use, instead of flow-based sensor chips, stirred microcuvettes, reducing the costs of the experimentation. PMID:14705890

  17. N-3 long-chain polyunsaturated fatty acids and risk of all-cause mortality among general populations: a meta-analysis.

    PubMed

    Chen, Guo-Chong; Yang, Jing; Eggersdorfer, Manfred; Zhang, Weiguo; Qin, Li-Qiang

    2016-01-01

    Prospective observational studies have shown inconsistent associations of dietary or circulating n-3 long-chain polyunsaturated fatty acids (LCPUFA) with risk of all-cause mortality. A meta-analysis was performed to evaluate the associations. Potentially eligible studies were identified by searching PubMed and EMBASE databases. The summary relative risks (RRs) with 95% confidence intervals (CIs) were calculated using the random-effects model. Eleven prospective studies involving 371 965 participants from general populations and 31 185 death events were included. The summary RR of all-cause mortality for high-versus-low n-3 LCPUFA intake was 0.91 (95% CI: 0.84-0.98). The summary RR for eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) intake was 0.83 (95% CI: 0.75-0.92) and 0.81 (95% CI: 0.74-0.95), respectively. In the dose-response analysis, each 0.3 g/d increment in n-3 LCPUFA intake was associated with 6% lower risk of all-cause mortality (RR = 0.94, 95% CI: 0.89-0.99); and each 1% increment in the proportions of circulating EPA and DHA in total fatty acids in blood was associated with 20% (RR = 0.80, 95% CI: 0.65-0.98) and 21% (RR = 0.79, 95% CI: 0.63-0.99) decreased risk of all-cause mortality, respectively. Moderate to high heterogeneity was observed across our anlayses. Our findings suggest that both dietary and circulating LCPUFA are inversely associated with all-cause mortality. PMID:27306836

  18. High Throughput Sequencing Analysis of the Immunoglobulin Heavy Chain Gene from Flow-Sorted B Cell Sub-Populations Define the Dynamics of Follicular Lymphoma Clonal Evolution.

    PubMed

    Carlotti, Emanuela; Wrench, David; Rosignoli, Guglielmo; Marzec, Jacek; Sangaralingam, Ajanthah; Hazanov, Lena; Michaeli, Miri; Hallam, Simon; Chaplin, Tracy; Iqbal, Sameena; Calaminici, Maria; Young, Bryan; Mehr, Ramit; Campbell, Peter; Fitzgibbon, Jude; Gribben, John G

    2015-01-01

    Understanding the dynamics of evolution of Follicular Lymphoma (FL) clones during disease progression is important for monitoring and targeting this tumor effectively. Genetic profiling of serial FL biopsies and examples of FL transmission following bone marrow transplant suggest that this disease may evolve by divergent evolution from a common ancestor cell. However where this ancestor cell resides and how it evolves is still unclear. The analysis of the pattern of somatic hypermutation of the immunoglobulin gene (Ig) is traditionally used for tracking the physiological clonal evolution of B cells within the germinal center and allows to discriminate those cells that have just entered the germinal center and display features of ancestor cells from those B cells that keep re-circulating across different lymphoid organs. Here we investigated the pattern of somatic hypermutation of the heavy chain of the immunoglobulin gene (IgH-VH) in 4 flow-sorted B cells subpopulations belonging to different stages of differentiation, from sequential lymph node biopsies of cases displaying diverse patterns of evolution, using the GS-FLX Titanium sequencing platform. We observed an unexpectedly high level of clonality, with hundreds of distinct tumor subclones in the different subpopulations from the same sample, the majority detected at a frequency <10-2. By using a lineage trees analysis we observed in all our FL and t-FL cases that the oligoclonal FL population was trapped in a narrow intermediate stage of maturation that maintains the capacity to undergo SHM, but was unable to further differentiate. The presence of such a complex architecture highlights challenges currently encountered in finding a cure for this disease. PMID:26325507

  19. Progesterone receptor isoform analysis by quantitative real-time polymerase chain reaction in formalin-fixed, paraffin-embedded canine mammary dysplasias and tumors.

    PubMed

    Guil-Luna, S; Stenvang, J; Brünner, N; Sánchez-Céspedes, R; Millán, Y; Gómez-Laguna, J; de las Mulas, J Martín

    2014-09-01

    Cloning and sequencing of the progesterone receptor gene in dogs have revealed 2 isoforms, A and B, transcribed from a single gene. Distribution of isoforms A and B in canine mammary lesions has hitherto been investigated only by Western blot analysis. This study analyzed progesterone receptor and its isoforms in formalin-fixed, paraffin-embedded tissue samples from canine mammary lesions (4 dysplasias, 10 benign tumors, and 46 carcinomas) using 1-step SYBR Green quantitative real-time polymerase chain reaction (RT-qPCR). Progesterone receptor was expressed in 75% of dysplasias, all benign tumors, and 59% of carcinomas. Carcinomas, and particularly simple epithelial-type carcinomas, displayed the lowest levels of expression. A high rate of agreement was recorded between RT-qPCR and immunohistochemical labeling. Isoforms A and B were successfully amplified, with correlation coefficients of 0.99 and amplification efficiencies close to 2, and were expressed in all lesion types analyzed. Predominance of A over B expression was observed in carcinomas and complex adenomas. Low-grade tumors exhibited higher progesterone receptor messenger RNA (mRNA) levels, but no difference was observed in the expression of isoform A versus B. Analysis of progesterone receptor mRNA isoforms by RT-qPCR was successful in routinely formalin-fixed, paraffin-embedded tissue samples and enabled the distribution of isoforms A and B to be identified for the first time in dysplasias, benign tumors, and malignant tumors of the canine mammary gland. These findings will facilitate future research into the role of progesterone receptor isoforms in the progression of canine mammary tumors. PMID:24249219

  20. Chain entanglements. I. Theory

    NASA Astrophysics Data System (ADS)

    Fixman, Marshall

    1988-09-01

    A model of concentrated polymer solution dynamics is described. The forces in a linear generalized Langevin equation for the motion of a probe chain are derived on the assumption that all relaxation of the forces is due to motion of the surrounding matrix. Vicinal chain displacements are classified as viscoelastic deformation, reptation, and minor residual fluctuations. The latter provide a torsional relaxation of the primitive path that minimizes the significance of transverse forces on the probe chain. All displacements of vicinal segments are assumed proportional to the forces that they exert on the probe chain. In response to an external force, the displacement of the probe chain relative to a laboratory frame is increased by viscoelastic deformation of the matrix, but reptative diffusion relative to the deforming matrix is slowed down. The net effect on translational diffusion is negligible if the probe and vicinal chains have the same chain length N, but the friction constant for reptative motion is increased by a factor N1-xs. xs=1/2 if Gaussian conformational statistics applies during the disengagement process, while xs =0.6 if excluded volume statistics applies. The translational friction constant is βp ˜N2, as in reptation theory, but the viscosity is η˜N4-xs . The persistence of entanglements during the translational diffusion of the probe chain across many radii of gyration is rationalized pictorially in terms of correlated reptative motion of the probe and vicinal chains.

  1. Immunohistochemical analysis of the skin in junctional epidermolysis bullosa using laminin 5 chain specific antibodies is of limited value in predicting the underlying gene mutation.

    PubMed

    McMillan, J R; McGrath, J A; Pulkkinen, L; Kon, A; Burgeson, R E; Ortonne, J P; Meneguzzi, G; Uitto, J; Eady, R A

    1997-06-01

    The anchoring filament protein laminin 5 is composed of three polypeptide chains (alpha 3, beta 3 and gamma 2) each encoded by separate genes (LAMA3, LAMB3 and LAMC2, respectively). Mutations in any of these three genes may give rise to the autosomal recessive blistering skin disease, junctional epidermolysis bullosa. At present, there is no easy way of predicting which of these three genes might harbour the pathogenetic laminin 5 mutations in a case of junctional epidermolysis bullosa. In this study, we assessed whether immunohistochemistry might be helpful in this regard. We performed immunohistochemical labelling of the dermal-epidermal junction using alpha 3, beta 3 and gamma 2 chain-specific antibodies in 11 patients with junctional epidermolysis bullosa, in whom the laminin 5 mutations had been previously delineated. Although, labelling for the laminin 5 chain bearing the mutations was attenuated or undetectable in all cases, a complete absence of labelling or a reduction in the staining intensity for the other two chains was also seen in all cases. The results showed that immunohistochemical labelling of the dermal-epidermal junction using alpha 3, beta 3 and gamma 2 chain-specific antibodies is not a specific indicator for which of the laminin 5 chain genes contains the pathogenetic mutations, and is therefore unreliable in screening for individual laminin 5 gene mutations in cases of junctional epidermolysis bullosa. PMID:9217810

  2. Systematic Analysis of Gene Expression Alterations and Clinical Outcomes for Long-Chain Acyl-Coenzyme A Synthetase Family in Cancer

    PubMed Central

    Chen, Wei-Ching; Wang, Chih-Yang; Hung, Yu-Hsuan; Weng, Tzu-Yang; Yen, Meng-Chi; Lai, Ming-Derg

    2016-01-01

    Dysregulated lipid metabolism contributes to cancer progression. Our previous study indicates that long-chain fatty acyl-Co A synthetase (ACSL) 3 is essential for lipid upregulation induced by endoplasmic reticulum stress. In this report, we aimed to identify the role of ACSL family in cancer with systematic analysis and in vitro experiment. We explored the ACSL expression using Oncomine database to determine the gene alteration during carcinogenesis and identified the association between ACSL expression and the survival of cancer patient using PrognoScan database. ACSL1 may play a potential oncogenic role in colorectal and breast cancer and play a potential tumor suppressor role in lung cancer. Co-expression analysis revealed that ACSL1 was coexpressed with MYBPH, PTPRE, PFKFB3, SOCS3 in colon cancer and with LRRFIP1, TSC22D1 in lung cancer. In accordance with PrognoScan analysis, downregulation of ACSL1 in colon and breast cancer cell line inhibited proliferation, migration, and anchorage-independent growth. In contrast, increase of oncogenic property was observed in lung cancer cell line by attenuating ACSL1. High ACSL3 expression predicted a better prognosis in ovarian cancer; in contrast, high ACSL3 predicted a worse prognosis in melanoma. ACSL3 was coexpressed with SNUPN, TRIP13, and SEMA5A in melanoma. High expression of ACSL4 predicted a worse prognosis in colorectal cancer, but predicted better prognosis in breast, brain and lung cancer. ACSL4 was coexpressed with SERPIN2, HNRNPCL1, ITIH2, PROCR, LRRFIP1. High expression of ACSL5 predicted good prognosis in breast, ovarian, and lung cancers. ACSL5 was coexpressed with TMEM140, TAPBPL, BIRC3, PTPRE, and SERPINB1. Low ACSL6 predicted a worse prognosis in acute myeloid leukemia. ACSL6 was coexpressed with SOX6 and DARC. Altogether, different members of ACSLs are implicated in diverse types of cancer development. ACSL-coexpressed molecules may be used to further investigate the role of ACSL family in

  3. Systematic Analysis of Gene Expression Alterations and Clinical Outcomes for Long-Chain Acyl-Coenzyme A Synthetase Family in Cancer.

    PubMed

    Chen, Wei-Ching; Wang, Chih-Yang; Hung, Yu-Hsuan; Weng, Tzu-Yang; Yen, Meng-Chi; Lai, Ming-Derg

    2016-01-01

    Dysregulated lipid metabolism contributes to cancer progression. Our previous study indicates that long-chain fatty acyl-Co A synthetase (ACSL) 3 is essential for lipid upregulation induced by endoplasmic reticulum stress. In this report, we aimed to identify the role of ACSL family in cancer with systematic analysis and in vitro experiment. We explored the ACSL expression using Oncomine database to determine the gene alteration during carcinogenesis and identified the association between ACSL expression and the survival of cancer patient using PrognoScan database. ACSL1 may play a potential oncogenic role in colorectal and breast cancer and play a potential tumor suppressor role in lung cancer. Co-expression analysis revealed that ACSL1 was coexpressed with MYBPH, PTPRE, PFKFB3, SOCS3 in colon cancer and with LRRFIP1, TSC22D1 in lung cancer. In accordance with PrognoScan analysis, downregulation of ACSL1 in colon and breast cancer cell line inhibited proliferation, migration, and anchorage-independent growth. In contrast, increase of oncogenic property was observed in lung cancer cell line by attenuating ACSL1. High ACSL3 expression predicted a better prognosis in ovarian cancer; in contrast, high ACSL3 predicted a worse prognosis in melanoma. ACSL3 was coexpressed with SNUPN, TRIP13, and SEMA5A in melanoma. High expression of ACSL4 predicted a worse prognosis in colorectal cancer, but predicted better prognosis in breast, brain and lung cancer. ACSL4 was coexpressed with SERPIN2, HNRNPCL1, ITIH2, PROCR, LRRFIP1. High expression of ACSL5 predicted good prognosis in breast, ovarian, and lung cancers. ACSL5 was coexpressed with TMEM140, TAPBPL, BIRC3, PTPRE, and SERPINB1. Low ACSL6 predicted a worse prognosis in acute myeloid leukemia. ACSL6 was coexpressed with SOX6 and DARC. Altogether, different members of ACSLs are implicated in diverse types of cancer development. ACSL-coexpressed molecules may be used to further investigate the role of ACSL family in

  4. Late Miocene to present-day exhumation and uplift of the Internal Zone of the Rif chain: Insights from low temperature thermochronometry and basin analysis

    NASA Astrophysics Data System (ADS)

    Romagny, A.; Ph. Münch; Cornée, J.-J.; Corsini, M.; Azdimousa, A.; Melinte-Dobrinescu, M. C.; Drinia, H.; Bonno, M.; Arnaud, N.; Monié, P.; Quillévéré, F.; Ben Moussa, A.

    2014-07-01

    Located on the margin of the west Alboran basin, the Gibraltar Arc (Betic-Rif mountain belt) displays post-Pliocene vertical movements evidenced by uplifted marine sedimentary basins and marine terraces. Quantification of vertical movements is an important clue to understand the origin of present-day relief generation in the Betic-Rif mountain chain together with the causes of the Messinian Salinity Crisis. In this paper, we present the results of a pluridisciplinary study combining an analysis of low temperature thermochronology and Pliocene basins evolution to constrain the exhumation history and surface uplift of internals units of the Rif belt (Northern Morocco). The mean (U-Th)/He apatite ages obtained from 11 samples are comprised between 14.1 and 17.8 Ma and display a wide dispersion, which could be explained by a great variability of apatite chemistries in the analyzed samples. No correlations between altitude and age have been found along altitudinal profile suggesting a rapid exhumation during this period. Thermal modeling using our (U-Th)/He apatite ages and geochronological data previously obtained in the same area (40Ar/39Ar and K/Ar data on biotite, zircon and apatite fission track) allow us to propose a cooling history. The rocks suffered a rapid cooling at 60-100 °C/Ma between 22.5 and 19 Ma, then cooled to temperatures around 40 °C between 19 and 18 Ma. They were re-heated at around 110 °C between 18 and 15 Ma then rapidly cooled and exhumed to reach the surface temperature at around 13 Ma. The re-heating could be related to a renewal in thrusting and burying of the inner zones. Between 15 and 13 Ma the cooling resumed at a rate of 50 °C/Ma indicating an exhumation rate of 0.8 mm/y considering an average 40 °C/km geothermal gradient. This exhumation may be linked to the extension in the Alboran Sea. Otherwise biostratigraphic and sedimentological analysis of Pliocene basins of the internal Rif provided informations on the more recent events

  5. Detection of Clonal T-Cell Receptor γ Gene Rearrangements in Paraffin-Embedded Tissue by Polymerase Chain Reaction and Nonradioactive Single-Strand Conformational Polymorphism Analysis

    PubMed Central

    Signoretti, Sabina; Murphy, Michael; Cangi, Maria Giulia; Puddu, Pietro; Kadin, Marshall E.; Loda, Massimo

    1999-01-01

    The diagnosis of T-cell lymphoproliferative disorders, which frequently involve the skin and other extranodal sites, is often problematic because of the difficulty in establishing clonality in paraffin-embedded tissue. To this end, we developed a simple, nonradioactive method to detect T-cell receptor γ (TCR-γ) gene rearrangements by polymerase chain reaction single-strand conformational polymorphism (PCR-SSCP) in paraffin-embedded tissue. Jurkat and HSB-2 cell lines and peripheral blood samples from normal individuals were used as monoclonal and polyclonal controls, respectively. DNA was extracted from 24 biopsies of T-cell lymphomas, 12 biopsies of reactive lymphoid infiltrates, and 2 biopsies of primary cutaneous large B-cell lymphomas. Vγ1–8, Vγ9, Vγ10, Vγ11, and Jγ1/Jγ2 consensus primers were used for TCR-γ gene rearrangement amplification and PCR products were analyzed by nonradioactive SSCP. Monoclonal controls yielded a well-defined banded pattern, whereas all polyclonal T-cell controls showed a reproducible pattern of smears. We detected monoclonality in 20/21 (95%) T-cell lymphoma cases, whereas no dominant T-cell clones were found in any of the reactive lymphoid infiltrates or B-cell lymphomas. Sensitivity of 1–5% was demonstrated by serially diluting Jurkat cells in mononuclear blood cells from normal individuals. We conclude that nonradioactive PCR-SSCP for TCR-γ gene rearrangement analysis is a useful adjunct to routine histological and immunophenotypic methods in the diagnosis of T-cell lymphoproliferative disorders in paraffin-embedded tissue. PMID:9916920

  6. Comparative evaluation of polymerase chain reaction and restriction enzyme analysis: two amplified targets, hsp65 and rpoB, for identification of cultured mycobacteria.

    PubMed

    Cheunoy, Wattana; Prammananan, Therdsak; Chaiprasert, Angkana; Foongladda, Suporn

    2005-03-01

    The increasing incidence of tuberculosis and other mycobacterial infections due to AIDS epidemic resulted in the need of rapid and accurate identification of isolated mycobacteria. The correct identification result leads to the selection of an appropriate therapeutic regimen. Polymerase chain reaction and restriction enzyme analysis (PCR-REA) has been developed since 1992 and used as the rapid method for identifying mycobacteria. Several genes or sequences have been used as an amplified target for PCR-REA. The present study aims to evaluate the potential use of PCR-REA of gene-encoding heat shock protein 65 kDa (hsp65) and beta-subunit RNA polymerase (rpoB) for the identification of mycobacteria compared with conventional biochemical identification. Two hundreds clinical isolates, consisting of 50 isolates of Mycobacterium tuberculosis and 150 isolates of nontuberculous mycobacteria (NTM), were submitted for identification using PCR-REA and biochemical method. The results demonstrated that PCR-REA identified 188 isolates of both M. tuberculosis and NTM concordantly with biochemical identification. Discordant identification results obtained from 12 isolates, comprised of 8 M. scrofulaceum, 1 M. avium complex, 1 M. malmoense, 1 M. terrae complex, and 1 M. chelonae/abscessus. Overall, the concordant percentage of results obtained from PCR-REA compared with biochemical method was 100%, 98.8%, and 83.3% for M. tuberculosis complex, rapidly growing, and slowly growing mycobacteria, respectively, and the results of hsp65 PCR-REA was in agreement with those obtained from rpoB PCR-REA. From this study, PCR-REA appears to be a simple, rapid, and reliable method for identifying mycobacteria in a routine microbiology laboratory. PMID:15766601

  7. Molecular typing of Iranian mycobacteria isolates by polymerase chain reaction-restriction fragment length polymorphism analysis of 360-bp rpoB gene

    PubMed Central

    Hadifar, Shima; Moghim, Sharareh; Fazeli, Hossein; GhasemianSafaei, Hajieh; Havaei, Seyed Asghar; Farid, Fariba; Esfahani, Bahram Nasr

    2015-01-01

    Background: Diagnosis and typing of Mycobacterium genus provides basic tools for investigating the epidemiology and pathogenesis of this group of bacteria. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) is an accurate method providing diagnosis and typing of species of mycobacteria. The present study is conducted by the purpose of determining restriction fragment profiles of common types of mycobacteria by PRA method of rpoB gene in this geographical region. Materials and Methods: Totally 60 clinical and environmental isolates from February to October, 2013 were collected and subcultured and identified by phenotypic methods. A 360 bp fragment of the rpoB gene amplified by PCR and products were digested by MspI and HaeIII enzymes. Results: In the present study, of all mycobacteria isolates identified by PRA method, 13 isolates (21.66%) were Mycobacterium tuberculosis, 34 isolates (56.66%) were rapidly growing Nontuberculosis Mycobacteria (NTM) that including 26 clinical isolates (43.33%) and 8 environmental isolates (13.33%), 11 isolates (18.33%) were clinical slowly growing NTM. among the clinical NTM isolates, Mycobacterium fortuitum Type I with the frequency of 57.77% was the most prevalent type isolates. Furthermore, an unrecorded of the PRA pattern of Mycobacterium conceptionense (HeaIII: 120/90/80, MspI: 120/105/80) was found. This study demonstrated that the PRA method was high discriminatory power for identification and typing of mycobacteria species and was able to identify 96.6% of all isolates. Conclusion: Based on the result of this study, rpoB gene could be a potentially useful tool for identification and investigation of molecular epidemiology of mycobacterial species. PMID:26380237

  8. Expression of steroidogenic enzymes and their transcription factors in cortisol-producing adrenocortical adenomas: immunohistochemical analysis and quantitative real-time polymerase chain reaction studies.

    PubMed

    Kubota-Nakayama, Fumie; Nakamura, Yasuhiro; Konosu-Fukaya, Sachiko; Azmahani, Abdullah; Ise, Kazue; Yamazaki, Yuto; Kitawaki, Yuko; Felizola, Saulo J A; Ono, Yoshikiyo; Omata, Kei; Morimoto, Ryo; Iwama, Noriyuki; Satoh, Fumitoshi; Sasano, Hironobu

    2016-08-01

    Adrenal Cushing syndrome (CS) is caused by the overproduction of cortisol in adrenocortical tumors including adrenal cortisol-producing adenoma (CPA). In CS, steroidogenic enzymes such as 17α-hydroxylase/17, 20-lase (CYP17A1), 3β-hydroxysteroid dehydrogenase (HSD3B), and 11β-hydroxylase (CYP11B1) are abundantly expressed in tumor cells. In addition, several transcriptional factors have been reported to play pivotal roles in the regulation of these enzymes in CPA, but their correlations with those enzymes above have still remained largely unknown. Therefore, in this study, we examined the status of steroidogenic enzymes and their transcriptional factors in 78 and 15 CPA cases by using immunohistochemistry and quantitative real-time polymerase chain reaction (qPCR), respectively. Immunoreactivity of HSD3B2, CYP11B1, CYP17A1, steroidogenic factor-1 (SF1[NR5A1]), GATA6, and nerve growth factor induced-B (NGFIB[NR4A1]) was detected in tumor cells. Results of qPCR analysis revealed that expression of HSD3B2 mRNA was significantly higher than that of HSD3B1, and CYP11B1 mRNA was significantly higher than CYP11B2. In addition, the expression of CYP11B1 mRNA was positively correlated with those of NR5A1, GATA6, and NR4A1. These results all indicated that HSD3B2 but not HSD3B1 was mainly involved in cortisol overproduction in CPA. In addition, NR5A1, GATA6, and NR4A1 were all considered to play important roles in cortisol overproduction through regulating CYP11B1 gene transcription. PMID:27085553

  9. Chain Reaction Polymerization.

    ERIC Educational Resources Information Center

    McGrath, James E.

    1981-01-01

    The salient features and importance of chain-reaction polymerization are discussed, including such topics as the thermodynamics of polymerization, free-radical polymerization kinetics, radical polymerization processes, copolymers, and free-radical chain, anionic, cationic, coordination, and ring-opening polymerizations. (JN)

  10. Critical Chain Exercises

    ERIC Educational Resources Information Center

    Doyle, John Kevin

    2010-01-01

    Critical Chains project management focuses on holding buffers at the project level vs. task level, and managing buffers as a project resource. A number of studies have shown that Critical Chain project management can significantly improve organizational schedule fidelity (i.e., improve the proportion of projects delivered on time) and reduce…

  11. Stepwise assembling of polypeptide chain energy distributions.

    PubMed

    Jacchieri, S G

    2001-03-01

    The principles and application of conformational analysis software that makes use of a new algorithm are described. It is known that the existence of a local energy minimum in the energy landscape is in general related to the clustering of polypeptide chain conformations near that energy value or, in other words, to a high density of states. A criterion based on this principle is part of an algorithm employed to select subsets of polypeptide chain conformations in broad energy ranges. Chain fragments belonging to these subsets are then combined to build larger polypeptide chains and the corresponding energy distributions. The functionality of the various operations employed in the process is described and the FORTRAN 77 source code that defines the algorithm is listed. The methodology is illustrated with a calculation involving three chain fragments belonging to the cellular prion protein (PrP(C)). PMID:11219430

  12. Botswana's Beef Global Commodity Chain: Explaining the Resistance to Change

    ERIC Educational Resources Information Center

    Ransom, Elizabeth

    2011-01-01

    In an era of increasing global agricultural trade, many firms and farms seek to upgrade their agricultural commodity chains to become better integrated into global markets. Utilizing a global commodity chain (GCC) approach, this analysis unravels the challenges to and the potential consequences of upgrading Botswana's beef commodity chain.…

  13. Liquid crystal alignment on ion-beam-treated polyimide with a long alkyl side chain: near edge X-ray absorption fine structure spectroscopy analysis.

    PubMed

    Seo, Joo-Hong; Hwang, Soo Won; Song, Dong Han; Shin, Jae Hoon; Yoon, Tae-Hoon; Kim, Jae Chang; Yi, Mi Hye

    2009-02-19

    Liquid crystal alignment on ion-beam-treated polyimides with a long alkyl side chain was investigated using near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The long alkyl side chains and the asymmetric distribution and orientational order of the pi-bonds of the polyimide surface can be determined by analyzing the angular dependent resonance intensities of the NEXAFS measurements. Herein, we demonstrate that the pretilt angle of the LC cell made by our method decreases as more long alkyl side chains are destroyed. Additionally, the tilt direction of the LC molecules can be determined from the asymmetric distribution of pi-bonds of the polyimide created by the ion beam irradiation. PMID:19161281

  14. Chain Effects: The Impact of Academy Chains on Low Income Students

    ERIC Educational Resources Information Center

    Hutchings, Merryn; Francis, Becky; De Vries, Robert

    2014-01-01

    The authors analysed school performance data to review how well disadvantaged pupils achieve in academy chains. They included chains only if they had at least three academies in 2013, and two sponsored secondary academies for the whole period from September 2010 to July 2013. This means that academies are included in our analysis only when there…

  15. SUMO chains: polymeric signals.

    PubMed

    Vertegaal, Alfred C O

    2010-02-01

    Ubiquitin and ubiquitin-like proteins are conjugated to a wide variety of target proteins that play roles in all biological processes. Target proteins are conjugated to ubiquitin monomers or to ubiquitin polymers that form via all seven internal lysine residues of ubiquitin. The fate of these target proteins is controlled in a chain architecture-dependent manner. SUMO (small ubiquitin-related modifier) shares the ability of ubiquitin to form chains via internal SUMOylation sites. Interestingly, a SUMO-binding site in Ubc9 is important for SUMO chain synthesis. Similar to ubiquitin-polymer cleavage by USPs (ubiquitin-specific proteases), SUMO chain formation is reversible. SUMO polymers are cleaved by the SUMO proteases SENP6 [SUMO/sentrin/SMT3 (suppressor of mif two 3)-specific peptidase 6], SENP7 and Ulp2 (ubiquitin-like protease 2). SUMO chain-binding proteins including ZIP1, SLX5/8 (synthetic lethal of unknown function 5/8), RNF4 (RING finger protein 4) and CENP-E (centromere-associated protein E) have been identified that interact non-covalently with SUMO chains, thereby regulating target proteins that are conjugated to SUMO multimers. SUMO chains play roles in replication, in the turnover of SUMO targets by the proteasome and during mitosis and meiosis. Thus signalling via polymers is an exciting feature of the SUMO family. PMID:20074033

  16. Translocation of reptating chains

    NASA Astrophysics Data System (ADS)

    Żurek, S.; Drzewiński, A.; van Leeuwen, J. M. J.

    2011-05-01

    Voltage-driven translocation is modeled with the Rubinstein-Duke rules for hopping reptons in one- and two-dimensional lattices. The chain is driven through the pore by a bias potential promoting the transition of stored length in one direction. Coupling states give a semi-periodicity of the process that enables us to relate the properties to the stationary state of the master equation. The exact solution for short chains and Monte Carlo simulations for longer chains are used to calculate displacements, velocities and the translocation time.

  17. Parameters optimization using experimental design for headspace solid phase micro-extraction analysis of short-chain chlorinated paraffins in waters under the European water framework directive.

    PubMed

    Gandolfi, F; Malleret, L; Sergent, M; Doumenq, P

    2015-08-01

    The water framework directives (WFD 2000/60/EC and 2013/39/EU) force European countries to monitor the quality of their aquatic environment. Among the priority hazardous substances targeted by the WFD, short chain chlorinated paraffins C10-C13 (SCCPs), still represent an analytical challenge, because few laboratories are nowadays able to analyze them. Moreover, an annual average quality standards as low as 0.4μgL(-1) was set for SCCPs in surface water. Therefore, to test for compliance, the implementation of sensitive and reliable analysis method of SCCPs in water are required. The aim of this work was to address this issue by evaluating automated solid phase micro-extraction (SPME) combined on line with gas chromatography-electron capture negative ionization mass spectrometry (GC/ECNI-MS). Fiber polymer, extraction mode, ionic strength, extraction temperature and time were the most significant thermodynamic and kinetic parameters studied. To determine the suitable factors working ranges, the study of the extraction conditions was first carried out by using a classical one factor-at-a-time approach. Then a mixed level factorial 3×2(3) design was performed, in order to give rise to the most influent parameters and to estimate potential interactions effects between them. The most influent factors, i.e. extraction temperature and duration, were optimized by using a second experimental design, in order to maximize the chromatographic response. At the close of the study, a method involving headspace SPME (HS-SPME) coupled to GC/ECNI-MS is proposed. The optimum extraction conditions were sample temperature 90°C, extraction time 80min, with the PDMS 100μm fiber and desorption at 250°C during 2min. Linear response from 0.2ngmL(-1) to 10ngmL(-1) with r(2)=0.99 and limits of detection and quantification, respectively of 4pgmL(-1) and 120pgmL(-1) in MilliQ water, were achieved. The method proved to be applicable in different types of waters and show key advantages, such

  18. Comparison of Enterococcus quantitative polymerase chain reaction analysis results from midwest U.S. river samples using EPA Method 1611 and Method 1609 PCR reagents

    EPA Science Inventory

    The U.S. Environmental Protection Agency (EPA) has provided recommended beach advisory values in its 2012 recreational water quality criteria (RWQC) for states wishing to use quantitative polymerase chain reaction (qPCR) for the monitoring of Enterococcus fecal indicator bacteria...

  19. Structural and Biochemical Analysis of a Single Amino-Acid Mutant of WzzBSF That Alters Lipopolysaccharide O-Antigen Chain Length in Shigella flexneri.

    PubMed

    Chang, Chiung-Wen; Tran, Elizabeth N H; Ericsson, Daniel J; Casey, Lachlan W; Lonhienne, Thierry; Benning, Friederike; Morona, Renato; Kobe, Bostjan

    2015-01-01

    Lipopolysaccharide (LPS), a surface polymer of Gram-negative bacteria, helps bacteria survive in different environments and acts as a virulence determinant of host infection. The O-antigen (Oag) component of LPS exhibits a modal chain-length distribution that is controlled by polysaccharide co-polymerases (PCPs). The molecular basis of the regulation of Oag chain-lengths remains unclear, despite extensive mutagenesis and structural studies of PCPs from Escherichia coli and Shigella. Here, we identified a single mutation (A107P) of the Shigella flexneri WzzBSF, by a random mutagenesis approach, that causes a shortened Oag chain-length distribution in bacteria. We determined the crystal structures of the periplasmic domains of wild-type WzzBSF and the A107P mutant. Both structures form a highly similar open trimeric assembly in the crystals, and show a similar tendency to self-associate in solution. Binding studies by bio-layer interferometry reveal cooperative binding of very short (VS)-core-plus-O-antigen polysaccharide (COPS) to the periplasmic domains of both proteins, but with decreased affinity for the A107P mutant. Our studies reveal that subtle and localized structural differences in PCPs can have dramatic effects on LPS chain-length distribution in bacteria, for example by altering the affinity for the substrate, which supports the role of the structure of the growing Oag polymer in this process. PMID:26378781

  20. A Meta-Analysis and Systematic Review of the Literature to Evaluate Potential Threats to Internal Validity in Probe Procedures for Chained Tasks

    ERIC Educational Resources Information Center

    Alexander, Jennifer L.; Smith, Katie A.; Mataras, Theologia; Shepley, Sally B.; Ayres, Kevin M.

    2015-01-01

    The two most frequently used methods for assessing performance on chained tasks are single opportunity probes (SOPs) and multiple opportunity probes (MOPs). Of the two, SOPs may be easier and less time-consuming but can suppress actual performance. In comparison, MOPs can provide more information but present the risk of participants acquiring…

  1. Structural and Biochemical Analysis of a Single Amino-Acid Mutant of WzzBSF That Alters Lipopolysaccharide O-Antigen Chain Length in Shigella flexneri

    PubMed Central

    Casey, Lachlan W.; Lonhienne, Thierry; Benning, Friederike; Morona, Renato; Kobe, Bostjan

    2015-01-01

    Lipopolysaccharide (LPS), a surface polymer of Gram-negative bacteria, helps bacteria survive in different environments and acts as a virulence determinant of host infection. The O-antigen (Oag) component of LPS exhibits a modal chain-length distribution that is controlled by polysaccharide co-polymerases (PCPs). The molecular basis of the regulation of Oag chain-lengths remains unclear, despite extensive mutagenesis and structural studies of PCPs from Escherichia coli and Shigella. Here, we identified a single mutation (A107P) of the Shigella flexneri WzzBSF, by a random mutagenesis approach, that causes a shortened Oag chain-length distribution in bacteria. We determined the crystal structures of the periplasmic domains of wild-type WzzBSF and the A107P mutant. Both structures form a highly similar open trimeric assembly in the crystals, and show a similar tendency to self-associate in solution. Binding studies by bio-layer interferometry reveal cooperative binding of very short (VS)-core-plus-O-antigen polysaccharide (COPS) to the periplasmic domains of both proteins, but with decreased affinity for the A107P mutant. Our studies reveal that subtle and localized structural differences in PCPs can have dramatic effects on LPS chain-length distribution in bacteria, for example by altering the affinity for the substrate, which supports the role of the structure of the growing Oag polymer in this process. PMID:26378781

  2. Decay Chain Deduction of Uranium Fission Products.

    PubMed

    Guo, Huiping; Tian, Chenyang; Wang, Xiaotian; Lv, Ning; Ma, Meng; Wei, Yingguang

    2016-07-01

    Delayed gamma spectrum is the fingerprint of uranium materials in arms control verification technology. The decay chain is simplified into basic state linear chain and excitation state linear chain to calculate and analyze the delayed gamma spectra of fission products. Formulas of the changing rule for nuclide number before and after zero-time are deduced. The C program for calculating the delayed gamma ray spectra data is constructed, and related experiments are conducted to verify this theory. Through analysis of the delayed gamma counts of several nuclides, the calculated results are found to be consistent with experimental values. PMID:27218290

  3. Spectroscopy of element 115 decay chains.

    PubMed

    Rudolph, D; Forsberg, U; Golubev, P; Sarmiento, L G; Yakushev, A; Andersson, L-L; Di Nitto, A; Düllmann, Ch E; Gates, J M; Gregorich, K E; Gross, C J; Heßberger, F P; Herzberg, R-D; Khuyagbaatar, J; Kratz, J V; Rykaczewski, K; Schädel, M; Åberg, S; Ackermann, D; Block, M; Brand, H; Carlsson, B G; Cox, D; Derkx, X; Eberhardt, K; Even, J; Fahlander, C; Gerl, J; Jäger, E; Kindler, B; Krier, J; Kojouharov, I; Kurz, N; Lommel, B; Mistry, A; Mokry, C; Nitsche, H; Omtvedt, J P; Papadakis, P; Ragnarsson, I; Runke, J; Schaffner, H; Schausten, B; Thörle-Pospiech, P; Torres, T; Traut, T; Trautmann, N; Türler, A; Ward, A; Ward, D E; Wiehl, N

    2013-09-13

    A high-resolution α, x-ray, and γ-ray coincidence spectroscopy experiment was conducted at the GSI Helmholtzzentrum für Schwerionenforschung. Thirty correlated α-decay chains were detected following the fusion-evaporation reaction 48Ca + 243Am. The observations are consistent with previous assignments of similar decay chains to originate from element Z=115. For the first time, precise spectroscopy allows the derivation of excitation schemes of isotopes along the decay chains starting with elements Z>112. Comprehensive Monte Carlo simulations accompany the data analysis. Nuclear structure models provide a first level interpretation. PMID:24074079

  4. Spectroscopy of element 115 decay chains

    SciTech Connect

    Rudolph, Dirk; Forsberg, U.; Golubev, P.; Sarmiento, L. G.; Yakushev, A.; Andersson, L.-L.; Di Nitto, A.; Duehllmann, Ch. E.; Gates, J. M.; Gregorich, K. E.; Gross, Carl J; Hessberger, F. P.; Herzberg, R.-D; Khuyagbaatar, J.; Kratz, J. V.; Rykaczewski, Krzysztof Piotr; Schaedel, M.; Aberg, S.; Ackermann, D.; Block, M.; Brand, H.; Carlsson, B. G.; Cox, D.; Derkx, X.; Eberhardt, K.; Even, J.; Fahlander, C.; Gerl, J.; Jaeger, E.; Kindler, B.; Krier, J.; Kojouharov, I.; Kurz, N.; Lommel, B.; Mistry, A.; Mokry, C.; Nitsche, H.; Omtvedt, J. P.; Papadakis, P.; Ragnarsson, I.; Runke, J.; Schaffner, H.; Schausten, B.; Thoerle-Pospiech, P.; Torres, T.; Traut, T.; Trautmann, N.; Tuerler, A.; Ward, A.; Ward, D. E.; Wiehl, N.

    2013-01-01

    A high-resolution a, X-ray and -ray coincidence spectroscopy experiment was conducted at the GSI Helmholtzzentrum fu r Schwerionenforschung. Thirty correlated a-decay chains were detected following the fusion-evaporation reaction 48Ca + 243Am. The observations are consistent with previous assignments of similar decay chains to originate from element Z = 115. The data includes first candidates of fingerprinting the decay step Mt --> Bh with characteristic X rays. For the first time, precise spectroscopy allows the derivation of excitation schemes of isotopes along the decay chains starting with elements Z > 112. Comprehensive Monte-Carlo simulations accompany the data analysis. Nuclear structure models provide a first level interpretation.

  5. Atomic Chain Electronics

    NASA Technical Reports Server (NTRS)

    Yamada, Toshishige; Saini, Subhash (Technical Monitor)

    1998-01-01

    Adatom chains, precise structures artificially created on an atomically regulated surface, are the smallest possible candidates for future nanoelectronics. Since all the devices are created by combining adatom chains precisely prepared with atomic precision, device characteristics are predictable, and free from deviations due to accidental structural defects. In this atomic dimension, however, an analogy to the current semiconductor devices may not work. For example, Si structures are not always semiconducting. Adatom states do not always localize at the substrate surface when adatoms form chemical bonds to the substrate atoms. Transport properties are often determined for the entire system of the chain and electrodes, and not for chains only. These fundamental issues are discussed, which will be useful for future device considerations.

  6. Factorialsum Number Chains.

    ERIC Educational Resources Information Center

    Lamb, John, Jr.

    1989-01-01

    Describes several phenomena in which interesting properties of numbers are demonstrated. Includes discussions of amicable, perfect, and sociable numbers. Presents computer programs for conducting a number chain search. (RT)

  7. Respiratory chain supercomplexes.

    PubMed

    Schägger, H

    2001-01-01

    Respiratory chain supercomplexes have been isolated from mammalian and yeast mitochondria, and bacterial membranes. Functional roles of respiratory chain supercomplexes are catalytic enhancement, substrate channelling, and stabilization of complex I by complex III in mammalian cells. Bacterial supercomplexes are characterized by their relatively high detergent-stability compared to yeast or mammalian supercomplexes that are stable to sonication. The mobility of substrate cytochrome c increases in the order bacterial, yeast, and mammalian respiratory chain. In bacterial supercomplexes, the electron transfer between complexes III and IV involves movement of the mobile head of a tightly bound cytochrome c, whereas the yeast S. cerevisiae seems to use substrate channelling of a mobile cytochrome c, and mammalian respiratory chains have been described to use a cytochrome c pool. Dimeric ATP synthase seems to be specific for mitochondrial OXPHOS systems. Monomeric complex V was found in Acetobacterium woodii and Paracoccus denitrificans. PMID:11798023

  8. Light chain nephropathy.

    PubMed

    Darouich, Sihem; Bettaieb, Ilhem; Aouadia, Raja; Hedri, Hafedh; Abderrahim, Ezzeddine; Goucha, Rym; Khedher, Adel

    2015-01-01

    Light chain deposition disease (LCDD) is characterized by the tissue deposition of monotypic immunoglobulin light chains of either kappa or lambda isotype. It is the archetypal systemic disease that is most frequently diagnosed on a kidney biopsy, although the deposits may involve several other organs. This brief review focuses on the clinicopathological features of LCDD-associated nephropathy with an emphasis on the diagnostic and therapeutic difficulties related to this elusive condition. PMID:26022011

  9. Analysis of the complementarity determining regions β-chain genomic rearrangement using high-throughput sequencing in periphery cytotoxic T lymphocytes of patients with chronic hepatitis B

    PubMed Central

    HUANG, YINUO; MA, HONG; WEI, SHUTANG; LUO, GANG; SUN, RUIMIN; FAN, ZHIBO; WU, LIPING; YANG, WENYI; FU, LIN; WANG, JUNHUI; HAN, DAZHENG; LU, JUN

    2016-01-01

    Cytotoxic T lymphocytes (CTLs) are important for the recognition of the hepatitis B virus (HBV), mediating immunoprotective mechanisms and determining the clinical outcome following HBV infection. CTLs recognize the invading virus via the T cell receptor (TCR). The aim of the current study was to investigate the variability of TCR in lymphocytes from patients with chronic hepatitis B and whether TCR genomic recombination is regulated by the current treatment strategies. Peripheral blood mononuclear cells (PBMCs) were isolated from patients with chronic hepatitis B and high-throughput sequencing was performed to analyze the gene expression diversity of β chain complementarity determining region. High-throughput sequencing produced ~380,000 reads. The sequences of V and J family mRNAs of the β chain V area were analyzed and databases were created for all 30 V family and J family genes. Using the Basic Local Alignment Search Tool, 15 genes were identified to be upregulated in the samples following treatment. Among them, the expression of T cell receptor β variable 28 (TRBV28)_T cell receptor β joining 1–5 (TRBJ1.5) and TRBV6_TRBJ2.10 were significantly different in the treated samples compared with samples taken prior to treatment. Genomic recombination patterns of TRBV and TRBJ of the β chain V area were observed to be different in the samples following treatment. The data of the current study demonstrated that the genomic rearrangement of the V and J segments of TCR β chain V area may be associated with the chronic progression of HBV and impact on treatment efficacy. PMID:27221081

  10. Identification and functional analysis of the essential and regulatory light chains of the only type II myosin Myo1p in Saccharomyces cerevisiae

    PubMed Central

    Luo, Jianying; Vallen, Elizabeth A.; Dravis, Christopher; Tcheperegine, Serguei E.; Drees, Becky; Bi, Erfei

    2004-01-01

    Cytokinesis in Saccharomyces cerevisiae involves coordination between actomyosin ring contraction and septum formation and/or targeted membrane deposition. We show that Mlc1p, a light chain for Myo2p (type V myosin) and Iqg1p (IQGAP), is the essential light chain for Myo1p, the only type II myosin in S. cerevisiae. However, disruption or reduction of Mlc1p–Myo1p interaction by deleting the Mlc1p binding site on Myo1p or by a point mutation in MLC1, mlc1-93, did not cause any obvious defect in cytokinesis. In contrast, a different point mutation, mlc1-11, displayed defects in cytokinesis and in interactions with Myo2p and Iqg1p. These data suggest that the major function of the Mlc1p–Myo1p interaction is not to regulate Myo1p activity but that Mlc1p may interact with Myo1p, Iqg1p, and Myo2p to coordinate actin ring formation and targeted membrane deposition during cytokinesis. We also identify Mlc2p as the regulatory light chain for Myo1p and demonstrate its role in Myo1p ring disassembly, a function likely conserved among eukaryotes. PMID:15210731

  11. Impacts to the ethylene supply chain from a hurricane disruption.

    SciTech Connect

    Sun, Amy Cha-Tien; Downes, Paula Sue; Heinen, Russell; Welk, Margaret Ellen

    2010-03-01

    Analysis of chemical supply chains is an inherently complex task, given the dependence of these supply chains on multiple infrastructure systems (e.g., the petroleum sector, transportation, etc.). This effort requires data and information at various levels of resolution, ranging from network-level distribution systems to individual chemical reactions. Sandia National Laboratories (Sandia) has integrated its existing simulation and infrastructure analysis capabilities with chemical data models to analyze the chemical supply chains of several nationally critical chemical commodities. This paper describes how Sandia models the ethylene supply chain; that is, the supply chain for the most widely used raw material for plastics production including a description of the types of data and modeling capabilities that are required to represent the ethylene supply chain. The paper concludes with a description of Sandia's use the model to project how the supply chain would be affected by and adapt to a disruptive scenario hurricane.

  12. Phasic Triplet Markov Chains.

    PubMed

    El Yazid Boudaren, Mohamed; Monfrini, Emmanuel; Pieczynski, Wojciech; Aïssani, Amar

    2014-11-01

    Hidden Markov chains have been shown to be inadequate for data modeling under some complex conditions. In this work, we address the problem of statistical modeling of phenomena involving two heterogeneous system states. Such phenomena may arise in biology or communications, among other fields. Namely, we consider that a sequence of meaningful words is to be searched within a whole observation that also contains arbitrary one-by-one symbols. Moreover, a word may be interrupted at some site to be carried on later. Applying plain hidden Markov chains to such data, while ignoring their specificity, yields unsatisfactory results. The Phasic triplet Markov chain, proposed in this paper, overcomes this difficulty by means of an auxiliary underlying process in accordance with the triplet Markov chains theory. Related Bayesian restoration techniques and parameters estimation procedures according to the new model are then described. Finally, to assess the performance of the proposed model against the conventional hidden Markov chain model, experiments are conducted on synthetic and real data. PMID:26353069

  13. Prevalence and mutation analysis of short/branched chain acyl-CoA dehydrogenase deficiency (SBCADD) detected on newborn screening in Wisconsin

    PubMed Central

    Van Calcar, Sandra C.; Baker, Mei W.; Williams, Phillip; Jones, Susan A.; Xiong, Blia; Thao, Mai Choua; Lee, Sheng; Yang, Mai Khou; Rice, Greg M.; Rhead, William; Vockley, Jerry; Hoffman, Gary; Durkin, Maureen S.

    2015-01-01

    Short/branched chain acyl-CoA dehydrogenase deficiency (SBCADD), also called 2-methylbutyryl CoA dehydrogenase deficiency (2-MBCDD), is a disorder of L-isoleucine metabolism of uncertain clinical significance. SBCADD is inadvertently detected on expanded newborn screening by elevated 2-methylbutyrylcarnitine (C5), which has the same mass to charge (m/s) on tandem mass spectrometry (MS/MS) as isovalerylcarnitine (C5), an analyte that is elevated in isovaleric acidemia (IVA), a disorder in leucine metabolism. SBCADD cases identified in the Hmong-American population have been found in association with the c.1165 A>G mutation in the ACADSB gene. The purposes of this study were to: (a) estimate the prevalence of SBCADD and carrier frequency of the c.1165 A>G mutation in the Hmong ethnic group; (b) determine whether the c.1 165 A>G mutation is common to all Hmong newborns screening positive for SBCADD; and (c) evaluate C5 acylcarnitine cut-off values to detect and distinguish between SBCADD and IVA diagnoses. During the first 10 years of expanded newborn screening using MS/MS in Wisconsin (2001–2011), 97 infants had elevated C5 values (≥0.44 μmol/L), of whom five were Caucasian infants confirmed to have IVA Of the remaining 92 confirmed SBCADD cases, 90 were of Hmong descent. Mutation analysis was completed on an anonymous, random sample of newborn screening cards (n = 1139) from Hmong infants. Fifteen infants, including nine who had screened positive for SBCADD based on a C5 acylcarnitine concentrations ≥0.44 μmol/L, were homozygous for the c.1165 A>G mutation. This corresponds to a prevalence in this ethnic group of being homozygous for the mutation of 1.3% (95% confidence interval 0.8–2.2%) and of being heterozygous for the mutation of 21.8% (95% confidence interval 19.4–24.3%), which is consistent with the Hardy-Weinberg equilibrium. Detection of homozygous individuals who were not identified on newborn screening suggests that the C5 screening cut

  14. Chain formation and chain dynamics in a dilute magnetorheological fluid.

    PubMed

    Hagenbüchle, M; Liu, J

    1997-10-20

    Magnetorheological fluids are suspensions of magnetizable particles that reversibly change from liquid to solid when subjected to a magnetic field. A field-induced structure of dipolar chains is responsible for these changes. Our work aimed at understanding chain dynamics and the kinetics of chain formation by using dynamic light scattering. Chain length is determined by measurement of the diffusion coefficient. Chain-length growth shows a Smoluchowski behavior. PMID:18264283

  15. Spatial Data Supply Chains

    NASA Astrophysics Data System (ADS)

    Varadharajulu, P.; Azeem Saqiq, M.; Yu, F.; McMeekin, D. A.; West, G.; Arnold, L.; Moncrieff, S.

    2015-06-01

    This paper describes current research into the supply of spatial data to the end user in as close to real time as possible via the World Wide Web. The Spatial Data Infrastructure paradigm has been discussed since the early 1990s. The concept has evolved significantly since then but has almost always examined data from the perspective of the supplier. It has been a supplier driven focus rather than a user driven focus. The current research being conducted is making a paradigm shift and looking at the supply of spatial data as a supply chain, similar to a manufacturing supply chain in which users play a significant part. A comprehensive consultation process took place within Australia and New Zealand incorporating a large number of stakeholders. Three research projects that have arisen from this consultation process are examining Spatial Data Supply Chains within Australia and New Zealand and are discussed within this paper.

  16. Supply-Chain Optimization Template

    NASA Technical Reports Server (NTRS)

    Quiett, William F.; Sealing, Scott L.

    2009-01-01

    The Supply-Chain Optimization Template (SCOT) is an instructional guide for identifying, evaluating, and optimizing (including re-engineering) aerospace- oriented supply chains. The SCOT was derived from the Supply Chain Council s Supply-Chain Operations Reference (SCC SCOR) Model, which is more generic and more oriented toward achieving a competitive advantage in business.

  17. Solitons in Granular Chains

    SciTech Connect

    Manciu, M.; Sen, S.; Hurd, A.J.

    1999-04-12

    The authors consider a chain of elastic (Hertzian) grains that repel upon contact according to the potential V = a{delta}{sup u}, u > 2, where {delta} is the overlap between the grains. They present numerical and analytical results to show that an impulse initiated at an end of a chain of Hertzian grains in contact eventually propagates as a soliton for all n > 2 and that no solitons are possible for n {le} 2. Unlike continuous, they find that colliding solitons in discrete media initiative multiple weak solitons at the point of crossing.

  18. INTERACTING QUANTUM SPIN CHAINS

    SciTech Connect

    ZHELUDEV,A.

    2001-09-09

    A brief review of recent advances in neutron scattering studies of low-dimensional quantum magnets is followed by a particular example. The separation of single-particle and continuum states in the weakly-coupled S = l/2 chains system BaCu{sub 2}Si{sub 2}O{sub 7} is described in some detail.

  19. Heavy Chain Diseases

    MedlinePlus

    ... cells often prevents proper absorption of nutrients from food (malabsorption), resulting in severe diarrhea and weight loss. A rare form that affects the respiratory tract also exists. Blood tests are done when alpha heavy chain disease is suspected. Serum protein electrophoresis, measurement of ...

  20. Polymerase chain reaction system

    DOEpatents

    Benett, William J.; Richards, James B.; Stratton, Paul L.; Hadley, Dean R.; Milanovich, Fred P.; Belgrader, Phil; Meyer, Peter L.

    2004-03-02

    A portable polymerase chain reaction DNA amplification and detection system includes one or more chamber modules. Each module supports a duplex assay of a biological sample. Each module has two parallel interrogation ports with a linear optical system. The system is capable of being handheld.

  1. Atwood's Heavy Chain

    ERIC Educational Resources Information Center

    Beeken, Paul

    2011-01-01

    While perusing various websites in search of a more challenging lab for my students, I came across a number of ideas where replacing the string in an Atwood's machine with a simple ball chain like the kind found in lamp pulls created an interesting system to investigate. The replacement of the string produced a nice nonuniform acceleration, but…

  2. Breaking the Chains

    ERIC Educational Resources Information Center

    Stanistreet, Paul

    2007-01-01

    In 1792 more than 350,000 people in Britain signed a petition calling for an end to the slave trade. It was, writes historian Adam Hochschild in his book "Bury the Chains," "the first time in history that a large number of people became outraged, and stayed outraged for many years, over someone else's rights". In 1807--after 15 years of…

  3. Supply chain optimization for pediatric perioperative departments.

    PubMed

    Davis, Janice L; Doyle, Robert

    2011-09-01

    Economic challenges compel pediatric perioperative departments to reduce nonlabor supply costs while maintaining the quality of patient care. Optimization of the supply chain introduces a framework for decision making that drives fiscally responsible decisions. The cost-effective supply chain is driven by implementing a value analysis process for product selection, being mindful of product sourcing decisions to reduce supply expense, creating logistical efficiency that will eliminate redundant processes, and managing inventory to ensure product availability. The value analysis approach is an analytical methodology for product selection that involves product evaluation and recommendation based on consideration of clinical benefit, overall financial impact, and revenue implications. PMID:21884843

  4. Cloning, expression, purification and preliminary crystallographic analysis of the short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica

    SciTech Connect

    Harmer, Nicholas J.; King, Jerry D.; Palmer, Colin M.; Preston, Andrew; Maskell, Duncan J.; Blundell, Tom L.

    2007-08-01

    The expression, purification, and crystallisation of the short-chain dehydrogenases WbmF, WbmG and WbmH from B. bronchiseptica are described. Native diffraction data to 1.5, 2.0, and 2.2 Å were obtained for the three proteins, together with complexes with nucleotides. The short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica were cloned into Escherichia coli expression vectors, overexpressed and purified to homogeneity. Crystals of all three wild-type enzymes were obtained using vapour-diffusion crystallization with high-molecular-weight PEGs as a primary precipitant at alkaline pH. Some of the crystallization conditions permitted the soaking of crystals with cofactors and nucleotides or nucleotide sugars, which are possible substrate compounds, and further conditions provided co-complexes of two of the proteins with these compounds. The crystals diffracted to resolutions of between 1.50 and 2.40 Å at synchrotron X-ray sources. The synchrotron data obtained were sufficient to determine eight structures of the three enzymes in complex with a variety of cofactors and substrate molecules.

  5. Effect of chain architecture on the size, shape, and intrinsic viscosity of chains in polymer solutions: A molecular simulation study

    NASA Astrophysics Data System (ADS)

    Khabaz, Fardin; Khare, Rajesh

    2014-12-01

    Effect of chain architecture on the chain size, shape, and intrinsic viscosity was investigated by performing molecular dynamics simulations of polymer solutions in a good solvent. Four types of chains - linear, comb shaped, H-shaped, and star - were studied for this purpose using a model in which the solvent particles were considered explicitly. Results indicated that the chain length (N) dependence of the mean squared radius of gyration of the chains followed a power-law behavior < {R_g^2 } rangle ^{1/2} ˜ N^\\upsilon with scaling exponents of υ = 0.605, 0.642, 0.602, and 0.608, for the linear, comb shaped, H-shaped, and star shaped chains, respectively. The simulation results for the geometrical shrinking factor were higher than the prior theoretical predictions for comb shaped chains. Analysis of chain shape demonstrated that the star chains were significantly smaller and more spherical than the others, while the comb and H-shaped polymer chains showed a more cylindrical shape. It is shown that the intrinsic viscosity of the chains can be calculated by plotting the specific viscosity determined from simulations against the solution concentration. The intrinsic viscosity exhibited linear behavior with the reciprocal of the overlap concentration for all chain architectures studied. The molecular weight dependence of the intrinsic viscosity followed the Mark-Houwink relation, [η] = KMa, for all chain architectures. When comparing the calculated values of exponent a with the literature experimental values, agreement was found only for the H and star chains, and a disagreement for the linear and comb chains. The viscosity shrinking factor of the branched chains was compared with the available experimental data and the theoretical predictions and a general agreement was found.

  6. Markov Chain Monte Carlo and Irreversibility

    NASA Astrophysics Data System (ADS)

    Ottobre, Michela

    2016-06-01

    Markov Chain Monte Carlo (MCMC) methods are statistical methods designed to sample from a given measure π by constructing a Markov chain that has π as invariant measure and that converges to π. Most MCMC algorithms make use of chains that satisfy the detailed balance condition with respect to π; such chains are therefore reversible. On the other hand, recent work [18, 21, 28, 29] has stressed several advantages of using irreversible processes for sampling. Roughly speaking, irreversible diffusions converge to equilibrium faster (and lead to smaller asymptotic variance as well). In this paper we discuss some of the recent progress in the study of nonreversible MCMC methods. In particular: i) we explain some of the difficulties that arise in the analysis of nonreversible processes and we discuss some analytical methods to approach the study of continuous-time irreversible diffusions; ii) most of the rigorous results on irreversible diffusions are available for continuous-time processes; however, for computational purposes one needs to discretize such dynamics. It is well known that the resulting discretized chain will not, in general, retain all the good properties of the process that it is obtained from. In particular, if we want to preserve the invariance of the target measure, the chain might no longer be reversible. Therefore iii) we conclude by presenting an MCMC algorithm, the SOL-HMC algorithm [23], which results from a nonreversible discretization of a nonreversible dynamics.

  7. Crystallization and Preliminary X-ray Analysis of the Human Long Myosin Light-Chain Kinase 1-Specific Domain IgCAM3

    SciTech Connect

    W Vallen Graham; A Magis; K Bailey; J Turner; D Ostrov

    2011-12-31

    Myosin light-chain kinase-dependent tight junction regulation is a critical event in inflammatory cytokine-induced increases in epithelial paracellular permeability. MLCK is expressed in human intestinal epithelium as two isoforms, long MLCK1 and long MLCK2, and MLCK1 is specifically localized to the tight junction, where it regulates paracellular permeability. The sole difference between these long MLCK splice variants is the presence of an immunoglobulin-like cell-adhesion molecule domain, IgCAM3, in MLCK1. To gain insight into the structure of the IgCAM3 domain, the IgCAM3 domain of MLCK1 has been expressed, purified and crystallized. Preliminary X-ray diffraction data were collected to 2.0 {angstrom} resolution and were consistent with the primitive trigonal space group P2{sub 1}2{sub 1}2{sub 1}.

  8. Rapid identification of Bordetella pertussis pertactin gene variants using LightCycler real-time polymerase chain reaction combined with melting curve analysis and gel electrophoresis.

    PubMed Central

    Mäkinen, J.; Viljanen, M. K.; Mertsola, J.; Arvilommi, H.; He, Q.

    2001-01-01

    Recently, eight allelic variants of the pertactin gene (prn1-8) have been characterized in Bordetella pertussis strains isolated in Europe and the United States. It has been suggested that the divergence of the pertactin types of clinical isolates from those of the B. pertussis vaccine strains is a result of vaccine-driven evolution. Sequencing of the prn, which is relatively time-consuming, has so far been the only method for the differentiation of prn types. We have developed a rapid real-time polymerase chain reaction assay suitable for large-scale screening of the prn type of the circulating strains. This method correctly identified the prn type of all tested 41 clinical isolates and two Finnish vaccine strains. The method is simple and reliable and provides an alternative for sequencing in pertussis research. PMID:11747721

  9. Mobility chains analysis of technologies for passenger cars and light duty vehicles fueled with biofuels : application of the Greet model to project the role of biomass in America's energy future (RBAEF) project.

    SciTech Connect

    Wu, M.; Wu, Y.; Wang, M; Energy Systems

    2008-01-31

    The Role of Biomass in America's Energy Future (RBAEF) is a multi-institution, multiple-sponsor research project. The primary focus of the project is to analyze and assess the potential of transportation fuels derived from cellulosic biomass in the years 2015 to 2030. For this project, researchers at Dartmouth College and Princeton University designed and simulated an advanced fermentation process to produce fuel ethanol/protein, a thermochemical process to produce Fischer-Tropsch diesel (FTD) and dimethyl ether (DME), and a combined heat and power plant to co-produce steam and electricity using the ASPEN Plus{trademark} model. With support from the U.S. Department of Energy (DOE), Argonne National Laboratory (ANL) conducted, for the RBAEF project, a mobility chains or well-to-wheels (WTW) analysis using the Greenhouse gases, Regulated Emissions, and Energy use in Transportation (GREET) model developed at ANL. The mobility chains analysis was intended to estimate the energy consumption and emissions associated with the use of different production biofuels in light-duty vehicle technologies.

  10. Construction and functional analysis of an anti-human cervical carcinoma/anti-human CD3 single-chain bispecific antibody.

    PubMed

    Wu, Hong; Yao, Li; Chou, Lin; Yang, Jin-Hua; Zhang, Yun-Xiu; Li, Xiao-Li; Shan, Bo-Er

    2016-07-01

    The aim of the present study was to construct a single-chain bispecific antibody (scBsAb) against cervical carcinoma and to investigate its biological activities. The scBsAb was constructed using a genetic cloning technique and antigen binding activities were detected by ELISA. The iodogen method was used to analyze the pharmacokinetics. The Rosette formation test was used to detect the binding ability between peripheral blood lymphocytes (PBLs) and Cs1213 cervical cancer cells. In addition, the MTT method was performed to detect the killing effect of PBLs. The molecular weight of the scBsAb was ~60 kDa. The antigen binding activities of scBsAbs were compared with the anti‑human cervical carcinoma antibody single‑chain Fv fragment (CSAs‑1 scFv) and anti‑cluster of differentiation (CD)3 scFv (P>0.05). In addition, a pharmacokinetics assay demonstrated that compared with the two corresponding scFvs, scBsAbs exhibited a significantly prolonged retention time in the body (P<0.01). In addition, the number of rosettes formed by PBLs and Cs1213 cells in the scBsAb group was markedly greater than that in the scFv groups or the RPMI‑1640 group (P<0.05 and P<0.01, respectively). The killing activity of PBLs against scBsAb‑mediated Cs1213 cells was significantly greater than that mediated by the other antibodies (P<0.05). When the concentration of scBsAb was 40 µg/ml, the killing rate was 64.5%. Thus, anti‑human cervical carcinoma/anti‑CD3 scBsAbs may possess two types of antigen binding activity, prolong the duration in vivo and improve the killing activity of PBLs against cancer cells. PMID:27220396

  11. Analyzing sites of OH radical attack (ring vs. side chain) in oxidation of substituted benzenes via dual stable isotope analysis (δ(13)C and δ(2)H).

    PubMed

    Zhang, Ning; Geronimo, Inacrist; Paneth, Piotr; Schindelka, Janine; Schaefer, Thomas; Herrmann, Hartmut; Vogt, Carsten; Richnow, Hans H

    2016-01-15

    OH radicals generated by the photolysis of H2O2 can degrade aromatic contaminants by either attacking the aromatic ring to form phenolic products or oxidizing the substituent. We characterized these competing pathways by analyzing the carbon and hydrogen isotope fractionation (εC and εH) of various substituted benzenes. For benzene and halobenzenes that only undergo ring addition, low values of εC (-0.7‰ to -1.0‰) were observed compared with theoretical values (-7.2‰ to -8‰), possibly owing to masking effect caused by pre-equilibrium between the substrate and OH radical preceding the rate-limiting step. In contrast, the addition of OH radicals to nitrobenzene ring showed a higher εC (-3.9‰), probably due to the lower reactivity. Xylene isomers, anisole, aniline, N,N-dimethylaniline, and benzonitrile yielded normal εH values (-2.8‰ to -29‰) indicating the occurrence of side-chain reactions, in contrast to the inverse εH (11.7‰ to 30‰) observed for ring addition due to an sp(2) to sp(3) hybridization change at the reacting carbon. Inverse εH values for toluene (14‰) and ethylbenzene (30‰) were observed despite the formation of side-chain oxidation products, suggesting that ring addition has a larger contribution to isotope fractionation. Dual element isotope slopes (∆δ(2)H/∆δ(13)C) therefore allow identification of significant degradation pathways of aromatic compounds by photochemically induced OH radicals. Issues that should be addressed in future studies include quantitative determination of the contribution of each competing pathway to the observed isotope fractionation and characterization of physical processes preceding the reaction that could affect isotope fractionation. PMID:26520272

  12. Association Analysis of Myosin Heavy-chain Genes mRNA Transcription with the Corresponding Proteins Expression of Longissimus Muscle in Growing Pigs.

    PubMed

    Men, X M; Deng, B; Tao, X; Qi, K K; Xu, Z W

    2016-04-01

    The goal of this work was to investigate the correlations between MyHC mRNA transcription and their corresponding protein expressions in porcine longissimus muscle (LM) during postnatal growth of pigs. Five DLY (Duroc×Landrace×Yorkshire) crossbred pigs were selected, slaughtered and sampled at postnatal 7, 30, 60, 120, and 180 days, respectively. Each muscle was subjected to quantity MyHCs protein contents through an indirect enzyme-linked immunosorbent assay (ELISA), to quantity myosin heavy-chains (MyHCs) mRNA abundances using real-time polymerase chain reaction. We calculated the proportion (%) of each MyHC to total of four MyHC for two levels, respectively. Moreover, the activities of several key energy metabolism enzymes were determined in LM. The result showed that mRNA transcription and protein expression of MyHC I, IIa, IIx and IIb in LM all presented some obvious changes with postnatal aging of pigs, especially at the early stage after birth, and their mRNA transcriptions were easy to be influenced than their protein expressions. The relative proportion of each MyHC mRNA was significantly positively related to that of its corresponding protein (p<0.01), and MyHC I mRNA proportion was positively correlated with creatine kinase (CK), succinate dehydrogenase (SDH), malate dehydrogenase (MDH) activities (p<0.05). These data suggested that MyHC mRNA transcription can be used to reflect MyHC expression, metabolism property and adaptive plasticity of porcine skeletal muscles, and MyHC mRNA composition could be a molecular index reflecting muscle fiber type characteristics. PMID:26949945

  13. Association Analysis of Myosin Heavy-chain Genes mRNA Transcription with the Corresponding Proteins Expression of Longissimus Muscle in Growing Pigs

    PubMed Central

    Men, X. M.; Deng, B.; Tao, X.; Qi, K. K.; Xu, Z. W.

    2016-01-01

    The goal of this work was to investigate the correlations between MyHC mRNA transcription and their corresponding protein expressions in porcine longissimus muscle (LM) during postnatal growth of pigs. Five DLY (Duroc×Landrace×Yorkshire) crossbred pigs were selected, slaughtered and sampled at postnatal 7, 30, 60, 120, and 180 days, respectively. Each muscle was subjected to quantity MyHCs protein contents through an indirect enzyme-linked immunosorbent assay (ELISA), to quantity myosin heavy-chains (MyHCs) mRNA abundances using real-time polymerase chain reaction. We calculated the proportion (%) of each MyHC to total of four MyHC for two levels, respectively. Moreover, the activities of several key energy metabolism enzymes were determined in LM. The result showed that mRNA transcription and protein expression of MyHC I, IIa, IIx and IIb in LM all presented some obvious changes with postnatal aging of pigs, especially at the early stage after birth, and their mRNA transcriptions were easy to be influenced than their protein expressions. The relative proportion of each MyHC mRNA was significantly positively related to that of its corresponding protein (p<0.01), and MyHC I mRNA proportion was positively correlated with creatine kinase (CK), succinate dehydrogenase (SDH), malate dehydrogenase (MDH) activities (p<0.05). These data suggested that MyHC mRNA transcription can be used to reflect MyHC expression, metabolism property and adaptive plasticity of porcine skeletal muscles, and MyHC mRNA composition could be a molecular index reflecting muscle fiber type characteristics. PMID:26949945

  14. X-ray diffraction analysis of the effects of myosin regulatory light chain phosphorylation and butanedione monoxime on skinned skeletal muscle fibers.

    PubMed

    Yamaguchi, Maki; Kimura, Masako; Li, Zhao-Bo; Ohno, Tetsuo; Takemori, Shigeru; Hoh, Joseph F Y; Yagi, Naoto

    2016-04-15

    The phosphorylation of the myosin regulatory light chain (RLC) is an important modulator of skeletal muscle performance and plays a key role in posttetanic potentiation and staircase potentiation of twitch contractions. The structural basis for these phenomena within the filament lattice has not been thoroughly investigated. Using a synchrotron radiation source at SPring8, we obtained X-ray diffraction patterns from skinned rabbit psoas muscle fibers before and after phosphorylation of myosin RLC in the presence of myosin light chain kinase, calmodulin, and calcium at a concentration below the threshold for tension development ([Ca(2+)] = 10(-6.8)M). After phosphorylation, the first myosin layer line slightly decreased in intensity at ∼0.05 nm(-1)along the equatorial axis, indicating a partial loss of the helical order of myosin heads along the thick filament. Concomitantly, the (1,1/1,0) intensity ratio of the equatorial reflections increased. These results provide a firm structural basis for the hypothesis that phosphorylation of myosin RLC caused the myosin heads to move away from the thick filaments towards the thin filaments, thereby enhancing the probability of interaction with actin. In contrast, 2,3-butanedione monoxime (BDM), known to inhibit contraction by impeding phosphate release from myosin, had exactly the opposite effects on meridional and equatorial reflections to those of phosphorylation. We hypothesize that these antagonistic effects are due to the acceleration of phosphate release from myosin by phosphorylation and its inhibition by BDM, the consequent shifts in crossbridge equilibria leading to opposite changes in abundance of the myosin-ADP-inorganic phosphate complex state associated with helical order of thick filaments. PMID:26911280

  15. Cross-contact chain

    NASA Technical Reports Server (NTRS)

    Lieneweg, Udo (Inventor)

    1988-01-01

    A system is provided for use with wafers that include multiple integrated circuits that include two conductive layers in contact at multiple interfaces. Contact chains are formed beside the integrated circuits, each contact chain formed of the same two layers as the circuits, in the form of conductive segments alternating between the upper and lower layers and with the ends of the segments connected in series through interfaces. A current source passes a current through the series-connected segments, by way of a pair of current tabs connected to opposite ends of the series of segments. While the current flows, voltage measurements are taken between each of a plurality of pairs of voltage tabs, the two tabs of each pair connected to opposite ends of an interface that lies along the series-connected segments. A plot of interface conductances on a normal probability chart, enables prediction of the yield of good integrated circuits from the wafer.

  16. Cross-contact chain

    NASA Technical Reports Server (NTRS)

    Lieneweg, U. (Inventor)

    1986-01-01

    A system is provided for use with wafers that include multiple integrated circuits that include two conductive layers in contact at multiple interfaces. Contact chains are formed beside the integrated circuits, each contact chain formed of the same two layers as the circuits, in the form of conductive segments alternating between the upper and lower layers and with the ends of the segments connected in series through interfaces. A current source passes a current through the series-connected segments, by way of a pair of current tabs connected to opposite ends of the series of segments. While the current flows, voltage measurements are taken between each of a plurality of pairs of voltage tabs, the two tabs of each pair connected to opposite ends of an interface that lies along the series-connected segments. A plot of interface conductances on normal probability chart enables prediction of the yield of good integrated circuits from the wafer.

  17. Streamlining the supply chain.

    PubMed

    Neumann, Lydon

    2003-07-01

    Effective management of the supply chain requires attention to: Product management--formulary development and maintenance, compliance, clinical involvement, standardization, and demand-matching. Sourcing and contracting--vendor consolidation, GPO portfolio management, price leveling, content management, and direct contracting Purchasing and payment-cycle--automatic placement, web enablement, centralization, evaluated receipts settlement, and invoice matching Inventory and distribution management--"unofficial" and "official" locations, vendor-managed inventory, automatic replenishment, and freight management. PMID:12866156

  18. Callisto Crater Chain Mosaic

    NASA Technical Reports Server (NTRS)

    1997-01-01

    This mosaic of three images shows an area within the Valhalla region on Jupiter's moon, Callisto. North is to the top of the mosaic and the Sun illuminates the surface from the left. The smallest details that can be discerned in this picture are knobs and small impact craters about 160 meters (175 yards) across. The mosaic covers an area approximately 45 kilometers (28 miles) across. It shows part of a prominent crater chain located on the northern part of the Valhalla ring structure.

    Crater chains can form from the impact of material ejected from large impacts (forming secondary chains) or by the impact of a fragmented projectile, perhaps similar to the Shoemaker-Levy 9 cometary impacts into Jupiter in July 1994. It is believed this crater chain was formed by the impact of a fragmented projectile. The images which form this mosaic were obtained by the solid state imaging system aboard NASA's Galileo spacecraft on Nov. 4, 1996 (Universal Time).

    Launched in October 1989, Galileo entered orbit around Jupiter on December 7, 1995. The spacecraft's mission is to conduct detailed studies of the giant planet, its largest moons and the Jovian magnetic environment. The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.

    This image and other images and data received from Galileo are posted on the World Wide Web Galileo mission home page at http://galileo.jpl.nasa.gov. Background information and educational context for the images can be found at http:// www.jpl.nasa.gov/galileo/sepo.

  19. The innovation value chain.

    PubMed

    Hansen, Morten T; Birkinshaw, Julian

    2007-06-01

    The challenges of coming up with fresh ideas and realizing profits from them are different for every company. One firm may excel at finding good ideas but may have weak systems for bringing them to market. Another organization may have a terrific process for funding and rolling out new products and services but a shortage of concepts to develop. In this article, Hansen and Birkinshaw caution executives against using the latest and greatest innovation approaches and tools without understanding the unique deficiencies in their companies' innovation systems. They offer a framework for evaluating innovation performance: the innovation value chain. It comprises the three main phases of innovation (idea generation, conversion, and diffusion) as well as the critical activities performed during those phases (looking for ideas inside your unit; looking for them in other units; looking for them externally; selecting ideas; funding them; and promoting and spreading ideas companywide). Using this framework, managers get an end-to-end view of their innovation efforts. They can pinpoint their weakest links and tailor innovation best practices appropriately to strengthen those links. Companies typically succumb to one of three broad "weakest-link" scenarios. They are idea poor, conversion poor, or diffusion poor. The article looks at the ways smart companies - including Intuit, P&G, Sara Lee, Shell, and Siemens- modify the best innovation practices and apply them to address those organizations' individual needs and flaws. The authors warn that adopting the chain-based view of innovation requires new measures of what can be delivered by each link in the chain. The approach also entails new roles for employees "external scouts" and "internal evangelists," for example. Indeed, in their search for new hires, companies should seek out those candidates who can help address particular weaknesses in the innovation value chain. PMID:17580654

  20. Determining Annealing Temperatures for Polymerase Chain Reaction

    ERIC Educational Resources Information Center

    Porta, Angela R.; Enners, Edward

    2012-01-01

    The polymerase chain reaction (PCR) is a common technique used in high school and undergraduate science teaching. Students often do not fully comprehend the underlying principles of the technique and how optimization of the protocol affects the outcome and analysis. In this molecular biology laboratory, students learn the steps of PCR with an…

  1. Requirements of supply chain management in differentiating European pork chains.

    PubMed

    Trienekens, Jacques; Wognum, Nel

    2013-11-01

    This paper summarizes results obtained by research into pork chain management in the EU Integrated Project Q-Porkchains. Changing demands for intrinsic and extrinsic quality attributes of pork products impact the way supply chain management should be organized from the farmer down to the consumer. The paper shows the importance of Quality Management Systems for integrating supply chains and enhancing consumer confidence. The paper also presents innovations in information system integration for aligning information exchange in the supply chain and logistics concepts based on innovative measurement technologies at the slaughterhouse stage. In the final section research challenges towards sustainable pork supply chains satisfying current consumer demands are presented. PMID:23611335

  2. In vitro analysis of the effect of alkyl-chain length of anionic surfactants on the skin by using a reconstructed human epidermal model.

    PubMed

    Yamaguchi, Fumiko; Watanabe, Shin-Ichi; Harada, Fusae; Miyake, Miyuki; Yoshida, Masaki; Okano, Tomomichi

    2014-01-01

    We investigated the effect of the alkyl-chain length of anionic surfactants on the skin using an in vitro model. The evaluated anionic surfactants were sodium alkyl sulfate (AS) and sodium fatty acid methyl ester sulfonate (MES), which had different alkyl-chain lengths (C8-C14). Skin tissue damage and permeability were examined using a reconstructed human epidermal model, LabCyte EPI-MODEL24. Skin tissue damage was examined by measuring cytotoxicity with an MTT assay. Liquid chromatography/tandem mass spectrometry (LC/MS-MS) and liquid chromatography/mass spectrometry (LC/MS) were used to detect surfactants that permeated into the assay medium through an epidermal model. To assess the permeation mechanism and cell damage caused by the surfactants through the epidermis, we evaluated the structural changes of Bovine Serum Albumin (BSA), used as a simple model protein, and the fluidity of 1,2-dipalmitoyl-sn-glycero-3-phosphpcholine (DPPC) liposome, which serves as one of the most abundant phospholipid models of living cell membranes in the epidermis. The effects of the surfactants on the proteins were measured using Circular Dichroism (CD) spectroscopy, while the effects on membrane fluidity were investigated by electron spin resonance (ESR) spectroscopy. ET50 (the 50% median effective time) increased as follows: C10 < C12 < C8 < C14 in AS and C8, C10 < C12 < C14 in MES. The order of permeation through the LabCyte EPI-MODEL24 was C10 > C12 > C14, for both AS and MES. For both AS and MES, the order parameter, which is the criteria for the microscopic viscosity of lipid bilayers, increased as follows: C10 < C12 < C14, which means the membrane fluidity is C10 > C12 > C14. It was determined that the difference in skin tissue damage in the LabCyte EPI-MODEL24 with C10 to C14 AS and MES was caused by the difference in permeation and cell membrane fluidity through the lipid bilayer path in the epidermis. PMID:25213449

  3. Structure and Stability of Monatomic Metallic Chains

    NASA Astrophysics Data System (ADS)

    Batra, Inder P.; Sen, Prasenjit; Ciraci, S.

    2001-03-01

    We have investigated atomic and electronic structure of Au and Al monatomic chains by using first-principle plane wave method within density-functional theory. Despite their different valencies, Au and Al form planar zigzag chains with each atom having four nearest neighbors. The zigzag structure is stable against linearization and non-planar deformations. We performed an extensive charge density analysis and finite temperature calculations to reveal the origin of the unusual atomic structure in these one dimensional metallic systems. The implications of the zigzag structure on the electronic properties and the balistic electron conduction have been examined.

  4. Rapid cloning, expression, and functional characterization of paired αβ and γδ T-cell receptor chains from single-cell analysis

    PubMed Central

    Guo, Xi-zhi J; Dash, Pradyot; Calverley, Matthew; Tomchuck, Suzanne; Dallas, Mari H; Thomas, Paul G

    2016-01-01

    Transgenic expression of antigen-specific T-cell receptor (TCR) genes is a promising approach for immunotherapy against infectious diseases and cancers. A key to the efficient application of this approach is the rapid and specific isolation and cloning of TCRs. Current methods are often labor-intensive, nonspecific, and/or relatively slow. Here, we describe an efficient system for antigen-specific αβTCR cloning and CDR3 substitution. We demonstrate the capability of cloning influenza-specific TCRs within 10 days using single-cell polymerase chain reaction (PCR) and Gibson Assembly techniques. This process can be accelerated to 5 days by generating receptor libraries, requiring only the exchange of the antigen-specific CDR3 region into an existing backbone. We describe the construction of this library for human γδ TCRs and report the cloning and expression of a TRGV9/TRDV2 receptor that is activated by zoledronic acid. The functional activity of these αβ and γδ TCRs can be characterized in a novel reporter cell line (Nur77-GFP Jurkat 76 TCRα–β–) for screening of TCR specificity and avidity. In summary, we provide a rapid method for the cloning, expression, and functional characterization of human and mouse TCRs that can assist in the development of TCR-mediated therapeutics. PMID:26858965

  5. Rapid cloning, expression, and functional characterization of paired αβ and γδ T-cell receptor chains from single-cell analysis.

    PubMed

    Guo, Xi-Zhi J; Dash, Pradyot; Calverley, Matthew; Tomchuck, Suzanne; Dallas, Mari H; Thomas, Paul G

    2016-01-01

    Transgenic expression of antigen-specific T-cell receptor (TCR) genes is a promising approach for immunotherapy against infectious diseases and cancers. A key to the efficient application of this approach is the rapid and specific isolation and cloning of TCRs. Current methods are often labor-intensive, nonspecific, and/or relatively slow. Here, we describe an efficient system for antigen-specific αβTCR cloning and CDR3 substitution. We demonstrate the capability of cloning influenza-specific TCRs within 10 days using single-cell polymerase chain reaction (PCR) and Gibson Assembly techniques. This process can be accelerated to 5 days by generating receptor libraries, requiring only the exchange of the antigen-specific CDR3 region into an existing backbone. We describe the construction of this library for human γδ TCRs and report the cloning and expression of a TRGV9/TRDV2 receptor that is activated by zoledronic acid. The functional activity of these αβ and γδ TCRs can be characterized in a novel reporter cell line (Nur77-GFP Jurkat 76 TCRα(-)β(-)) for screening of TCR specificity and avidity. In summary, we provide a rapid method for the cloning, expression, and functional characterization of human and mouse TCRs that can assist in the development of TCR-mediated therapeutics. PMID:26858965

  6. Proteomics Analysis of the Non-Muscle Myosin Heavy Chain IIa-Enriched Actin-Myosin Complex Reveals Multiple Functions within the Podocyte

    PubMed Central

    Hays, Thomas; Ma’ayan, Avi; Clark, Neil R.; Tan, Christopher M.; Teixeira, Avelino; Teixeira, Angela; Choi, Jae W.; Burdis, Nora; Jung, Sung Yun; Bajaj, Amol O.; O’Malley, Bert W.; He, John C.; Hyink, Deborah P.; Klotman, Paul E.

    2014-01-01

    MYH9 encodes non-muscle myosin heavy chain IIA (NMMHCIIA), the predominant force-generating ATPase in non-muscle cells. Several lines of evidence implicate a role for MYH9 in podocytopathies. However, NMMHCIIA‘s function in podocytes remains unknown. To better understand this function, we performed immuno-precipitation followed by mass-spectrometry proteomics to identify proteins interacting with the NMMHCIIA-enriched actin-myosin complexes. Computational analyses revealed that these proteins belong to functional networks including regulators of cytoskeletal organization, metabolism and networks regulated by the HIV-1 gene nef. We further characterized the subcellular localization of NMMHCIIA within podocytes in vivo, and found it to be present within the podocyte major foot processes. Finally, we tested the effect of loss of MYH9 expression in podocytes in vitro, and found that it was necessary for cytoskeletal organization. Our results provide the first survey of NMMHCIIA-enriched actin-myosin-interacting proteins within the podocyte, demonstrating the important role of NMMHCIIA in organizing the elaborate cytoskeleton structure of podocytes. Our characterization of NMMHCIIA’s functions goes beyond the podocyte, providing important insights into its general molecular role. PMID:24949636

  7. Molecular cloning and mRNA expression analysis of myosin heavy chain (MyHC) from fast skeletal muscle of grass carp, Ctenopharyngodon idella

    NASA Astrophysics Data System (ADS)

    Chu, Wuying; Fu, Guihong; Bing, Shiyu; Meng, Tao; Zhou, Ruixue; Cheng, Jia; Zhao, Falan; Zhang, Hongfang; Zhang, Jianshe

    2010-03-01

    The myosin heavy chain (MyHC) is one of the major structural and contracting proteins of muscle. We have isolated the cDNA clone encoding MyHC of the grass carp, Ctenopharyngodon idella. The sequence comprises 5 934 bp, including a 5 814 bp open reading frame encoding an amino acid sequence of 1 937 residues. The deduced amino acid sequence showed 69% homology to rabbit fast skeletal MyHC and 73%-76% homology to the MyHCs from the mandarin fish, walleye pollack, white croaker, chum salmon, and carp. The putative sequences of subfragment-1 and the light meromyosin region showed 61.4%-80% homology to the corresponding regions of other fish MyHCs. The tissue-specific and developmental stage-specific expressions of the MyHC gene were analyzed by quantitative real-time PCR. The MyHC gene showed the highest expression in the muscles compared with the kidney, spleen and intestine. Developmentally, there was a gradual increase in MyHC mRNA expression from the neural formation stage to the tail bud stage. The highest expression was detected in hatching larva. Our work on the MyHC gene from the grass carp has provided useful information for fish molecular biology and fish genomics.

  8. Synthesis of magnetic molecularly imprinted polymers by reversible addition fragmentation chain transfer strategy and its application in the Sudan dyes residue analysis.

    PubMed

    Xie, Xiaoyu; Chen, Liang; Pan, Xiaoyan; Wang, Sicen

    2015-07-31

    Magnetic molecularly imprinted polymers (MMIPs) have become a hotspot owing to the dual functions of target recognition and magnetic separation. In this study, the MMIPs were obtained by the surface-initiated reversible addition fragmentation chain transfer (RAFT) polymerization using Sudan I as the template. The resultant MMIPs were characterized by transmission electron microscope, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, vibrating sample magnetometer, and X-ray diffraction. Benefiting from the controlled/living property of the RAFT strategy, the uniform MIP layer was successfully grafted on the surface of RAFT agent-modified Fe3O4@SiO2 nanoparticles, favoring the fast mass transfer and rapid binding kinetics. The developed MMIPs were used as the solid-phase extraction sorbents to selectively extract four Sudan dyes (Sudan I, II, III, and IV) from chili powder samples. The recoveries of the spiked samples in chili powder samples ranged from 74.1 to 93.3% with RSD lower than 6.4% and the relative standard uncertainty lower than 0.029. This work provided a good platform for the extraction and removal of Sudan dyes in complicated matrixes and demonstrated a bright future for the application of the well-constructed MMIPs in the field of solid-phase extraction. PMID:26077971

  9. Analysis of the conformation and thermal stability of the high-affinity IgE Fc receptor β chain polymorphic proteins.

    PubMed

    Terada, Tomoyoshi; Takahashi, Teppei; Arikawa, Hajime; Era, Seiichi

    2016-07-01

    The high-affinity IgE Fc receptor (FcεRI) β chain acts as a signal amplifier through the immunoreceptor tyrosine-based activation motif in its C-terminal intracellular region. Polymorphisms in FcεRI β have been linked to atopy, asthma, and allergies. We investigated the secondary structure, conformation, and thermal stability of FcεRI β polymorphic (β-L172I, β-L174V, and β-E228G) proteins. Polymorphisms did not affect the secondary structure and conformation of FcεRI β. However, we calculated Gibbs free energy of unfolding (ΔGunf) and significant differences were observed in ΔGunf values between the wild-type FcεRI β (β-WT) and β-E228G. These results suggested that β-E228G affected the thermal stability of FcεRI β. The role of β-E228G in biological functions and its involvement in allergic reactions have not yet been elucidated in detail; therefore, differences in the thermal stability of β-E228G may affect the function of FcεRI β. PMID:26940508

  10. Aberrant expression of anaplastic lymphoma kinase in lung adenocarcinoma: Analysis of circulating free tumor RNA using one-step reverse transcription-polymerase chain reaction.

    PubMed

    Bruno, Rossella; Giordano, Mirella; Giannini, Riccardo; Alì, Greta; Puppo, Gianfranco; Ribechini, Alessandro; Chella, Antonio; Fontanini, Gabriella

    2016-09-01

    Lung adenocarcinoma patients harboring anaplastic lymphoma kinase (ALK) gene rearrangements respond well to approved ALK inhibitors. However, to date, limited evidence is available regarding whether using circulating free tumor mRNA to identify aberrant ALK expression is possible, and its feasibility remains to be clearly addressed. The present study evaluated ALK expression by a one-step reverse transcription‑polymerase chain reaction (PCR) assay on the circulating free tumor mRNA from 12 lung adenocarcinoma patients. Additionally, the present study tested for ALK rearrangements by fluorescence in situ hybridization (FISH) and immunohistochemistry. A molecular genetic characterization was performed on tumor tissues and plasma samples. Aberrant ALK expression was detected in 2/12 patients using mRNA purified from plasma specimens and the results agreed with the FISH and immunohistochemistry findings of solid biopsy samples. The detection of aberrant ALK expression on circulating free tumor RNA may be feasible using a one‑step real‑time PCR assay and may be particularly helpful when a solid biopsy sample is not available. PMID:27430882

  11. Radiology's value chain.

    PubMed

    Enzmann, Dieter R

    2012-04-01

    A diagnostic radiology value chain is constructed to define its main components, all of which are vulnerable to change, because digitization has caused disaggregation of the chain. Some components afford opportunities to improve productivity, some add value, while some face outsourcing to lower labor cost and to information technology substitutes, raising commoditization risks. Digital image information, because it can be competitive at smaller economies of scale, allows faster, differential rates of technological innovation of components, initiating a centralization-to-decentralization technology trend. Digitization, having triggered disaggregation of radiology's professional service model, may soon usher in an information business model. This means moving from a mind-set of "reading images" to an orientation of creating and organizing information for greater accuracy, faster speed, and lower cost in medical decision making. Information businesses view value chain investments differently than do small professional services. In the former model, producing a better business product will extend image interpretation beyond a radiologist's personal fund of knowledge to encompass expanding external imaging databases. A follow-on expansion with integration of image and molecular information into a report will offer new value in medical decision making. Improved interpretation plus new integration will enrich and diversify radiology's key service products, the report and consultation. A more robust, information-rich report derived from a "systems" and "computational" radiology approach will be facilitated by a transition from a professional service to an information business. Under health care reform, radiology will transition its emphasis from volume to greater value. Radiology's future brightens with the adoption of a philosophy of offering information rather than "reads" for decision making. Staunchly defending the status quo via turf wars is unlikely to constitute a

  12. Musical Markov Chains

    NASA Astrophysics Data System (ADS)

    Volchenkov, Dima; Dawin, Jean René

    A system for using dice to compose music randomly is known as the musical dice game. The discrete time MIDI models of 804 pieces of classical music written by 29 composers have been encoded into the transition matrices and studied by Markov chains. Contrary to human languages, entropy dominates over redundancy, in the musical dice games based on the compositions of classical music. The maximum complexity is achieved on the blocks consisting of just a few notes (8 notes, for the musical dice games generated over Bach's compositions). First passage times to notes can be used to resolve tonality and feature a composer.

  13. Monte Carlo without chains

    SciTech Connect

    Chorin, Alexandre J.

    2007-12-12

    A sampling method for spin systems is presented. The spin lattice is written as the union of a nested sequence of sublattices, all but the last with conditionally independent spins, which are sampled in succession using their marginals. The marginals are computed concurrently by a fast algorithm; errors in the evaluation of the marginals are offset by weights. There are no Markov chains and each sample is independent of the previous ones; the cost of a sample is proportional to the number of spins (but the number of samples needed for good statistics may grow with array size). The examples include the Edwards-Anderson spin glass in three dimensions.

  14. Characterization of the molecular species of glycerophospholipids from rabbit kidney: an alternative approach to the determination of the fatty acyl chain position by negative ion fast atom bombardment combined with mass-analysed ion kinetic energy analysis.

    PubMed

    Chen, S; Curcuruto, O; Catinella, S; Traldi, P; Menon, G

    1992-12-01

    An alternative approach to identifying fatty acid chain position in the molecular species of glycerophospholipids has been studied and developed. The fatty acyl groups esterified to the glycerol backbone in isomeric glycerophosphatidyl-choline, -serine and -ethanolamine as well as glycerophosphatidic acid can be detected by the presence of a pair of anions derived from phosphatidic acid parent ions (M minus the polar head groups in glycerophospholipids), designed to be [M--polar head--R2COOH]- and [M--polar head--R2CO--H]-, produced by negative ion fast atom bombardment combined with mass-analysed ion kinetic energy analysis. Because of the significant abundance of [M--polar head--R2COOH]- anion, fatty acid chains differing by 2 Da can be distinguished by accurate measurements of the electrostatic voltage related to this ion. Three-volt differences can be evidenced. Using this approach, the molecular species of glycerophosphatidyl-choline, -serine, -ethanolamine and -inositol from rabbit kidney were characterized after the separation of both class and species by normal and reversed-phase high-performance liquid chromatography, respectively. We identified 11 arachidonoyl-containing molecular species of glycerophospholipids and the other 17 lipid molecules in this biological material. A couple of 1- alkenyl-2-arachidonoyl-sn-glycerol-3-phosphoethanolamine species, identified as plasmalogen GPE 16:0-20:4 and plasmalogen GPE 18:0-20:4, were found for the first time in rabbit kidney. PMID:1477110

  15. Chain termination in polyhydroxyalkanoate synthesis: involvement of exogenous hydroxy-compounds as chain transfer agents.

    PubMed

    Madden, L A; Anderson, A J; Shah, D T; Asrar, J

    1999-01-01

    We have identified a range of compounds which, when present during poly(3-hydroxybutyrate) [P(3HB)] accumulation by Ralstonia eutropha (reclassified from Alcaligenes eutrophus), can act as chain transfer agents in the chain termination step of polymerization. End-group analysis by 31P NMR of polymer derivatized with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane revealed that all these compounds were covalently linked to P(3HB) at the carboxyl terminus. All chain transfer agents possessed one or more hydroxyl groups, and glycerol was selected for further investigation. The number-average molecular mass (Mn) of P(3HB) produced by R. eutropha from glycerol was substantially lower than for polymer produced from glucose, and we identified two new end-group structures. These were attributed to a glycerol molecule bound to the P(3HB) chain via the primary or secondary hydroxyl groups. When a primary hydroxyl group of glycerol is involved in chain transfer, the end-group structure is in both [R] and [S] configurations, implying that chain transfer to glycerol is a random transesterification and that PHA synthase does not catalyse chain transfer. 3-Hydroxybutyric acid is the most probable chain transfer agent in vivo, with propagation and termination reactions involving transfer of the P(3HB) chain to enzyme-bound and free 3-hydroxybutyrate, respectively. Only carboxyl end-groups were detected in P(3HB) extracted from exponentially growing bacteria. It is proposed that a compound other than 3-hydroxybutyryl-CoA acts as a primer in the initiation of polymer synthesis. PMID:10416649

  16. System Dynamics Modeling for Supply Chain Information Sharing

    NASA Astrophysics Data System (ADS)

    Feng, Yang

    In this paper, we try to use the method of system dynamics to model supply chain information sharing. Firstly, we determine the model boundaries, establish system dynamics model of supply chain before information sharing, analyze the model's simulation results under different changed parameters and suggest improvement proposal. Then, we establish system dynamics model of supply chain information sharing and make comparison and analysis on the two model's simulation results, to show the importance of information sharing in supply chain management. We wish that all these simulations would provide scientific supports for enterprise decision-making.

  17. T cell receptor β-chain repertoire analysis reveals intratumour heterogeneity of tumour-infiltrating lymphocytes in oesophageal squamous cell carcinoma.

    PubMed

    Chen, Zengchao; Zhang, Chaoting; Pan, Yaqi; Xu, Ruiping; Xu, Changqing; Chen, Ziping; Lu, Zheming; Ke, Yang

    2016-08-01

    Oesophageal squamous cell carcinoma (ESCC) has a generally poor prognosis, due to the lack of effective treatment methods. Immunotherapeutic approaches based on tumour-infiltrating lymphocytes (TILs) have demonstrated that durable responses are produced in some patients with solid tumours, which suggests the potential feasibility of clinical application of immunotherapy for ESCC. However, many of the basic characteristics of TILs in ESCC are poorly understood, including clonality, specificity and spatial heterogeneity of the response of TILs, which depends on the interaction between antigens and T cell receptors (TCRs). We used ultra-deep sequencing of rearranged genes in TCR β-chain (TCRβ) to profile the basic characteristics of T cells in tumour tissues (four to six regions from each tumour) as well as matched adjacent normal tissue and peripheral blood from seven patients diagnosed with primary ESCC. We found that T cell clones within ESCCs were quite different from those of the peripheral blood and even the adjacent normal tissues in general. Although there was a relatively higher degree of overlap of intratumoural TCRβ repertoires than those between the tumour and other tissues, intratumoural TCRβ repertoires were spatially heterogeneous. Due to the restricted sampling, high-throughput TCRβ sequencing could characterize the diversity and composition of a limited (compartment-dependent) fraction of the respective T cell clones in any individual ESCC, expanding our understanding of immune behaviour and immune response and shedding more light on ESCC immunotherapy. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. PMID:27171315

  18. Evaluation of a Campylobacter fetus subspecies venerealis real-time quantitative polymerase chain reaction for direct analysis of bovine preputial samples

    PubMed Central

    Chaban, Bonnie; Chu, Shirley; Hendrick, Steven; Waldner, Cheryl; Hill, Janet E.

    2012-01-01

    The detection and subspeciation of Campylobacter fetus subsp. venerealis (CFV) from veterinary samples is important for both clinical and economic reasons. Campylobacter fetus subsp. venerealis is the causative agent of bovine genital campylobacteriosis, a venereal disease that can lead to serious reproductive problems in cattle, and strict international regulations require animals and animal products to be CFV-free for trade. This study evaluated methods reported in the literature for CFV detection and reports the translation of an extensively tested CFV-specific polymerase chain reaction (PCR) primer set; including the VenSF/VenSR primers and a real-time, quantitative PCR (qPCR) platform using SYBR Green chemistry. Three methods of preputial sample preparation for direct qPCR were evaluated and a heat lysis DNA extraction method was shown to allow for CFV detection at the level of approximately one cell equivalent per reaction (or 1.0 × 103 CFU/mL) from prepuce. The optimized sample preparation and qPCR protocols were then used to evaluate 3 western Canadian bull cohorts, which included 377 bulls, for CFV. The qPCR assay detected 11 positive bulls for the CFV-specific parA gene target. DNA sequence data confirmed the identity of the amplified product and revealed that positive samples were comprised of 2 sequence types; one identical to previously reported CFV parA gene sequences and one with a 9% sequence divergence. These results add valuable information towards our understanding of an important CFV subspeciation target and offer a significantly improved format for an internationally recognized PCR test. PMID:23277694

  19. Real-time Polymerase Chain Reaction Analysis of Sewage Samples to Determine Oral Polio Vaccine Circulation Duration and Mutation After Mexican National Immunization Weeks

    PubMed Central

    Troy, Stephanie B.; Ferreyra-Reyes, Leticia; Canizales-Quintero, Sergio; Huang, ChunHong; Lee, Yu-Jin; Báez-Saldaña, Renata; Ferreira-Guerrero, Elizabeth; García-García, Lourdes; Maldonado, Yvonne

    2012-01-01

    Background. Oral polio vaccine (OPV) can mutate and cause outbreaks of paralytic poliomyelitis with prolonged replication. After poliovirus eradication, global use of inactivated polio vaccine (IPV) may be needed until all OPV stops circulating. Mexico, where children receive routine IPV but where OPV is given only during biannual national immunization weeks (NIWs), provides a natural setting to study duration of OPV circulation in a community primarily vaccinated with IPV. Methods. One-liter sewage samples from four separate arroyos (creeks) near Orizaba, Mexico, were collected monthly for 12 months. Concentrated sewage underwent RNA extraction, reverse transcription, and real-time polymerase chain reaction (PCR) to detect OPV serotypes 1, 2, and 3 and their variants containing the serotype-specific point mutation in the 5′ untranslated region associated with neurovirulence. Results. OPV was detected 3, 4, 5, and 7 months after the May 2010 NIW, but was not detected at 6 or 8 months. A second and third NIW occurred in February 2011 and May 2011, and OPV was detected in the sewage monthly after both of these NIW through July 2011 when collection stopped. The OPV detected was primarily serotype 2 and predominantly contained the point mutations in the 5′ untranslated region associated with increased neurovirulence. Conclusions. OPV was detected in sewage as late as 7 months after an NIW in a Mexican community primarily vaccinated with IPV, but was not detected at 8 months, suggesting that OPV circulation may have ceased. These data suggest that in communities with high vaccination rates, 1 or 2 years of IPV administration after OPV cessation could be sufficient to prevent outbreaks of paralytic poliomyelitis from vaccine-derived strains. PMID:23667738

  20. Pasteurella multocida in backyard chickens in Upper Egypt: incidence with polymerase chain reaction analysis for capsule type, virulence in chicken embryos and antimicrobial resistance.

    PubMed

    Mohamed, Moemen A; Mohamed, Mohamed-Wael A; Ahmed, Ahmed I; Ibrahim, Awad A; Ahmed, Mohamed S

    2012-01-01

    The prevalence of Pasteurella multocida strains among 275 backyard chickens from different regions of Upper Egypt was studied. A total of 21 isolates of P. multocida were recovered in 21 out of 275 chickens tested (7.6%) and were confirmed using phenotypic characterisation. Somatic serotyping of the 21 isolates resulted in 12 isolates being classed as serotype A:1 (57.14%), 4 as serotype A:3 (19.05%) and 5 could not be typed (23.8%). Capsular typing, using multiplex polymerase chain reaction (PCR), demonstrated that 18 strains were capsular type A (85.7%), and 3 were type D (14.3%). The present findings suggest that a multiplex capsular PCR could be valuable for the rapid identification of P. multocida in cases of fowl cholera infection. A total of 5 isolates of P. multocida were selected to study their pathogenicity in embryonated chicken eggs instead of conducting a study in mature chickens. The results showed a variation in pathogenicity between the strains tested, namely: serotype A:1 strains caused 80% mortality, in contrast to 20% mortality by type D strains. Pathological findings included severe congestion of the entire embryo, haemorrhaging of the skin, feather follicles and toe, and ecchymotic haemorrhages on the liver of the inoculated embryos. The observations in this study indicate that P. multocida serogroup A could be highly pathogenic for mature chickens and therefore might be a cause of considerable economic losses in commercial production. A total of 10 isolates were subjected to antimicrobial susceptibility to determine the minimal inhibitory concentration of 7 antimicrobials. All isolates were susceptible to ciprofloxacin, florfenicol, streptomycin and sulphamethoxazol with trimethoprim and with varying degrees of sensitivity to the other agents. PMID:22485004

  1. Segregation and chain extension of overlapping semiflexible macromolecules in channel

    NASA Astrophysics Data System (ADS)

    Cifra, Peter; Racko, Dusan

    2014-03-01

    Decrease of overall chain extension in channel by local backfolding together with an increased extension of sequences running parallel have been reported to complicate linearization experiments under moderate confinements. Less known related effect occurs in two overlapping chains in channel. Investigation of overlap and segregation of polymer coils in channel was extended here relative to previous studies from flexible to semiflexible chains. Results are based on simulation of confinement free energy of a chain and on direct simulation of coil segregation process. For confinement free energy we confirm the predicted opposite trend with increasing chain stiffness for the weak and strong confinement regimes. Results of two different approaches are consistent, in agreement with theoretical analysis and indicate a stronger segregation tendency of flexible chains relative to semiflexible chains, both in its extent and dynamics. Mutual excluded volume between confined chains leads to extension of overlapping chains along channel and this effect is stronger for flexible chains but weak for stiffer macromolecules such as DNA. Support from Slovak Res. and Develop. Agency (SRDA-0451-11) is acknowledged. D. Racko, P. Cifra, J. Chem. Phys. 138, 184904 (2013)

  2. [Trophic chains in soil].

    PubMed

    2013-01-01

    Trophic links of soil animals are extensively diverse but also flexible. Moreover, feeding activity of large soil saprotrophs often cascades into a range of ecosystem-level consequences via the ecological engineering. Better knowledge on the main sources of energy utilized by soil animals is needed for understanding functional structure of soil animal communities and their participation in the global carbon cycling. Using published and original data, we consider the relative importance of dead organic matter and saprotrophic microorganisms as a basal energy source in the detritus-based food chains, the feeding of endogeic macrofauna on the stabilized soil organic matter, and the role of recent photosynthate in the energy budget of soil communities. Soil food webs are spatially and functionally compartmentalized, though the separation of food chains into bacteria- and fungi-based channels seems to be an over-simplification. The regulation of the litter decomposition rates via top-down trophic interactions across more than one trophic level is only partly supported by experimental data, but mobile litter-dwelling predators play a crucial role in integrating local food webs within and across neighboring ecosystems. PMID:25508107

  3. [Trophic chains in soil].

    PubMed

    Goncharov, A A; Tiunov, A V

    2013-01-01

    Trophic links of soil animals are extensively diverse but also flexible. Moreover, feeding activity of large soil saprotrophs often cascades into a range of ecosystem-level consequences via the ecological engineering. Better knowledge on the main sources of energy utilized by soil animals is needed for understanding functional structure of soil animal communities and their participation in the global carbon cycling. Using published and original data, we consider the relative importance of dead organic matter and saprotrophic microorganisms as a basal energy source in the detritus-based food chains, the feeding of endogeic macrofauna on the stabilized soil organic matter, and the role of recent photosynthate in the energy budget of soil communities. Soil food webs are spatially and functionally compartmentalized, though the separation of food chains into bacteria- and fungi-based channels seems to be an over-simplification. The regulation of the litter decomposition rates via top-down trophic interactions across more than one trophic level is only partly supported by experimental data, but mobile litter-dwelling predators play a crucial role in integrating local food webs within and across neighboring ecosystems. PMID:25438576

  4. Practicality of spin chain wiring in diamond quantum technologies.

    PubMed

    Ping, Yuting; Lovett, Brendon W; Benjamin, Simon C; Gauger, Erik M

    2013-03-01

    Coupled spin chains are promising candidates for wiring up qubits in solid-state quantum computing (QC). In particular, two nitrogen-vacancy centers in diamond can be connected by a chain of implanted nitrogen impurities; when driven by suitable global fields the chain can potentially enable quantum state transfer at room temperature. However, our detailed analysis of error effects suggests that foreseeable systems may fall far short of the fidelities required for QC. Fortunately the chain can function in the more modest role as a mediator of noisy entanglement, enabling QC provided that we use subsequent purification. For instance, a chain of 5 spins with interspin distances of 10 nm has finite entangling power as long as the T(2) time of the spins exceeds 0.55 ms. Moreover we show that repurposing the chain this way can remove the restriction to nearest-neighbor interactions, so eliminating the need for complicated dynamical decoupling sequences. PMID:23521240

  5. Doping of Semiconducting Atomic Chains

    NASA Technical Reports Server (NTRS)

    Toshishige, Yamada; Kutler, Paul (Technical Monitor)

    1997-01-01

    Due to the rapid progress in atom manipulation technology, atomic chain electronics would not be a dream, where foreign atoms are placed on a substrate to form a chain, and its electronic properties are designed by controlling the lattice constant d. It has been shown theoretically that a Si atomic chain is metallic regardless of d and that a Mg atomic chain is semiconducting or insulating with a band gap modified with d. For electronic applications, it is essential to establish a method to dope a semiconducting chain, which is to control the Fermi energy position without altering the original band structure. If we replace some of the chain atoms with dopant atoms randomly, the electrons will see random potential along the chain and will be localized strongly in space (Anderson localization). However, if we replace periodically, although the electrons can spread over the chain, there will generally appear new bands and band gaps reflecting the new periodicity of dopant atoms. This will change the original band structure significantly. In order to overcome this dilemma, we may place a dopant atom beside the chain at every N lattice periods (N > 1). Because of the periodic arrangement of dopant atoms, we can avoid the unwanted Anderson localization. Moreover, since the dopant atoms do not constitute the chain, the overlap interaction between them is minimized, and the band structure modification can be made smallest. Some tight-binding results will be discussed to demonstrate the present idea.

  6. Myosin light-chain phosphatase.

    PubMed Central

    Morgan, M; Perry, S V; Ottaway, J

    1976-01-01

    1. A method for the isolation of a new enzyme, myosin light-chain phosphatase, from rabbit white skeletal muscle by using a Sepharose-phosphorylated myosin light-chain affinity column is described. 2. The enzyme migrated as a single component on electrophoresis in sodium dodecyl sulphate/polyacrylamide gel at pH7.0, with apparent mol.wt. 70000. 3. The enzyme was highly specific for the phosphorylated P-light chain of myosin, had pH optima at 6.5 and 8.0 and was not inhibited by NaF. 4. A Ca2+-sensitive 'ATPase' (adenosine triphosphatase) system consisting of myosin light-chain kinase, myosin light-chain phosphatase and the P-light chain is described. 5. Evidence is presented for a phosphoryl exchange between Pi, phosphorylated P-light chain and myosin light-chain phosphatase. 6. Heavy meromyosin prepared by chymotryptic digestion can be phosphorylated by myosin light-chain kinase. 7. The ATPase activities of myosin and heavy meromyosin, in the presence and absence of F-actin, were not significantly changed (+/- 10%) by phosphorylation of the P-light chain. Images PLATE 1 PMID:186030

  7. Comparative Analysis of Real-Time Polymerase Chain Reaction Methods to Typing HLA-B*57:01 in HIV-1-Positive Patients.

    PubMed

    Falasca, Francesca; Dello Russo, Cinzia; Mora, Barbara; Pirazzoli, Antonella; Fantauzzi, Alessandra; Navarra, Pierluigi; Pizzuti, Antonio; De Vito, Corrado; Antonelli, Guido; Turriziani, Ombretta

    2016-07-01

    The HLA-B*57:01 allele is strongly associated with the hypersensitivity reaction to Abacavir (ABC). Therefore, treatment guidelines recommend that patients initiating ABC are preventively tested for the presence of this allele. To date, four different commercial assays based on the real-time quantitative polymerase chain reaction (Q-PCR) technique are available for the detection of HLA-B*57:01: Duplicα-RealTime Reagent Set HLA-B*57:01 by Euroclone, HLA-B*57:01 Real-TM by Sacace Biotechnologies, COBAS AmpliPrep/COBAS TaqMan HLA-B*57:01 Screening Test by Roche Diagnostic, and HLA-B*57:01 by Nuclear Laser Medicine. The study was carried out to compare the performance of the first three commercially available Q-PCR kits in a routine clinical setting. A total of 98 samples from Policlinico Umberto I Hospital were tested. Results obtained by the Duplicα-RealTime Genotyping kit and AmpliPrep/TaqMan system were 100% concordant. In contrast, genotyping by the HLA-B*57:01 Real-TM kit showed poor agreement with the other systems, that is, 12 out of 33 positive samples were detected as HLA-B*57:01 negative. To confirm the correct genotype of these discordant samples, two additional methods with rapid turnaround times and already implemented into routine clinical practice were used, that is, a PCR-based microsequence-specific primer DNA typing test and a laboratory-developed screening test in Q-PCR. All 12 discordant samples were genotyped as HLA-B*57:01-positive samples using these two additional methods in a single-blinded manner, thus confirming the low sensitivity of HLA-B*57:01 Real-TM test. These findings underline the need to compare results obtained with commercial assays before choosing a test suitable for use in a routine clinical laboratory. PMID:26750774

  8. Responses of feeding prebiotics on nutrient digestibility, faecal microbiota composition and short-chain fatty acid concentrations in dogs: a meta-analysis.

    PubMed

    Patra, A K

    2011-09-01

    The effects of prebiotics on digestibility, short-chain fatty acid (SCFA) concentrations and bacterial populations in the faeces and immunity in dogs were evaluated by meta-analyses. Overall, data from 15 published studies containing 65 different treatment means of 418 observations from different breeds of dogs were included in the data set. Feeding of prebiotics to dogs did not affect the nutrient intake (P > 0.10), nor did prebiotics change (P > 0.10) the digestibility of dry matter (DM) and fat. However, crude protein (CP) digestibility tended to decrease quadratically (P = 0.06) with increasing dosages of prebiotics, although the degree of prediction was low (R(2) = 0.33). The concentration of total SCFA (P = 0.08; R(2) = 0.90) tended to increase linearly, whereas concentration of acetate (R(2) = 0.25), propionate (R(2) = 0.88) and butyrate (R(2) = 0.85) increased quadratically with increasing dosage of prebiotics in the faeces of dogs. The numbers of beneficial bifidobacteria (P < 0.01; R(2) = 0.62) increased quadratically, but lactobacilli (P < 0.01; R(2) = 0.66) increased linearly with increasing supplementation of prebiotics. The changes in healthy bacterial numbers were affected by the interaction of initial bacterial numbers and dose of prebiotics; bacterial numbers increased relatively more when initial bacterial numbers were low. Dietary composition did not influence the response of prebiotics on lactobacilli and bifidobacterial numbers in this study. The numbers of pathogenic Clostridium perfringens and Escherichia coli were not affected by prebiotics. Prebiotics did not affect the serum immunoglobulin (Ig) concentrations such as IgG, IgA and IgM in dogs. Although prebiotics may tend to have an adverse effect on CP digestibility, prebiotics at doses up to 1.40% food intake (DM basis) might increase the beneficial bacterial populations and SCFA concentrations in the faeces of dogs. Thus, the feeding of prebiotics has a great prospective to improve the

  9. Low Blood Long Chain Omega-3 Fatty Acids in UK Children Are Associated with Poor Cognitive Performance and Behavior: A Cross-Sectional Analysis from the DOLAB Study

    PubMed Central

    Montgomery, Paul; Burton, Jennifer R.; Sewell, Richard P.; Spreckelsen, Thees F.; Richardson, Alexandra J.

    2013-01-01

    Background Omega-3 long-chain polyunsaturated fatty acids (LC-PUFA), especially DHA (docosahexaenonic acid) are essential for brain development and physical health. Low blood Omega-3 LC-PUFA have been reported in children with ADHD and related behavior/learning difficulties, as have benefits from dietary supplementation. Little is known, however, about blood fatty acid status in the general child population. We therefore investigated this in relation to age-standardized measures of behavior and cognition in a representative sample of children from mainstream schools. Participants 493 schoolchildren aged 7–9 years from mainstream Oxfordshire schools, selected for below average reading performance in national assessments at age seven. Method Whole blood fatty acids were obtained via fingerstick samples. Reading and working memory were assessed using the British Ability Scales (II). Behaviour (ADHD-type symptoms) was rated using the revised Conners’ rating scales (long parent and teacher versions). Associations were examined and adjusted for relevant demographic variables. Results DHA and eicosapentaenoic acid (EPA), accounted for only 1.9% and 0.55% respectively of total blood fatty acids, with DHA showing more individual variation. Controlling for sex and socio-economic status, lower DHA concentrations were associated with poorer reading ability (std. OLS coeff. = 0.09, p = <.042) and working memory performance (0.14, p = <.001). Lower DHA was also associated with higher levels of parent rated oppositional behavior and emotional lability (−0.175, p = <.0001 and −0.178, p = <.0001). Conclusions In these healthy UK children with below average reading ability, concentrations of DHA and other Omega-3 LC-PUFA were low relative to adult cardiovascular health recommendations, and directly related to measures of cognition and behavior. These findings require confirmation, but suggest that the benefits from dietary supplementation with Omega-3 LC

  10. Comparative Analysis of Real-Time Polymerase Chain Reaction Methods to Typing HLA-B*57:01 in HIV-1-Positive Patients

    PubMed Central

    Falasca, Francesca; Russo, Cinzia Dello; Mora, Barbara; Pirazzoli, Antonella; Fantauzzi, Alessandra; Navarra, Pierluigi; Pizzuti, Antonio; De Vito, Corrado; Antonelli, Guido

    2016-01-01

    Abstract The HLA-B*57:01 allele is strongly associated with the hypersensitivity reaction to Abacavir (ABC). Therefore, treatment guidelines recommend that patients initiating ABC are preventively tested for the presence of this allele. To date, four different commercial assays based on the real-time quantitative polymerase chain reaction (Q-PCR) technique are available for the detection of HLA-B*57:01: Duplicα-RealTime Reagent Set HLA-B*57:01 by Euroclone, HLA-B*57:01 Real-TM by Sacace Biotechnologies, COBAS AmpliPrep/COBAS TaqMan HLA-B*57:01 Screening Test by Roche Diagnostic, and HLA-B*57:01 by Nuclear Laser Medicine. The study was carried out to compare the performance of the first three commercially available Q-PCR kits in a routine clinical setting. A total of 98 samples from Policlinico Umberto I Hospital were tested. Results obtained by the Duplicα-RealTime Genotyping kit and AmpliPrep/TaqMan system were 100% concordant. In contrast, genotyping by the HLA-B*57:01 Real-TM kit showed poor agreement with the other systems, that is, 12 out of 33 positive samples were detected as HLA-B*57:01 negative. To confirm the correct genotype of these discordant samples, two additional methods with rapid turnaround times and already implemented into routine clinical practice were used, that is, a PCR-based microsequence-specific primer DNA typing test and a laboratory-developed screening test in Q-PCR. All 12 discordant samples were genotyped as HLA-B*57:01-positive samples using these two additional methods in a single-blinded manner, thus confirming the low sensitivity of HLA-B*57:01 Real-TM test. These findings underline the need to compare results obtained with commercial assays before choosing a test suitable for use in a routine clinical laboratory. PMID:26750774

  11. NNSA TRITIUM SUPPLY CHAIN

    SciTech Connect

    Wyrick, Steven; Cordaro, Joseph; Founds, Nanette; Chambellan, Curtis

    2013-08-21

    Savannah River Site plays a critical role in the Tritium Production Supply Chain for the National Nuclear Security Administration (NNSA). The entire process includes: • Production of Tritium Producing Burnable Absorber Rods (TPBARs) at the Westinghouse WesDyne Nuclear Fuels Plant in Columbia, South Carolina • Production of unobligated Low Enriched Uranium (LEU) at the United States Enrichment Corporation (USEC) in Portsmouth, Ohio • Irradiation of TPBARs with the LEU at the Tennessee Valley Authority (TVA) Watts Bar Reactor • Extraction of tritium from the irradiated TPBARs at the Tritium Extraction Facility (TEF) at Savannah River Site • Processing the tritium at the Savannah River Site, which includes removal of nonhydrogen species and separation of the hydrogen isotopes of protium, deuterium and tritium.

  12. The glassy wormlike chain

    NASA Astrophysics Data System (ADS)

    Kroy, Klaus; Glaser, Jens

    2007-11-01

    We introduce a new model for the dynamics of a wormlike chain (WLC) in an environment that gives rise to a rough free energy landscape, which we name the glassy WLC. It is obtained from the common WLC by an exponential stretching of the relaxation spectrum of its long-wavelength eigenmodes, controlled by a single parameter \\boldsymbol{\\cal E} . Predictions for pertinent observables such as the dynamic structure factor and the microrheological susceptibility exhibit the characteristics of soft glassy rheology and compare favourably with experimental data for reconstituted cytoskeletal networks and live cells. We speculate about the possible microscopic origin of the stretching, implications for the nonlinear rheology, and the potential physiological significance of our results.

  13. Polymerase chain displacement reaction.

    PubMed

    Harris, Claire L; Sanchez-Vargas, Irma J; Olson, Ken E; Alphey, Luke; Fu, Guoliang

    2013-02-01

    Quantitative PCR assays are now the standard method for viral diagnostics. These assays must be specific, as well as sensitive, to detect the potentially low starting copy number of viral genomic material. We describe a new technique, polymerase chain displacement reaction (PCDR), which uses multiple nested primers in a rapid, capped, one-tube reaction that increases the sensitivity of normal quantitative PCR (qPCR) assays. Sensitivity was increased by approximately 10-fold in a proof-of-principle test on dengue virus sequence. In PCDR, when extension occurs from the outer primer, it displaces the extension strand produced from the inner primer by utilizing a polymerase that has strand displacement activity. This allows a greater than 2-fold increase of amplification product for each amplification cycle and therefore increased sensitivity and speed over conventional PCR. Increased sensitivity in PCDR would be useful in nucleic acid detection for viral diagnostics. PMID:23384180

  14. Fuzzy Entropy Method for Quantifying Supply Chain Networks Complexity

    NASA Astrophysics Data System (ADS)

    Zhang, Jihui; Xu, Junqin

    Supply chain is a special kind of complex network. Its complexity and uncertainty makes it very difficult to control and manage. Supply chains are faced with a rising complexity of products, structures, and processes. Because of the strong link between a supply chain’s complexity and its efficiency the supply chain complexity management becomes a major challenge of today’s business management. The aim of this paper is to quantify the complexity and organization level of an industrial network working towards the development of a ‘Supply Chain Network Analysis’ (SCNA). By measuring flows of goods and interaction costs between different sectors of activity within the supply chain borders, a network of flows is built and successively investigated by network analysis. The result of this study shows that our approach can provide an interesting conceptual perspective in which the modern supply network can be framed, and that network analysis can handle these issues in practice.

  15. Comparative analysis of respiratory chain and oxidative phosphorylation in Leishmania tarentolae, Crithidia fasciculata, Phytomonas serpens and procyclic stage of Trypanosoma brucei.

    PubMed

    Verner, Zdeněk; Cermáková, Petra; Skodová, Ingrid; Kováčová, Bianka; Lukeš, Julius; Horváth, Anton

    2014-01-01

    Trypanosomatids are unicellular parasites living in a wide range of host environments, which to large extent shaped their mitochondrial energy metabolism, resulting in quite large differences even among closely related flagellates. In a comparative manner, we analyzed the activities and composition of mitochondrial respiratory complexes in four species (Leishmania tarentolae, Crithidia fasciculata, Phytomonas serpens and Trypanosoma brucei), which represent the main model trypanosomatids. Moreover, we measured the activity of mitochondrial glycerol-3-phosphate dehydrogenase, the overall oxygen consumption and the mitochondrial membrane potential in each species. The comparative analysis suggests an inverse relationship between the activities of respiratory complexes I and II, as well as the overall activity of the canonical complexes and glycerol-3-phosphate dehydrogenase. Our comparative analysis shows that mitochondrial functions are highly variable in these versatile parasites. PMID:24556248

  16. Chains, bombs, potrzebies and slugs

    NASA Astrophysics Data System (ADS)

    Jewess, Mike; McDowell, Alex; Maxfield, Stephen; Hunt, A. G.; Hicks, Bruce

    2010-03-01

    I read with pleasure Robert Crease's article on unusual units (February pp17-19). However, the article stated that an acre is 10×10 chains, when it is in fact 10×1 chains. Incidentally, a distance of 10 chains (220 yards) is known as a furlong, a word that suggests the length of a ploughed furrow and that is still used in horse-racing.

  17. Supply Chain Coordination in Hospitals

    NASA Astrophysics Data System (ADS)

    Rego, Nazaré; de Sousa, Jorge Pinho

    This paper presents an innovative approach to support the definition of strategies for the design of alternative configurations of hospital supply chains. This approach was developed around a hybrid Tabu Search / Variable Neighbourhood Search metaheuristic, that uses several neighbourhood structures. The flexibility of the procedure allows its application to supply chains with different topologies and atypical cost characteristics. A preliminary computational experience shows the approach potential in solving large scale supply chain configuration problems. The future incorporation of this approach in a broader Decision Support System (DSS) will provide a tool that can significantly contribute to an increase of healthcare supply chains efficiency and encourage the establishment of collaborative partnerships between their members.

  18. Dynamical Aspects of Inextensible Chains

    NASA Astrophysics Data System (ADS)

    Ferrari, Franco; Pyrka, Maciej

    In the present work, a method to impose the inextensibility constraints on the dynamics of a chain fluctuating in a thermal bath at fixed temperature is investigated. The final goal is to construct the probability function of the chain and the generating functional of the correlation functions of the relevant degrees of freedom of the system. First, we study the dynamics of a freely hinged chain composed by massive beads connected together by massless segments of fixed length. It is shown that a system of this kind may be described by a set of Langevin equations in which the noise is characterized by a non-gaussian probability distribution. Starting from these Langevin equations, the generating functional of the freely hinged chain is derived in path integral form. A connection with a stochastic process governed by a Fokker-Planck equation is established. Next, a chain composed by one-dimensional bars with constant mass distribution is considered. A path integral expression of the generating functional for a chain of this type is derived. Finally, it is verified that in the limit in which the chain becomes continuous, both generating functionals of the freely hinged chain and of the freely jointed bar chain converge to the same result as expected.

  19. In Silico Analysis of the cadF Gene and Development of a Duplex Polymerase Chain Reaction for Species-Specific Identification of Campylobacter jejuni and Campylobacter coli

    PubMed Central

    Shams, Saeed; Bakhshi, Bita; Tohidi Moghadam, Tahereh

    2016-01-01

    Background Campylobacteriosis is a zoonotic infectious disease caused by Campylobacter jejuni and C. coli. The cadF gene is considered as a genus-specific gene while other genes are mainly used for discrimination at the species level. Objectives This study aimed to analyze the cadF gene and to develop a duplex PCR assay for simultaneous detection of C. coli and C. jejuni, the two commonly encountered species. Materials and Methods In silico analysis of the cadF gene was carried out by several software and available online tools. A duplex PCR optimized with specific primers was used for detection and differentiation of both species. To evaluate specificity and sensitivity of the test, a panel of different Campylobacter spp. together with several intestinal bacterial pathogens was tested. The limit of detection (LOD) of method was determined using serial dilutions of standard genomes. Results The analysis of the full size cadF gene indicated variations in this gene, which can be used to differentiate C. jejuni and C. coli. The duplex PCR designed in this study showed that it could simultaneously detect and differentiate both C. jejuni and C. coli with product sizes of 737 bp and 461 bp, respectively. This assay, with 100% specificity and sensitivity, had a limit of detection (LOD) of about 14 and 0.7 µg/mL for C. jejuni and C. coli, respectively. Conclusions In silico analysis of the cadF full-gene showed variations between the two species that can be used as a molecular target for differentiating C. jejuni and C. coli in a single-step duplex-PCR assay with high specificity and sensitivity. PMID:27127589

  20. Chain Dynamics in Magnetorheological Suspensions

    NASA Technical Reports Server (NTRS)

    Gast, A. P.; Furst, E. M.

    1999-01-01

    Magnetorheological (MR) suspensions are composed of colloidal particles which acquire dipole moments when subjected to an external magnetic field. At sufficient field strengths and concentrations, the dipolar particles rapidly aggregate to form long chains. Subsequent lateral cross-linking of the dipolar chains is responsible for a rapid liquid-to-solid-like rheological transition. The unique, magnetically-activated rheological properties of MR suspensions make them ideal for interfacing mechanical systems to electronic controls. Additionally, the ability to experimentally probe colloidal suspensions interacting through tunable anisotropic potentials is of fundamental interest. Our current experimental work has focused on understanding the fluctuations of dipolar chains. It has been proposed by Halsey and Toor (HT) that the strong Landau-Peierls thermal fluctuations of dipolar chains could be responsible for long-range attractions between chains. Such interactions will govern the long-time relaxation of MR suspensions. We have synthesized monodisperse neutrally buoyant MR suspensions by density matching stabilized ferrofluid emulsion droplets with D2O. This allows us to probe the dynamics of the dipolar chains using light scattering without gravitational, interfacial, and polydispersity effects to resolve the short-wavelength dynamics of the dipolar chains. We used diffusing wave spectroscopy to measure these dynamics. The particle displacements at short times that show an independence to the field strength, but at long times exhibit a constrained, sub-diffusive motion that slows as the dipole strength is increased. The experiments are in good qualitative agreement with Brownian dynamics simulations of dipolar chains. Although there have been several important and detailed studies of the structure and interactions in MR suspensions, there has not been conclusive evidence that supports or contradicts the HT model prediction that long-range interactions exist between

  1. CD44 variant exon 6 expressions in colon cancer assessed by quantitative analysis using real time reverse transcriptase-polymerase chain reaction.

    PubMed

    Yamada, Yoichi; Itano, Naoki; Narimatsu, Hisashi; Kudo, Takashi; Hirohashi, Setsuo; Ochiai, Atsushi; Tohnai, Iwai; Ueda, Minoru; Kimata, Koji

    2003-01-01

    CD44 is a family of transmembrane glycoproteins that serve as a major receptor for hyaluronate and the splice variants play a very important role in tumor progression and metastasis. We examined the relationship between cancer progression and mRNA levels of CD44 variant exon 6 (CD44v6) in specimens of colon cancer at different diagnostic stages from 31 patients using real time RT-PCR analysis. Increased mRNA levels of CD44v6 were observed in 82% of the specimens in comparison with those in the corresponding non-cancerous tissue specimens. A statistically significant correlation between the CD44v6 expression and the cancerous state was found in most specimens at all Dukes stages. None of the other parameters were related to the expression in the cancerous specimens. Quantitative real time RT-PCR analysis showed that there was no correlation of CD44v6 expression with tumor progression, although CD44v6 is upregulated in transformation. Thus, CD44v6 expression may be a clinically useful indicator of colon cancer. PMID:14534719

  2. Exploring membrane respiratory chains.

    PubMed

    Marreiros, Bruno C; Calisto, Filipa; Castro, Paulo J; Duarte, Afonso M; Sena, Filipa V; Silva, Andreia F; Sousa, Filipe M; Teixeira, Miguel; Refojo, Patrícia N; Pereira, Manuela M

    2016-08-01

    Acquisition of energy is central to life. In addition to the synthesis of ATP, organisms need energy for the establishment and maintenance of a transmembrane difference in electrochemical potential, in order to import and export metabolites or to their motility. The membrane potential is established by a variety of membrane bound respiratory complexes. In this work we explored the diversity of membrane respiratory chains and the presence of the different enzyme complexes in the several phyla of life. We performed taxonomic profiles of the several membrane bound respiratory proteins and complexes evaluating the presence of their respective coding genes in all species deposited in KEGG database. We evaluated 26 quinone reductases, 5 quinol:electron carriers oxidoreductases and 18 terminal electron acceptor reductases. We further included in the analyses enzymes performing redox or decarboxylation driven ion translocation, ATP synthase and transhydrogenase and we also investigated the electron carriers that perform functional connection between the membrane complexes, quinones or soluble proteins. Our results bring a novel, broad and integrated perspective of membrane bound respiratory complexes and thus of the several energetic metabolisms of living systems. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi. PMID:27044012

  3. Identification of tuna species in commercial cans by minor groove binder probe real-time polymerase chain reaction analysis of mitochondrial DNA sequences.

    PubMed

    Terio, Valentina; Di Pinto, Pietro; Decaro, Nicola; Parisi, Antonio; Desario, Costantina; Martella, Vito; Buonavoglia, Canio; Tantillo, Marilia Giuseppina

    2010-12-01

    Three different minor groove binder (MGB) probe assays have been developed for rapid and accurate identification of the species commonly used for production of canned tuna, i.e. yellowfin (Thunnus albacares), bluefin (Thunnus thynnus) and albacore (Thunnus alalunga) tunas. The assays targeting the mitochondrial cytochrome b gene were able to discriminate efficiently between the three species contained in fresh or canned tunas and did not react with other Scombroidei that were tested. A correct species prediction was obtained even from artificial mixtures prepared with different amounts of the reference tuna species and subjected to the sterilisation treatment. Testing of 27 commercial canned tunas by PCR-RFLP, MGB probe assays and sequence analysis showed a concordance of 100% between the last two techniques, whereas by using PCR-RFLP several samples were uncharacterised or mischaracterised. These results make the established MGB probe assays an attractive tool for direct and rapid species identification in canned tuna. PMID:20691254

  4. Long-Chain Omega-3 Fatty Acids Eicosapentaenoic Acid and Docosahexaenoic Acid and Blood Pressure: A Meta-Analysis of Randomized Controlled Trials

    PubMed Central

    Van Elswyk, Mary; Alexander, Dominik D.

    2014-01-01

    BACKGROUND Although a large body of literature has been devoted to examining the relationship between eicosapentaenoic and docosahexaenoic acids (EPA+DHA) and blood pressure, past systematic reviews have been hampered by narrow inclusion criteria and a limited scope of analytical subgroups. In addition, no meta-analysis to date has captured the substantial volume of randomized controlled trials (RCTs) published in the past 2 years. The objective of this meta-analysis was to examine the effect of EPA+DHA, without upper dose limits and including food sources, on blood pressure in RCTs. METHODS Random-effects meta-analyses were used to generate weighted group mean differences and 95% confidence intervals (CIs) between the EPA+DHA group and the placebo group. Analyses were conducted for subgroups defined by key subject or study characteristics. RESULTS Seventy RCTs were included. Compared with placebo, EPA+DHA provision reduced systolic blood pressure (−1.52mm Hg; 95% confidence interval (CI) = −2.25 to −0.79) and diastolic blood pressure (−0.99mm Hg; 95% CI = −1.54 to −0.44) in the meta-analyses of all studies combined. The strongest effects of EPA+DHA were observed among untreated hypertensive subjects (systolic blood pressure = −4.51mm Hg, 95% CI = −6.12 to −2.83; diastolic blood pressure = −3.05mm Hg, 95% CI = −4.35 to −1.74), although blood pressure also was lowered among normotensive subjects (systolic blood pressure = −1.25mm Hg, 95% CI = −2.05 to −0.46; diastolic blood pressure = −0.62mm Hg, 95% CI = −1.22 to −0.02). CONCLUSIONS Overall, available evidence from RCTs indicates that provision of EPA+DHA reduces systolic blood pressure, while provision of ≥2 grams reduces diastolic blood pressure. PMID:24610882

  5. Analysis of gamma delta V region usage in normal and diseased human intestinal biopsies and peripheral blood by polymerase chain reaction (PCR) and flow cytometry.

    PubMed Central

    Bucht, A; Söderström, K; Esin, S; Grunewald, J; Hagelberg, S; Magnusson, I; Wigzell, H; Grönberg, A; Kiessling, R

    1995-01-01

    The intestinal population of gamma delta T cell receptor (TCR)-bearing cells was characterized with regard to V delta and V gamma subtype expression. For this purpose, we utilized V gene-specific PCR of mRNA prepared from intestinal biopsies. Predominant expression of the V delta 1 subtype was demonstrated in the small intestine of patients with coeliac disease and in the inflamed colon of patients with inflammatory bowel diseases (IBD: ulcerative colitis and Crohn's disease) as well as in colon biopsies taken from macroscopically normal areas of colon. Although intestinal gamma delta T cells preferentially expressed V delta 1, other V delta transcripts could be detected, of which V delta 2 and V delta 5 were commonly expressed. Analysis of biopsies from mesenteric lymph nodes demonstrated a V delta repertoire similar to the mucosa. In peripheral blood on the other hand, high expression of both V delta 2 and V delta 1 was found. The predominant expression of V delta 1 transcripts in the intestinal mucosa of IBD patients correlated well with protein cell surface expression as analysed by flow cytometry using V delta 1- and V delta 2-specific antibodies. Selective expansion of gamma delta T cells could not be demonstrated within the inflamed mucosa as shown by mRNA analysis and flow cytometry. Instead, IBD patients demonstrated a decreased proportion of TCR gamma delta-carrying T cells in the inflamed mucosa compared with macroscopically normal area of colon. On the other hand, a significantly increased percentage of T cells bearing the gamma delta TCR was found in peripheral blood of patients with Crohn's disease compared with healthy individuals, indicating that local mucosal inflammation may influence the circulating gamma delta T cell population. Images Fig. 1 PMID:7813110

  6. Verifying the Hanging Chain Model

    ERIC Educational Resources Information Center

    Karls, Michael A.

    2013-01-01

    The wave equation with variable tension is a classic partial differential equation that can be used to describe the horizontal displacements of a vertical hanging chain with one end fixed and the other end free to move. Using a web camera and TRACKER software to record displacement data from a vibrating hanging chain, we verify a modified version…

  7. Preparation of a bifunctional pyrazosulfuron-ethyl imprinted polymer with hydrophilic external layers by reversible addition-fragmentation chain transfer polymerization and its application in the sulfonylurea residue analysis.

    PubMed

    Yang, Meixian; Zhang, Yingying; Lin, Shen; Yang, Xinlin; Fan, Zhijin; Yang, Lixia; Dong, Xiangchao

    2013-09-30

    A new bifunctional pyrazosulfuron-ethyl imprinted polymer was synthesized by the combination of molecular imprinting technology and living radical polymerization. In the synthesis, the pyrazosulfuron-ethyl imprinted polymer was obtained by the reversible addition-fragmentation chain transfer (RAFT) precipitation polymerization followed by grafting poly(glyceryl monomethacrylate) (pGMMA) by the post-RAFT polymerization. In this research, we used polyethylene glycol (PEG) as the polymeric porogen in order to increase the porosity of the material which is a new porogen application in the precipitation polymerization. The imprinted polymer has selectivity for the template and ability of humic acids exclusion which has shown the merits of molecularly imprinted polymers and restricted access materials. An online solid-phase extraction/HPLC method for the analysis of three sulfonylurea residues in soil samples has been developed and validated. The recovery of 81-99% in the spiked levels of 40-200 μg kg(-1) was obtained and the limit of detection (LOD) and limit of quantification (LOQ) were less than 4.8 and 15.9 μg kg(-1) respectively. The results demonstrated that this bifunctional material can be used for the efficient pyrazosulfuron-ethyl extraction in the sulfonylurea residue analysis from environmental samples. PMID:23953454

  8. Proton-Induced X-ray Emission (PIXE) Analysis and DNA-chain Break study in rat hepatocarcinogenesis: A possible chemopreventive role by combined supplementation of vanadium and beta-carotene.

    PubMed

    Chattopadhyay, Mitali Basu; Mukherjee, Sutapa; Kulkarni, Indira; Vijayan, V; Doloi, Manika; Kanjilal, Nb; Chatterjee, Malay

    2005-05-26

    Combined effect of vanadium and beta-carotene on rat liver DNA-chain break and Proton induced X-ray emission (PIXE) analysis was studied during a necrogenic dose (200 mg/kg of body weight) of Diethyl Nitrosamine (DENA) induced rat liver carcinogenesis. Morphological and histopathological changes were observed as an end point biomarker. Supplementation of vanadium (0.5 ppm ad libitum) in drinking water and beta-carotene in the basal diet (120 mg/Kg of body weight) were performed four weeks before DENA treatment and continued till the end of the experiment (16 weeks). PIXE analysis revealed the restoration of near normal value of zinc, copper, and iron, which were substantially altered when compared to carcinogen treated groups. Supplementation of both vanadium and beta-carotene four weeks before DENA injection was found to offer significant (64.73%, P < 0.001) protection against generation of single-strand breaks when compared with the carcinogen control counter parts. A significant stabilization of hepatic architecture of the cells was observed as compared to carcinogen control in vanadium plus beta-carotene treated group. This study thus suggests that vanadium, a prooxidant but potential therapeutic agent yield safe and effective pharmacological formulation with beta-carotene, an antioxidant, in the inhibition of experimental rat hepatocarcinogenesis. PMID:15918908

  9. Detection of Babesia canis vogeli and Hepatozoon canis in canine blood by a single-tube real-time fluorescence resonance energy transfer polymerase chain reaction assay and melting curve analysis.

    PubMed

    Kongklieng, Amornmas; Intapan, Pewpan M; Boonmars, Thidarut; Thanchomnang, Tongjit; Janwan, Penchom; Sanpool, Oranuch; Lulitanond, Viraphong; Taweethavonsawat, Piyanan; Chungpivat, Sudchit; Maleewong, Wanchai

    2015-03-01

    A real-time fluorescence resonance energy transfer polymerase chain reaction (qFRET PCR) coupled with melting curve analysis was developed for detection of Babesia canis vogeli and Hepatozoon canis infections in canine blood samples in a single tube assay. The target of the assay was a region within the 18S ribosomal RNA gene amplified in either species by a single pair of primers. Following amplification from the DNA of infected dog blood, a fluorescence melting curve analysis was done. The 2 species, B. canis vogeli and H. canis, could be detected and differentiated in infected dog blood samples (n = 37) with high sensitivity (100%). The detection limit for B. canis vogeli was 15 copies of a positive control plasmid, and for H. canis, it was 150 copies of a positive control plasmid. The assay could simultaneously distinguish the DNA of both parasites from the DNA of controls. Blood samples from 5 noninfected dogs were negative, indicating high specificity. Several samples can be run at the same time. The assay can reduce misdiagnosis and the time associated with microscopic examination, and is not prone to the carryover contamination associated with the agarose gel electrophoresis step of conventional PCR. In addition, this qFRET PCR method would be useful to accurately determine the range of endemic areas or to discover those areas where the 2 parasites co-circulate. PMID:25776544

  10. O6-Methylguanine-DNA methyltransferase protein expression by immunohistochemistry in brain and non-brain systemic tumours: systematic review and meta-analysis of correlation with methylation-specific polymerase chain reaction

    PubMed Central

    2011-01-01

    Background The DNA repair protein O6-Methylguanine-DNA methyltransferase (MGMT) confers resistance to alkylating agents. Several methods have been applied to its analysis, with methylation-specific polymerase chain reaction (MSP) the most commonly used for promoter methylation study, while immunohistochemistry (IHC) has become the most frequently used for the detection of MGMT protein expression. Agreement on the best and most reliable technique for evaluating MGMT status remains unsettled. The aim of this study was to perform a systematic review and meta-analysis of the correlation between IHC and MSP. Methods A computer-aided search of MEDLINE (1950-October 2009), EBSCO (1966-October 2009) and EMBASE (1974-October 2009) was performed for relevant publications. Studies meeting inclusion criteria were those comparing MGMT protein expression by IHC with MGMT promoter methylation by MSP in the same cohort of patients. Methodological quality was assessed by using the QUADAS and STARD instruments. Previously published guidelines were followed for meta-analysis performance. Results Of 254 studies identified as eligible for full-text review, 52 (20.5%) met the inclusion criteria. The review showed that results of MGMT protein expression by IHC are not in close agreement with those obtained with MSP. Moreover, type of tumour (primary brain tumour vs others) was an independent covariate of accuracy estimates in the meta-regression analysis beyond the cut-off value. Conclusions Protein expression assessed by IHC alone fails to reflect the promoter methylation status of MGMT. Thus, in attempts at clinical diagnosis the two methods seem to select different groups of patients and should not be used interchangeably. PMID:21269507

  11. Developing sustainable food supply chains.

    PubMed

    Smith, B Gail

    2008-02-27

    This paper reviews the opportunities available for food businesses to encourage consumers to eat healthier and more nutritious diets, to invest in more sustainable manufacturing and distribution systems and to develop procurement systems based on more sustainable forms of agriculture. The important factors in developing more sustainable supply chains are identified as the type of supply chain involved and the individual business attitude to extending responsibility for product quality into social and environmental performance within their own supply chains. Interpersonal trust and working to standards are both important to build more sustainable local and many conserved food supply chains, but inadequate to transform mainstream agriculture and raw material supplies to the manufactured and commodity food markets. Cooperation among food manufacturers, retailers, NGOs, governmental and farmers' organizations is vital in order to raise standards for some supply chains and to enable farmers to adopt more sustainable agricultural practices. PMID:17766237

  12. Simplex and duplex polymerase chain reaction analysis of Herculex RW (59122) maize based on one reference molecule including separated fragments of 5' integration site and endogenous gene.

    PubMed

    Li, Xiang; Yang, Litao; Zhang, Jianzhong; Wang, Shu; Shen, Kailin; Pan, Liangwen; Zhang, Dabing

    2009-01-01

    Reference molecules, as positive controls and calibrators, have been recently developed in genetically modified organism analysis as a potential substitute for reference materials derived from plant raw materials. In this study, a novel reference molecule p59122, including the revealed 5' integration sequence of maize Herculex RW (59122), was constructed that was suitable for simplex and duplex event-specific qualitative and quantitative PCR detections. The LOD values were 10 copies both for simplex and duplex qualitative PCR when p59122 was used as the calibrator. These values were comparable to those of using genomic DNA samples with 0.01 and 0.05%, approximately 5 and 25 hyploid genomic DNA copies, respectively. The absolute LOD and LOQ values were confirmed to be as low as 10 and 25 copies of p59122 DNA both in simplex and duplex quantitative systems. Furthermore, ideal quantification data with low bias, SD and RSD values were obtained from the practical samples analyses in simplex and duplex real-time PCR systems using the reference molecule p59122 as a calibrator. All these results suggested that the developed reference molecule p59122 and the qualitative and quantitative PCR detection methods are suitable for identification and quantification of GM maize 59122 and its derived products. PMID:19916386

  13. Deformation history during chain building deduced by outcrop structural analysis: The case of the Sicilian fold-and-thrust belt (Central Mediterranean)

    NASA Astrophysics Data System (ADS)

    Napoli, G.; Nigro, F.; Favara, R.; Renda, P.; Salvaggio, G.

    2015-11-01

    The Sicilian fold-and-thrust belt is located in the central Mediterranean area, and it represents the south-eastern arcuate segment of the Apennine-Maghrebide orogen. The tectonic evolution of the Sicilian belt is documented after outcrop analysis of small-scale structural features carried out throughout the region. Results are consistent with the following four main deformation stages having affected the study area, from the oldest to the youngest: (i) multilayer weakening; (ii) folding-and-thrusting, (iii) extension, and (iv) renewed thrusting. The first deformation stage included three different substages (layer-parallel shortening, bed-parallel simple shear and fold nucleation), the second one by both thrusting and fold amplification and tightening. The third deformation stage involved re-activation of the pre-existing mechanical discontinuities and formation of low-to-high angle normal faults. Out-of-sequence thrusting postdated the aforementioned extensional stage, and formed the latest orogenic deformation stage that affected the Sicilian belt.

  14. Enantioselective analysis of ketone bodies in patients with beta-ketothiolase deficiency, medium-chain acyl coenzyme A dehydrogenase deficiency and ketonemic vomiting.

    PubMed

    Heil, M; Podebrad, F; Prado, E; Beck, T; Mosand, A; Sewell, A C; Böhles, H; Lehnert, W

    2000-03-10

    Enantioselective multidimensional gas chromatography-mass spectrometry (enantio-MDGC-MS) is a valuable tool for the differentiation of enantiomers from complex matrices when present in trace amounts. The separation of chiral compounds provides further information on the diagnosis of diseases, and on normal and abnormal biochemical pathways. The formation of the normal urinary metabolite 3-hydroxy-2-methylbutanoic acid (HMBA), excreted in abnormally high amounts in beta-ketothiolase deficiency, is not absolutely clarified. Metabolic pathways involving this metabolite are isoleucine catabolism, as well as presumably beta-oxidation of fatty acids and ketogenesis. The latter two pathways are distinguishable in their enantioselectivity. Enantioselective analysis gives further information on interfering metabolic pathways and the selectivity of the enzyme(s) forming HMBA. Different ratios of the stereoisomers of HMBA in control urine samples and patients with beta-ketothiolase deficiency were detected. Analogous to HMBA urinary 3-hydroxybutanoic acid (HBA) was investigated in several diseases. The formation of HBA and HMBA is expected to result from the same or similar metabolic pathways. Differences in the enantiomeric ratio of HMBA may originate from the enantioselectivity of different enzyme systems. PMID:10755375

  15. Extended haplotype analysis of ovine ADRB3 using polymerase chain reaction single strand conformational polymorphism on two regions of the gene.

    PubMed

    Yang, Guo; Hickford, Jon G H; Zhou, Huitong; Fang, Qian; Forrest, Rachel H

    2011-07-01

    The β3 adrenergic receptor (ADRB3) plays a critical role in the regulation of energy metabolism in mammals. In sheep, intronic polymorphism of the ADRB3 gene has been associated with lamb survival and various production traits. This study investigates variation in the ovine ADRB3 3' untranslated region (3'UTR), a region that may impact expression of the gene. Using PCR- single strand conformational polymorphism (SSCP), six unique patterns (named a-f) were observed in an approximately 304-bp amplicon. Sequencing revealed three single-nucleotide polymorphisms (c.*233A>C, c.*271G>C, c.*357A>T) and a single-nucleotide deletion (c.*257delG). Haplotype analyses showed that the previously described allele A defined by variation in the ovine ADRB3 intron can be divided into three haplotypes (Aa, Ab, and Ac). In total, 16 haplotypes through ovine ADRB3 were detected. This study suggests that ovine ADRB3 is highly polymorphic and that the extended haplotype analysis through the promoter, 5'UTR, coding sequence, intron, and 3'UTR needs to be performed to define the full extent of variation in this gene. PMID:21348572

  16. Single-Step RNA Extraction from Different Hydrogel-Embedded Mesenchymal Stem Cells for Quantitative Reverse Transcription-Polymerase Chain Reaction Analysis.

    PubMed

    Köster, Nat